Homo sapiens complex locus COG2, encoding component of oligomeric golgi complex 2.
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SUMMARY back to top
RefSeq summary
[COG2] This gene encodes a subunit of the conserved oligomeric Golgi complex that is required for maintaining normal structure and activity of the Golgi complex. The encoded protein specifically interacts with the USO1 vesicle docking protein and may be necessary for normal Golgi ribbon formation and trafficking of Golgi enzymes. Mutations of this gene are associated with abnormal glycosylation within the Golgi apparatus. Alternative splicing results in multiple transcript variants.

RefSeq annotates 2 representative transcripts (NM included in AceView variants .a and .b), but Homo sapiens cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 13 spliced variants.

AceView synopsis, each blue text links to tables and details
Note that this locus is complex: it appears to produce several proteins with no sequence overlap.
Expression: According to AceView, this gene is expressed at high level, 3.6 times the average gene in this release. The sequence of this gene is defined by 418 GenBank accessions from 372 cDNA clones, some from brain (seen 29 times), testis (24), lung (23), eye (17), tongue, tumor tissue (14), kidney (13), germinal center B cell (8) and 120 other tissues. We annotate structural defects or features in 7 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 29 distinct introns (28 gt-ag, 1 gc-ag). Transcription produces 16 different mRNAs, 13 alternatively spliced variants and 3 unspliced forms. There are 6 probable alternative promotors, 6 non overlapping alternative last exons and 6 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 2 cassette exons, overlapping exons with different boundaries, splicing versus retention of 6 introns.
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant bAug10, fAug10, jAug10).
Function: There are 10 articles specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in processes (Golgi organization, intra-Golgi vesicle-mediated transport, intracellular protein transport, oligosaccharide biosynthetic process, protein amino acid glycosylation). Proteins are expected to have molecular functions (protein binding, protein transporter activity) and to localize in various compartments (Golgi stack, Golgi transport complex, nucleus, Golgi apparatus, Golgi membrane). Putative protein interactors have been described (COG3, COG4).
Protein coding potential: 12 spliced mRNAs putatively encode good proteins, altogether 12 different isoforms (8 complete, 2 COOH complete, 2 partial), some containing COG (conserved oligomeric Golgi) complex component, COG2 domain [Pfam], a second peroximal domain, a coiled coil stretch [Psort2]. The remaining 4 mRNA variants (1 spliced, 3 unspliced) appear not to encode good proteins. Finally proteins from this gene may be modulated by acetylation; ubiquitination, as detailed at PhosphoSite.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 1, links to other databases and other names
Map: This gene COG2 maps on chromosome 1, at 1q42.2 according to Entrez Gene. In AceView, it covers 51.54 kb, from 230778202 to 230829736 (NCBI 37, August 2010), on the direct strand.
Links to: manual annotations from PhosphoSite, the SNP view, gene overviews from Entrez Gene 22796, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as COG2, RP11-543E8.3 or LDLC, LOC22796. It has been described as conserved oligomeric Golgi complex subunit 2, COG complex subunit 2, conserved oligomeric Golgi complex protein 2, brefeldin A-sensitive, peripheral Golgi protein, low density lipoprotein receptor defect C complementing, low density lipoprotein receptor defect C-complementing protein.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Cog2 (e=0.0).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene cogc-2 (e=10-05), which may contain interesting functional annotation.
The closest A.thaliana gene, according to BlastP, is the AceView gene AT4G24840 (e=10-62), which may contain interesting functional annotation
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
COG2 Gene expression in 15 primates, 16 tissues, from the NHPRTR project in sFPKM BAB SkeletalMuscle WholeBlood CHP Kidney Liver Lung Spleen CMC CMM Cerebellum HUM Brain Colon Heart LymphNode Ovary Testis JMI BoneMarrow MLM OWL PTM RMC RMI Pituitary SQM Thymus MST SMY RTL 7.13 26.6 9.41 2.70 3.10 8.19 4.71 3.57 26.6 24.8 30.6 10.1 7.13 16.4 18.8 7.64 4.71 10.8 16.4 13.3 17.6 15.3 21.6 13.3 12.4 12.4 12.4 10.8 18.8 21.6 23.2 17.6 23.2 23.2 11.6 21.6 4.71 6.65 8.19 17.6 35.1 17.6 26.6 15.3 18.8 17.6 30.6 26.6 6.21 13.3 18.8 14.3 17.6 20.2 14.3 7.64 23.2 24.8 23.2 11.6 6.21 7.13 10.1 12.4 5.40 11.6 15.3 11.6 17.6 16.4 17.6 10.1 7.13 24.8 21.6 23.2 23.2 15.3 21.6 17.6 18.8 10.1 28.5 26.6 16.4 26.6 24.8 12.4 21.6 28.5 17.6 20.2 12.4 23.2 10.1 21.6 32.8 9.41 28.5 28.5 18.8 23.2 30.6 20.2 13.3 32.8 20.2 32.8 32.8 26.6 21.6 16.4 18.8 23.2 16.4 8.19 6.21 18.8 24.8 23.2 23.2 23.2 12.4 26.6 12.4 23.2 14.3 18.8 26.6 35.1 26.6 17.6 17.6 28.5 18.8 24.8 32.8 17.6 14.3 11.6 21.6 13.3 16.4 7.64 15.3 6.21 21.6 23.2 17.6 15.3 16.4 21.6 16.4 30.6 24.8 21.6 14.3 Expression quantiles None Weak 1 2 3 4 5 6 7 8 10 20 This gene All genes log2 distributions RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
Read more...
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene COG2 5' 3' encoded on plus strand of chromosome 1 from 230,778,202 to 230,829,736 25018 27275 29408 29907 28503 23917 25344 30662 25875 30556 32238 45315 31579 44644 48644 48209 a [NM] 25018 27275 29408 29907 28503 23917 25344 30662 25875 30556 32238 45315 31579 44644 48644 48209 b [NM] 25 27275 29408 29907 28503 23917 25344 30662 25875 30556 32238 45315 31579 44644 48644 48209 c 25018 27275 99 67 29907 28503 23917 25344 30662 25875 30556 32238 45315 31579 44644 48644 48209 d 25018 27275 29408 29907 28503 g 193 30556 32238 45315 31579 44644 48644 48209 e 87 27275 29408 29907 28503 23917 468 f 26 45315 31579 j 25018 27275 29408 29907 28503 44 30662 25875 48209 h 17 27275 29408 29907 28503 i 48644 k n-u p-u o 44644 l m-u 5kb 0 223 bp exon 223 bp exon 16785 bp [gt-ag] intron 162 GenBank accessions 24856 RNA-seq supporting reads 4069 UHR pooled cells 2749 Brain 2568 Blood 15374 Neuroblastoma 96 Other (also 5590 Primates bodymap) 162 bp exon 1132 bp [gt-ag] intron 169 GenBank accessions 27106 RNA-seq supporting reads 4450 UHR pooled cells 3188 Brain 3669 Blood 15710 Neuroblastoma 89 Other (also 5991 Primates bodymap) 66 bp exon 2317 bp [gt-ag] intron 160 GenBank accessions 29248 RNA-seq supporting reads 4670 UHR pooled cells 3209 Brain 4441 Blood 16813 Neuroblastoma 115 Other (also 5963 Primates bodymap) 81 bp exon 1262 bp [gt-ag] intron 154 GenBank accessions 29753 RNA-seq supporting reads 4028 UHR pooled cells 2857 Brain 6720 Blood 15992 Neuroblastoma 156 Other (also 6162 Primates bodymap) 104 bp exon 4088 bp [gt-ag] intron 58 GenBank accessions 28445 RNA-seq supporting reads 4214 UHR pooled cells 3139 Brain 5738 Blood 15210 Neuroblastoma 144 Other (also 5934 Primates bodymap) 109 bp exon 571 bp [gt-ag] intron 38 GenBank accessions 23879 RNA-seq supporting reads 4114 UHR pooled cells 2946 Brain 3308 Blood 13374 Neuroblastoma 137 Other (also 4095 Primates bodymap) 180 bp exon 1980 bp [gt-ag] intron 36 GenBank accessions 25308 RNA-seq supporting reads 4159 UHR pooled cells 2971 Brain 4463 Blood 13589 Neuroblastoma 126 Other (also 5184 Primates bodymap) 125 bp exon 3357 bp [gt-ag] intron 35 GenBank accessions 30627 RNA-seq supporting reads 5061 UHR pooled cells 3303 Brain 4037 Blood 18018 Neuroblastoma 208 Other (also 6204 Primates bodymap) 127 bp exon 3788 bp [gt-ag] intron 38 GenBank accessions 25837 RNA-seq supporting reads 4526 UHR pooled cells 2956 Brain 2527 Blood 15638 Neuroblastoma 190 Other (also 4799 Primates bodymap) 140 bp exon 4521 bp [gt-ag] intron 33 GenBank accessions 30523 RNA-seq supporting reads 5427 UHR pooled cells 3863 Brain 2886 Blood 18169 Neuroblastoma 178 Other (also 3624 Primates bodymap) 62 bp exon 1449 bp [gt-ag] intron 30 GenBank accessions 32208 RNA-seq supporting reads 5469 UHR pooled cells 4019 Brain 2937 Blood 19590 Neuroblastoma 193 Other (also 3394 Primates bodymap) 152 bp exon 1698 bp [gt-ag] intron 32 GenBank accessions 45283 RNA-seq supporting reads 7538 UHR pooled cells 5804 Brain 4758 Blood 26988 Neuroblastoma 195 Other (also 5780 Primates bodymap) 198 bp exon 938 bp [gt-ag] intron 37 GenBank accessions 31542 RNA-seq supporting reads 5503 UHR pooled cells 3739 Brain 4025 Blood 18091 Neuroblastoma 184 Other (also 3591 Primates bodymap) 73 bp exon 276 bp [gt-ag] intron 33 GenBank accessions 22973 RNA-seq supporting reads 4037 UHR pooled cells 2898 Brain 2035 Blood 13878 Neuroblastoma 125 Other (also 2350 Primates bodymap) 143 bp exon 1451 bp [gt-ag] intron 41 GenBank accessions 44603 RNA-seq supporting reads 7236 UHR pooled cells 5473 Brain 5294 Blood 26439 Neuroblastoma 161 Other (also 5210 Primates bodymap) 140 bp exon 1230 bp [gt-ag] intron 50 GenBank accessions 48594 RNA-seq supporting reads 8108 UHR pooled cells 6112 Brain 3910 Blood 30255 Neuroblastoma 209 Other (also 4540 Primates bodymap) 181 bp exon 1727 bp [gt-ag] intron 61 GenBank accessions 48148 RNA-seq supporting reads 8112 UHR pooled cells 5992 Brain 4991 Blood 28911 Neuroblastoma 142 Other (also 5091 Primates bodymap) 694 bp exon 65 accessions, NM_007357.2 some from eye (seen 4 times) lung (4), prostate (4) ductal carcinoma, cell line (3) pancreas (3) Validated 3' end, 2 accessions Validated 3' end, 12 accessions 694 bp exon 223 bp exon 223 bp exon 108 bp uORF 223 bp exon 223 bp exon 16785 bp [gt-ag] intron 162 GenBank accessions 24856 RNA-seq supporting reads 4069 UHR pooled cells 2749 Brain 2568 Blood 15374 Neuroblastoma 96 Other (also 5590 Primates bodymap) 162 bp exon 162 bp exon 1132 bp [gt-ag] intron 169 GenBank accessions 27106 RNA-seq supporting reads 4450 UHR pooled cells 3188 Brain 3669 Blood 15710 Neuroblastoma 89 Other (also 5991 Primates bodymap) 66 bp exon 66 bp exon 2317 bp [gt-ag] intron 160 GenBank accessions 29248 RNA-seq supporting reads 4670 UHR pooled cells 3209 Brain 4441 Blood 16813 Neuroblastoma 115 Other (also 5963 Primates bodymap) 81 bp exon 81 bp exon 1262 bp [gt-ag] intron 154 GenBank accessions 29753 RNA-seq supporting reads 4028 UHR pooled cells 2857 Brain 6720 Blood 15992 Neuroblastoma 156 Other (also 6162 Primates bodymap) 104 bp exon 104 bp exon 4088 bp [gt-ag] intron 58 GenBank accessions 28445 RNA-seq supporting reads 4214 UHR pooled cells 3139 Brain 5738 Blood 15210 Neuroblastoma 144 Other (also 5934 Primates bodymap) 109 bp exon 109 bp exon 571 bp [gt-ag] intron 38 GenBank accessions 23879 RNA-seq supporting reads 4114 UHR pooled cells 2946 Brain 3308 Blood 13374 Neuroblastoma 137 Other (also 4095 Primates bodymap) 180 bp exon 180 bp exon 1980 bp [gt-ag] intron 36 GenBank accessions 25308 RNA-seq supporting reads 4159 UHR pooled cells 2971 Brain 4463 Blood 13589 Neuroblastoma 126 Other (also 5184 Primates bodymap) 125 bp exon 125 bp exon 3357 bp [gt-ag] intron 35 GenBank accessions 30627 RNA-seq supporting reads 5061 UHR pooled cells 3303 Brain 4037 Blood 18018 Neuroblastoma 208 Other (also 6204 Primates bodymap) 127 bp exon 127 bp exon 3788 bp [gt-ag] intron 38 GenBank accessions 25837 RNA-seq supporting reads 4526 UHR pooled cells 2956 Brain 2527 Blood 15638 Neuroblastoma 190 Other (also 4799 Primates bodymap) 140 bp exon 140 bp exon 4521 bp [gt-ag] intron 33 GenBank accessions 30523 RNA-seq supporting reads 5427 UHR pooled cells 3863 Brain 2886 Blood 18169 Neuroblastoma 178 Other (also 3624 Primates bodymap) 62 bp exon 62 bp exon 1449 bp [gt-ag] intron 30 GenBank accessions 32208 RNA-seq supporting reads 5469 UHR pooled cells 4019 Brain 2937 Blood 19590 Neuroblastoma 193 Other (also 3394 Primates bodymap) 152 bp exon 152 bp exon 1698 bp [gt-ag] intron 32 GenBank accessions 45283 RNA-seq supporting reads 7538 UHR pooled cells 5804 Brain 4758 Blood 26988 Neuroblastoma 195 Other (also 5780 Primates bodymap) 198 bp exon 198 bp exon 938 bp [gt-ag] intron 37 GenBank accessions 31542 RNA-seq supporting reads 5503 UHR pooled cells 3739 Brain 4025 Blood 18091 Neuroblastoma 184 Other (also 3591 Primates bodymap) 73 bp exon 73 bp exon 279 bp [gt-ag] intron 6 GenBank accessions 1420 RNA-seq supporting reads 191 UHR pooled cells 212 Brain 100 Blood 907 Neuroblastoma 10 Other (also 133 Primates bodymap) 140 bp exon 140 bp exon 1451 bp [gt-ag] intron 41 GenBank accessions 44603 RNA-seq supporting reads 7236 UHR pooled cells 5473 Brain 5294 Blood 26439 Neuroblastoma 161 Other (also 5210 Primates bodymap) 140 bp exon 140 bp exon 1230 bp [gt-ag] intron 50 GenBank accessions 48594 RNA-seq supporting reads 8108 UHR pooled cells 6112 Brain 3910 Blood 30255 Neuroblastoma 209 Other (also 4540 Primates bodymap) 181 bp exon 181 bp exon 1727 bp [gt-ag] intron 61 GenBank accessions 48148 RNA-seq supporting reads 8112 UHR pooled cells 5992 Brain 4991 Blood 28911 Neuroblastoma 142 Other (also 5091 Primates bodymap) 693 bp exon 693 bp exon 194 accessions, NM_001145036.1 some from brain (seen 15 times) testis (13), tongue, tumor tissue (11) liver (6), lung (6) capped 5' end, 81 accessions Validated 3' end, 2 accessions 693 bp exon 230 bp exon 16423 bp [gt-ag] intron 2 GenBank accessions 23 RNA-seq supporting reads 2 UHR pooled cells 5 Brain 16 Neuroblastoma 162 bp exon 162 bp exon 1132 bp [gt-ag] intron 169 GenBank accessions 27106 RNA-seq supporting reads 4450 UHR pooled cells 3188 Brain 3669 Blood 15710 Neuroblastoma 89 Other (also 5991 Primates bodymap) 66 bp exon 2317 bp [gt-ag] intron 160 GenBank accessions 29248 RNA-seq supporting reads 4670 UHR pooled cells 3209 Brain 4441 Blood 16813 Neuroblastoma 115 Other (also 5963 Primates bodymap) 81 bp exon 1262 bp [gt-ag] intron 154 GenBank accessions 29753 RNA-seq supporting reads 4028 UHR pooled cells 2857 Brain 6720 Blood 15992 Neuroblastoma 156 Other (also 6162 Primates bodymap) 104 bp exon 4088 bp [gt-ag] intron 58 GenBank accessions 28445 RNA-seq supporting reads 4214 UHR pooled cells 3139 Brain 5738 Blood 15210 Neuroblastoma 144 Other (also 5934 Primates bodymap) 109 bp exon 571 bp [gt-ag] intron 38 GenBank accessions 23879 RNA-seq supporting reads 4114 UHR pooled cells 2946 Brain 3308 Blood 13374 Neuroblastoma 137 Other (also 4095 Primates bodymap) 180 bp exon 1980 bp [gt-ag] intron 36 GenBank accessions 25308 RNA-seq supporting reads 4159 UHR pooled cells 2971 Brain 4463 Blood 13589 Neuroblastoma 126 Other (also 5184 Primates bodymap) 125 bp exon 3357 bp [gt-ag] intron 35 GenBank accessions 30627 RNA-seq supporting reads 5061 UHR pooled cells 3303 Brain 4037 Blood 18018 Neuroblastoma 208 Other (also 6204 Primates bodymap) 127 bp exon 3788 bp [gt-ag] intron 38 GenBank accessions 25837 RNA-seq supporting reads 4526 UHR pooled cells 2956 Brain 2527 Blood 15638 Neuroblastoma 190 Other (also 4799 Primates bodymap) 140 bp exon 4521 bp [gt-ag] intron 33 GenBank accessions 30523 RNA-seq supporting reads 5427 UHR pooled cells 3863 Brain 2886 Blood 18169 Neuroblastoma 178 Other (also 3624 Primates bodymap) 62 bp exon 1449 bp [gt-ag] intron 30 GenBank accessions 32208 RNA-seq supporting reads 5469 UHR pooled cells 4019 Brain 2937 Blood 19590 Neuroblastoma 193 Other (also 3394 Primates bodymap) 152 bp exon 1698 bp [gt-ag] intron 32 GenBank accessions 45283 RNA-seq supporting reads 7538 UHR pooled cells 5804 Brain 4758 Blood 26988 Neuroblastoma 195 Other (also 5780 Primates bodymap) 198 bp exon 938 bp [gt-ag] intron 37 GenBank accessions 31542 RNA-seq supporting reads 5503 UHR pooled cells 3739 Brain 4025 Blood 18091 Neuroblastoma 184 Other (also 3591 Primates bodymap) 73 bp exon 276 bp [gt-ag] intron 33 GenBank accessions 22973 RNA-seq supporting reads 4037 UHR pooled cells 2898 Brain 2035 Blood 13878 Neuroblastoma 125 Other (also 2350 Primates bodymap) 143 bp exon 1451 bp [gt-ag] intron 41 GenBank accessions 44603 RNA-seq supporting reads 7236 UHR pooled cells 5473 Brain 5294 Blood 26439 Neuroblastoma 161 Other (also 5210 Primates bodymap) 140 bp exon 1230 bp [gt-ag] intron 50 GenBank accessions 48594 RNA-seq supporting reads 8108 UHR pooled cells 6112 Brain 3910 Blood 30255 Neuroblastoma 209 Other (also 4540 Primates bodymap) 181 bp exon 1727 bp [gt-ag] intron 61 GenBank accessions 48148 RNA-seq supporting reads 8112 UHR pooled cells 5992 Brain 4991 Blood 28911 Neuroblastoma 142 Other (also 5091 Primates bodymap) 694 bp exon 82 accessions, some from lung (seen 11 times) brain (8), kidney (8) glioblastoma (pooled) (6) testis (6) Validated 3' end, 1 accession Validated 3' end, 18 accessions 694 bp exon 195 bp exon 16785 bp [gt-ag] intron 162 GenBank accessions 24856 RNA-seq supporting reads 4069 UHR pooled cells 2749 Brain 2568 Blood 15374 Neuroblastoma 96 Other (also 5590 Primates bodymap) 162 bp exon 1132 bp [gt-ag] intron 169 GenBank accessions 27106 RNA-seq supporting reads 4450 UHR pooled cells 3188 Brain 3669 Blood 15710 Neuroblastoma 89 Other (also 5991 Primates bodymap) 66 bp exon 501 bp [gt-ag] intron 3 GenBank accessions 96 RNA-seq supporting reads 10 UHR pooled cells 24 Brain 7 Blood 55 Neuroblastoma (also 2 Primates bodymap) 233 bp exon 1583 bp [gt-ag] intron 1 GenBank accession 66 RNA-seq supporting reads 9 UHR pooled cells 24 Brain 9 Blood 24 Neuroblastoma (also 4 Primates bodymap) 81 bp exon 81 bp exon 1262 bp [gt-ag] intron 154 GenBank accessions 29753 RNA-seq supporting reads 4028 UHR pooled cells 2857 Brain 6720 Blood 15992 Neuroblastoma 156 Other (also 6162 Primates bodymap) 104 bp exon 4088 bp [gt-ag] intron 58 GenBank accessions 28445 RNA-seq supporting reads 4214 UHR pooled cells 3139 Brain 5738 Blood 15210 Neuroblastoma 144 Other (also 5934 Primates bodymap) 109 bp exon 571 bp [gt-ag] intron 38 GenBank accessions 23879 RNA-seq supporting reads 4114 UHR pooled cells 2946 Brain 3308 Blood 13374 Neuroblastoma 137 Other (also 4095 Primates bodymap) 180 bp exon 1980 bp [gt-ag] intron 36 GenBank accessions 25308 RNA-seq supporting reads 4159 UHR pooled cells 2971 Brain 4463 Blood 13589 Neuroblastoma 126 Other (also 5184 Primates bodymap) 125 bp exon 3357 bp [gt-ag] intron 35 GenBank accessions 30627 RNA-seq supporting reads 5061 UHR pooled cells 3303 Brain 4037 Blood 18018 Neuroblastoma 208 Other (also 6204 Primates bodymap) 127 bp exon 3788 bp [gt-ag] intron 38 GenBank accessions 25837 RNA-seq supporting reads 4526 UHR pooled cells 2956 Brain 2527 Blood 15638 Neuroblastoma 190 Other (also 4799 Primates bodymap) 140 bp exon 4521 bp [gt-ag] intron 33 GenBank accessions 30523 RNA-seq supporting reads 5427 UHR pooled cells 3863 Brain 2886 Blood 18169 Neuroblastoma 178 Other (also 3624 Primates bodymap) 62 bp exon 1449 bp [gt-ag] intron 30 GenBank accessions 32208 RNA-seq supporting reads 5469 UHR pooled cells 4019 Brain 2937 Blood 19590 Neuroblastoma 193 Other (also 3394 Primates bodymap) 152 bp exon 1698 bp [gt-ag] intron 32 GenBank accessions 45283 RNA-seq supporting reads 7538 UHR pooled cells 5804 Brain 4758 Blood 26988 Neuroblastoma 195 Other (also 5780 Primates bodymap) 198 bp exon 938 bp [gt-ag] intron 37 GenBank accessions 31542 RNA-seq supporting reads 5503 UHR pooled cells 3739 Brain 4025 Blood 18091 Neuroblastoma 184 Other (also 3591 Primates bodymap) 73 bp exon 276 bp [gt-ag] intron 33 GenBank accessions 22973 RNA-seq supporting reads 4037 UHR pooled cells 2898 Brain 2035 Blood 13878 Neuroblastoma 125 Other (also 2350 Primates bodymap) 143 bp exon 1451 bp [gt-ag] intron 41 GenBank accessions 44603 RNA-seq supporting reads 7236 UHR pooled cells 5473 Brain 5294 Blood 26439 Neuroblastoma 161 Other (also 5210 Primates bodymap) 140 bp exon 1230 bp [gt-ag] intron 50 GenBank accessions 48594 RNA-seq supporting reads 8108 UHR pooled cells 6112 Brain 3910 Blood 30255 Neuroblastoma 209 Other (also 4540 Primates bodymap) 181 bp exon 1727 bp [gt-ag] intron 61 GenBank accessions 48148 RNA-seq supporting reads 8112 UHR pooled cells 5992 Brain 4991 Blood 28911 Neuroblastoma 142 Other (also 5091 Primates bodymap) 334 bp exon 3 accessions, some from testis (seen 2 times) amygdala (once) capped 5' end, 1 accession 334 bp exon 195 bp exon 195 bp exon 16785 bp [gt-ag] intron 162 GenBank accessions 24856 RNA-seq supporting reads 4069 UHR pooled cells 2749 Brain 2568 Blood 15374 Neuroblastoma 96 Other (also 5590 Primates bodymap) 162 bp exon 1132 bp [gt-ag] intron 169 GenBank accessions 27106 RNA-seq supporting reads 4450 UHR pooled cells 3188 Brain 3669 Blood 15710 Neuroblastoma 89 Other (also 5991 Primates bodymap) 66 bp exon 2317 bp [gt-ag] intron 160 GenBank accessions 29248 RNA-seq supporting reads 4670 UHR pooled cells 3209 Brain 4441 Blood 16813 Neuroblastoma 115 Other (also 5963 Primates bodymap) 81 bp exon 1262 bp [gt-ag] intron 154 GenBank accessions 29753 RNA-seq supporting reads 4028 UHR pooled cells 2857 Brain 6720 Blood 15992 Neuroblastoma 156 Other (also 6162 Primates bodymap) 104 bp exon 4088 bp [gt-ag] intron 58 GenBank accessions 28445 RNA-seq supporting reads 4214 UHR pooled cells 3139 Brain 5738 Blood 15210 Neuroblastoma 144 Other (also 5934 Primates bodymap) 251 bp exon 1 accession from tongue tumor tissue 251 bp exon 150 bp exon 135 bp [gt-ag] intron 2 GenBank accessions 191 RNA-seq supporting reads 71 Brain 120 Neuroblastoma 140 bp exon 4521 bp [gt-ag] intron 33 GenBank accessions 30523 RNA-seq supporting reads 5427 UHR pooled cells 3863 Brain 2886 Blood 18169 Neuroblastoma 178 Other (also 3624 Primates bodymap) 62 bp exon 1449 bp [gt-ag] intron 30 GenBank accessions 32208 RNA-seq supporting reads 5469 UHR pooled cells 4019 Brain 2937 Blood 19590 Neuroblastoma 193 Other (also 3394 Primates bodymap) 152 bp exon 1698 bp [gt-ag] intron 32 GenBank accessions 45283 RNA-seq supporting reads 7538 UHR pooled cells 5804 Brain 4758 Blood 26988 Neuroblastoma 195 Other (also 5780 Primates bodymap) 198 bp exon 938 bp [gt-ag] intron 37 GenBank accessions 31542 RNA-seq supporting reads 5503 UHR pooled cells 3739 Brain 4025 Blood 18091 Neuroblastoma 184 Other (also 3591 Primates bodymap) 73 bp exon 276 bp [gt-ag] intron 33 GenBank accessions 22973 RNA-seq supporting reads 4037 UHR pooled cells 2898 Brain 2035 Blood 13878 Neuroblastoma 125 Other (also 2350 Primates bodymap) 143 bp exon 1451 bp [gt-ag] intron 41 GenBank accessions 44603 RNA-seq supporting reads 7236 UHR pooled cells 5473 Brain 5294 Blood 26439 Neuroblastoma 161 Other (also 5210 Primates bodymap) 140 bp exon 1230 bp [gt-ag] intron 50 GenBank accessions 48594 RNA-seq supporting reads 8108 UHR pooled cells 6112 Brain 3910 Blood 30255 Neuroblastoma 209 Other (also 4540 Primates bodymap) 181 bp exon 1727 bp [gt-ag] intron 61 GenBank accessions 48148 RNA-seq supporting reads 8112 UHR pooled cells 5992 Brain 4991 Blood 28911 Neuroblastoma 142 Other (also 5091 Primates bodymap) 163 bp exon 2 accessions, some from testis (seen 2 times) 163 bp exon 138 bp exon 138 bp exon 132 bp uORF 16789 bp [gt-ag] intron 1 GenBank accession 86 RNA-seq supporting reads 8 UHR pooled cells 20 Brain 5 Blood 53 Neuroblastoma (also 18 Primates bodymap) 132 bp uORF 158 bp exon 158 bp exon 158 bp exon 1132 bp [gt-ag] intron 169 GenBank accessions 27106 RNA-seq supporting reads 4450 UHR pooled cells 3188 Brain 3669 Blood 15710 Neuroblastoma 89 Other (also 5991 Primates bodymap) 66 bp exon 66 bp exon 2317 bp [gt-ag] intron 160 GenBank accessions 29248 RNA-seq supporting reads 4670 UHR pooled cells 3209 Brain 4441 Blood 16813 Neuroblastoma 115 Other (also 5963 Primates bodymap) 81 bp exon 81 bp exon 1262 bp [gt-ag] intron 154 GenBank accessions 29753 RNA-seq supporting reads 4028 UHR pooled cells 2857 Brain 6720 Blood 15992 Neuroblastoma 156 Other (also 6162 Primates bodymap) 104 bp exon 104 bp exon 4088 bp [gt-ag] intron 58 GenBank accessions 28445 RNA-seq supporting reads 4214 UHR pooled cells 3139 Brain 5738 Blood 15210 Neuroblastoma 144 Other (also 5934 Primates bodymap) 109 bp exon 109 bp exon 571 bp [gt-ag] intron 38 GenBank accessions 23879 RNA-seq supporting reads 4114 UHR pooled cells 2946 Brain 3308 Blood 13374 Neuroblastoma 137 Other (also 4095 Primates bodymap) 180 bp exon 180 bp exon 1723 bp [gt-ag] intron 1 GenBank accession 467 RNA-seq supporting reads 29 UHR pooled cells 15 Brain 118 Blood 301 Neuroblastoma 4 Other 337 bp exon 337 bp exon 2 accessions, some from hypothalamus (seen once) tongue, tumor tissue (once) capped 5' end, 1 accession 337 bp exon 118 bp exon 118 bp exon 87 bp uORF 644 bp [gt-ag] intron 1 GenBank accession 25 RNA-seq supporting reads 6 UHR pooled cells 3 Brain 16 Neuroblastoma 87 bp uORF 152 bp exon 152 bp exon 152 bp exon 1698 bp [gt-ag] intron 32 GenBank accessions 45283 RNA-seq supporting reads 7538 UHR pooled cells 5804 Brain 4758 Blood 26988 Neuroblastoma 195 Other (also 5780 Primates bodymap) 198 bp exon 198 bp exon 938 bp [gt-ag] intron 37 GenBank accessions 31542 RNA-seq supporting reads 5503 UHR pooled cells 3739 Brain 4025 Blood 18091 Neuroblastoma 184 Other (also 3591 Primates bodymap) 73 bp exon 73 bp exon 276 bp [gt-ag] intron 33 GenBank accessions 22973 RNA-seq supporting reads 4037 UHR pooled cells 2898 Brain 2035 Blood 13878 Neuroblastoma 125 Other (also 2350 Primates bodymap) 109 bp exon 109 bp exon 1 accession from normal nasopharynx 109 bp exon 191 bp exon 191 bp exon 16785 bp [gt-ag] intron 162 GenBank accessions 24856 RNA-seq supporting reads 4069 UHR pooled cells 2749 Brain 2568 Blood 15374 Neuroblastoma 96 Other (also 5590 Primates bodymap) 162 bp exon 1132 bp [gt-ag] intron 169 GenBank accessions 27106 RNA-seq supporting reads 4450 UHR pooled cells 3188 Brain 3669 Blood 15710 Neuroblastoma 89 Other (also 5991 Primates bodymap) 66 bp exon 2317 bp [gt-ag] intron 160 GenBank accessions 29248 RNA-seq supporting reads 4670 UHR pooled cells 3209 Brain 4441 Blood 16813 Neuroblastoma 115 Other (also 5963 Primates bodymap) 81 bp exon 1262 bp [gt-ag] intron 154 GenBank accessions 29753 RNA-seq supporting reads 4028 UHR pooled cells 2857 Brain 6720 Blood 15992 Neuroblastoma 156 Other (also 6162 Primates bodymap) 104 bp exon 4088 bp [gt-ag] intron 58 GenBank accessions 28445 RNA-seq supporting reads 4214 UHR pooled cells 3139 Brain 5738 Blood 15210 Neuroblastoma 144 Other (also 5934 Primates bodymap) 109 bp exon 142 bp [gt-ag] intron 1 GenBank accession 42 RNA-seq supporting reads 2 UHR pooled cells 7 Brain 8 Blood 24 Neuroblastoma 1 Other 196 bp exon 196 bp exon 233 bp [gt-ag] intron 1 GenBank accession 43 RNA-seq supporting reads 7 UHR pooled cells 2 Brain 16 Blood 17 Neuroblastoma 1 Other 2285 bp exon 3357 bp [gt-ag] intron 35 GenBank accessions 30627 RNA-seq supporting reads 5061 UHR pooled cells 3303 Brain 4037 Blood 18018 Neuroblastoma 208 Other (also 6204 Primates bodymap) 127 bp exon 3788 bp [gt-ag] intron 38 GenBank accessions 25837 RNA-seq supporting reads 4526 UHR pooled cells 2956 Brain 2527 Blood 15638 Neuroblastoma 190 Other (also 4799 Primates bodymap) 4957 bp exon Sequence gap 7586 bp 109 bp exon 1727 bp [gt-ag] intron 61 GenBank accessions 48148 RNA-seq supporting reads 8112 UHR pooled cells 5992 Brain 4991 Blood 28911 Neuroblastoma 142 Other (also 5091 Primates bodymap) 20 accessions, some from eye (seen 7 times) retina (6), uterus (2) well-differentiated endometrialadenocarcinoma 7 pooled tumors (2), breast (once) 442 bp exon 16 bp exon 16 bp exon 16583 bp [gt-ag] intron 2 GenBank accessions 15 RNA-seq supporting reads 7 Brain 1 Blood 6 Neuroblastoma 1 Other 162 bp exon 1132 bp [gt-ag] intron 169 GenBank accessions 27106 RNA-seq supporting reads 4450 UHR pooled cells 3188 Brain 3669 Blood 15710 Neuroblastoma 89 Other (also 5991 Primates bodymap) 66 bp exon 2317 bp [gt-ag] intron 160 GenBank accessions 29248 RNA-seq supporting reads 4670 UHR pooled cells 3209 Brain 4441 Blood 16813 Neuroblastoma 115 Other (also 5963 Primates bodymap) 81 bp exon 1262 bp [gt-ag] intron 154 GenBank accessions 29753 RNA-seq supporting reads 4028 UHR pooled cells 2857 Brain 6720 Blood 15992 Neuroblastoma 156 Other (also 6162 Primates bodymap) 104 bp exon 4088 bp [gt-ag] intron 58 GenBank accessions 28445 RNA-seq supporting reads 4214 UHR pooled cells 3139 Brain 5738 Blood 15210 Neuroblastoma 144 Other (also 5934 Primates bodymap) 2 accessions, some from colon (seen once) 109 bp exon 176 bp exon 1230 bp [gt-ag] intron 50 GenBank accessions 48594 RNA-seq supporting reads 8108 UHR pooled cells 6112 Brain 3910 Blood 30255 Neuroblastoma 209 Other (also 4540 Primates bodymap) 436 bp exon 2 accessions 436 bp exon 634 bp exon 634 bp exon 2 accessions, some from uterus (seen once) capped 5' end, 1 accession 634 bp exon 541 bp exon 541 bp exon 2 accessions, some from brain (seen once) colon ins (once), tumor 5 pooled (see description) (once) Validated 3' end, 1 accession 541 bp exon 399 bp exon 399 bp exon 399 bp exon 96 bp [gc-ag] intron 1 GenBank accession 55 RNA-seq supporting reads 7 UHR pooled cells 9 Blood 39 Neuroblastoma 1 accession from cerebellum capped 5' end, 1 accession 152 bp exon 575 bp exon 575 bp exon 42 bp uORF 575 bp exon 575 bp exon 1451 bp [gt-ag] intron 41 GenBank accessions 44603 RNA-seq supporting reads 7236 UHR pooled cells 5473 Brain 5294 Blood 26439 Neuroblastoma 161 Other (also 5210 Primates bodymap) 250 bp exon 250 bp exon 2 accessions, some from brain (seen once) 250 bp exon 1281 bp exon 1281 bp exon 4 accessions, some from lung (seen 2 times) carcinoid (once), multiple sclerosis lesions (once) skin (once), squamous cell carcinoma (once) 1281 bp exon Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
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Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR uORF Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
aAug10 2960 bp 738 aa 151 bp 592 bp 2kb possibly including promoter 51530 bp 1kb
bAug10 2956 bp 737 aa 151 bp 591 bp 105 bp 2kb including Promoter 51529 bp 1kb
cAug10 2967 bp 679 aa 335 bp 592 bp 2kb possibly including promoter 51175 bp 1kb
dAug10 2805 bp 622 aa 704 bp 232 bp 2kb including Promoter 51142 bp 1kb
eAug10 1402 bp 446 aa 61 bp 2kb 14827 bp 1kb
fAug10 1173 bp 223 aa 239 bp 262 bp 129 bp 2kb including Promoter 29055 bp 1kb
gAug10 859 bp 220 aa 123 bp 73 bp 2kb probably including promoter 26443 bp 1kb
hAug10 9517 bp 205 aa 119 bp 8780 bp 2kb probably including promoter 51246 bp 1kb
iAug10 538 bp 179 aa 2kb 25920 bp 1kb
jAug10 650 bp 153 aa 189 bp 84 bp 2kb possibly including promoter 4206 bp 1kb
kAug10 612 bp 145 aa 174 bp 2kb 1842 bp 1kb
lAug10 825 bp 93 aa 437 bp 106 bp 39 bp 2kb possibly including promoter 2276 bp 1kb
mAug10-unspliced 1281 bp 78 aa 1026 bp 18 bp 2kb 1281 bp 1kb
nAug10-unspliced 634 bp 89 aa 97 bp 267 bp 2kb including Promoter 634 bp 1kb
oAug10 551 bp 36 aa 199 bp 241 bp 2kb including Promoter 647 bp 1kb
pAug10-unspliced 541 bp 49 aa 378 bp 13 bp 2kb 541 bp 1kb

Gene neighbors and Navigator on chromosome 1q42.2 back to top
C COG2 C I R P CAPN9 D C R P R ARV1 C R P R C D C R P PGBD5 C D C I R P AGT C C R P C1orf198 C R P TTC13 C R FAM89A 100kb 0 GALNT2, 494 accessions 19 variants reyoha, 2 accessions COG2, 393 accessions, 16 variants CAPN9, 38 accessions, 7 variants mosiyo, 12 accessions 5 variants ARV1, 234 accessions, 14 variants blanawbu, 1 accession blunawbu, 1 accession blonawbu, 2 accessions blarnawbu, 1 accession blasabu, 1 accession bleenawbu, 1 accession blernawbu, 1 accession nerweybo, 4 accessions bloynawbu, 2 accessions neyweybo, 2 accessions niyaro, 3 accessions flynawbu, 2 accessions noyweybo, 1 accession pyweybo, 1 accession blersabu, 1 accession goylobo, 2 accessions flarnawbu, 1 accession kowabo, 1 accession klersabu, 1 accession fleynawbu, 1 accession smawsabu, 1 accession smerrobo, 3 accessions perweybo, 1 accession glanawbu, 2 accessions glynawbu, 1 accession porweybo, 1 accession gleynawbu, 1 accession slaply, 1 accession poyweybo, 1 accession gloynawbu, 1 accession klanawbu, 1 accession voylor, 6 accessions smeyrobo, 4 accessions kolobo, 2 accessions mesiyo, 1 accession steesabu, 1 accession klernawbu, 1 accession nuyaro, 9 accessions kleynawbu, 1 accession ruweybo, 1 accession dersybu, 1 accession snarrobo, 1 accession deysybu, 2 accessions sneerobo, 4 accessions karwabo, 1 accession pleynawbu, 1 accession plornawbu, 2 accessions yayoha, 3 accessions, 2 variants larlobo, 1 accession skynawbu, 1 accession skonawbu, 1 accession lorlobo, 3 accessions meysybu, 1 accession tarsybu, 1 accession veysybu, 1 accession slanawbu, 2 accessions vorsybu, 1 accession slonawbu, 2 accessions rawweybo, 1 accession reeweybo, 1 accession slernawbu, 1 accession slornawbu, 2 accessions blersybu, 1 accession meelobo, 1 accession smawnawbu, 1 accession sheynawbu, 1 accession shornawbu, 1 accession shoynawbu, 1 accession blynawbu, 1 accession blawnawbu, 1 accession gerlobo, 1 accession blornawbu, 6 accessions flanawbu, 1 accession gorlobo, 1 accession norweybo, 1 accession puweybo, 1 accession poweybo, 1 accession parweybo, 3 accessions flernawbu, 1 accession peeweybo, 1 accession jeerobo, 1 accession skoyply, 22 accessions flornawbu, 1 accession floynawbu, 1 accession jarlobo, 1 accession peyweybo, 1 accession jawlobo, 1 accession glonawbu, 1 accession glarnawbu, 1 accession glawnawbu, 1 accession gleenawbu, 1 accession glernawbu, 1 accession jerlobo, 1 accession glornawbu, 1 accession kesimo, 3 accessions, 2 variants klunawbu, 2 accessions jorlobo, 1 accession kokoyo, 3 accessions, 2 variants klarnawbu, 1 accession kalobo, 2 accessions kylobo, 1 accession smorrobo, 2 accessions keelobo, 1 accession kerlobo, 1 accession seeber, 1 accession ryweybo, 1 accession royoha, 2 accessions, 2 variants kloynawbu, 1 accession bawsybu, 1 accession planawbu, 1 accession plunawbu, 1 accession plawnawbu, 1 accession pleenawbu, 1 accession lulobo, 2 accessions wawama, 1 accession rawama, 1 accession ploynawbu, 1 accession kusybu, 2 accessions soyber, 1 accession skanawbu, 1 accession skunawbu, 1 accession lerlobo, 3 accessions roweybo, 1 accession musybu, 5 accessions rarweybo, 1 accession skernawbu, 2 accessions skeynawbu, 1 accession skornawbu, 1 accession skoynawbu, 1 accession loylobo, 1 accession riwama, 1 accession malobo, 1 accession slarply, 8 accessions slunawbu, 2 accessions wasybu, 1 accession mylobo, 5 accessions slarnawbu, 1 accession mulobo, 1 accession sleynawbu, 1 accession plubar, 2 accessions pleybar, 1 accession sloynawbu, 1 accession wysybu, 1 accession smonawbu, 1 accession rerweybo, 1 accession smarnawbu, 1 accession skeeply, 11 accessions 4 variants karobo, 1 accession PGBD5, 113 accessions 4 variants jeelobo, 1 accession AGT, 413 accessions, 11 variants fersybu, 1 accession C1orf198, 499 accessions 7 variants TTC13, 147 accessions 12 variants FAM89A, 163 accessions 7 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               10 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i, .j, .k, .l, .m-u, .n-u, .o, .p-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes CI

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

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