Homo sapiens complex locus PSMC6, encoding proteasome (prosome, macropain) 26S subunit, ATPase, 6.
TABLE OF CONTENTS / OPEN CLOSE ALL PARAGRAPHS
SUMMARY back to top
RefSeq summary
[PSMC6] The 26S proteasome is a multicatalytic proteinase complex with a highly ordered structure composed of 2 complexes, a 20S core and a 19S regulator. The 20S core is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. The 19S regulator is composed of a base, which contains 6 ATPase subunits and 2 non-ATPase subunits, and a lid, which contains up to 10 non-ATPase subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes one of the ATPase subunits, a member of the triple-A family of ATPases which have a chaperone-like activity. Pseudogenes have been identified on chromosomes 8 and 12. [provided by RefSeq].

RefSeq annotates one representative transcript (NM included in AceView variant.a), 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, 2.4 times the average gene in this release. The sequence of this gene is defined by 661 GenBank accessions, some from placenta (seen 18 times), uterus (17), placenta cot 25-normalized (14), lung (10), eye (8), brain (7), leiomyosarcoma (7) and 108 other tissues. We annotate structural defects or features in 7 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 22 distinct gt-ag introns. Transcription produces 14 different mRNAs, 13 alternatively spliced variants and 1 unspliced form. There are 2 probable alternative promotors, 5 non overlapping alternative last exons and 8 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 5 cassette exons, overlapping exons with different boundaries, splicing versus retention of 6 introns.
2 variants were isolated in vivo, despite the fact that they are predicted targets of nonsense mediated mRNA decay (NMD).
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 aAug10, eAug10).
Function: There are 45 articles specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in pathway (Proteasome) and a process (protein catabolic process). Proteins are expected to have molecular functions (ATP binding, hydrolase activity, nucleotide binding) and to localize in cytoplasm. Putative protein interactors have been described (ATXN7, C1ORF216, CCDC85B, CRK, PAAF1, PMS2, PSMC5, PSMC6, PSMD6, PSMD7, PSMD9ANDWDR66, PSMD10, PSMD13, PSMD14, UCHL5, USP14).
Protein coding potential: 9 spliced mRNAs putatively encode good proteins, altogether 9 different isoforms (8 complete, 1 partial), some containing domains ATPase family associated with various cellular activities (AAA), ATPase family associated with various cellular activities (AAA) [Pfam], a second peroximal domain, a coiled coil stretch [Psort2]. The remaining 5 mRNA variants (4 spliced, 1 unspliced; 1 partial) appear not to encode good proteins.
Isoform PSMC6.eAug10 is annotated using as Met a Kozak-compatible g..AGGg start, thereby gaining 73 amino acids N-terminal to the first AUG. Finally proteins from this gene may be modulated by acetylation; phosphorylation; 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 14, links to other databases and other names
Map: This gene PSMC6 maps on chromosome 14, at 14q22.1 according to Entrez Gene. In AceView, it covers 21.41 kb, from 53173902 to 53195307 (NCBI 37, August 2010), on the direct strand.
Links to: manual annotations from KEGG_03050, PhosphoSite, the SNP view, gene overviews from Entrez Gene 5706, 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 PSMC6, P44, p42, SUG2, CADP44, MGC12520 or LOC5706, joynawby. It has been described as 26S protease regulatory subunit 10B, proteasome subunit p42, proteasome 26S subunit ATPase 6, conserved ATPase domain protein 44, 26S protease regulatory subunit S10B, 26S proteasome AAA-ATPase subunit RPT4.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Psmc6 (e= 10-102).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene rpt-4 (e=6 10-84), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes AT1G45000 (e=8 10-75), RPT4A (e=3 10-74), 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
PSMC6 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 35.1 16.4 26.6 17.6 18.8 37.6 24.8 21.6 11.6 18.8 11.6 40.3 32.8 46.3 43.2 46.3 28.5 28.5 28.5 32.8 37.6 28.5 32.8 21.6 46.3 46.3 53.2 199 32.8 17.6 18.8 18.8 57.1 37.6 37.6 13.3 16.4 21.6 23.2 16.4 28.5 30.6 26.6 35.1 30.6 21.6 30.6 30.6 23.2 30.6 46.3 46.3 30.6 32.8 43.2 43.2 32.8 40.3 37.6 28.5 40.3 35.1 28.5 40.3 23.2 26.6 30.6 40.3 32.8 28.5 28.5 57.1 40.3 35.1 32.8 32.8 32.8 37.6 21.6 23.2 30.6 49.7 40.3 32.8 32.8 32.8 35.1 37.6 28.5 26.6 35.1 28.5 40.3 35.1 24.8 23.2 37.6 49.7 32.8 32.8 37.6 32.8 40.3 46.3 43.2 37.6 32.8 37.6 43.2 46.3 32.8 24.8 32.8 30.6 37.6 30.6 57.1 30.6 30.6 32.8 32.8 37.6 43.2 43.2 43.2 37.6 35.1 92.7 37.6 35.1 30.6 30.6 21.6 26.6 30.6 46.3 57.1 106 75.3 43.2 37.6 43.2 35.1 21.6 23.2 43.2 35.1 40.3 37.6 40.3 26.6 26.6 32.8 40.3 26.6 26.6 16.4 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 PSMC6 5' 3' encoded on plus strand of chromosome 14 from 53,173,902 to 53,195,307 106162 101630 114846 150571 155141 115112 113330 147240 159313 175781 a [NM] 106162 101630 114846 150571 155141 115112 b 106162 101630 1715 150571 155141 115112 425 175781 c 1050 114846 150571 155141 115112 d 175781 j 1779 101630 114846 150571 155141 115112 e n-u 99 101630 114846 150571 155141 f 106162 101630 g 2098 175781 l 106162 101630 6674 150571 155141 h 175781 k 106162 101630 i 1779 101630 10 m 1 2kb 0 121 bp exon 121 bp exon 108 bp uORF 121 bp exon 1004 bp [gt-ag] intron 135 GenBank accessions 106027 RNA-seq supporting reads 20569 UHR pooled cells 13891 Brain 4400 Blood 65865 Neuroblastoma 1302 Other (also 23206 Primates bodymap) 108 bp uORF 80 bp exon 80 bp exon 94 bp [gt-ag] intron 146 GenBank accessions 101484 RNA-seq supporting reads 19941 UHR pooled cells 14101 Brain 5951 Blood 60519 Neuroblastoma 972 Other (also 12570 Primates bodymap) 40 bp exon 40 bp exon 241 bp [gt-ag] intron 142 GenBank accessions 109059 RNA-seq supporting reads 21369 UHR pooled cells 15094 Brain 6868 Blood 64731 Neuroblastoma 997 Other (also 25460 Primates bodymap) 53 bp exon 53 bp exon 2284 bp [gt-ag] intron 133 GenBank accessions 114713 RNA-seq supporting reads 23531 UHR pooled cells 16757 Brain 7486 Blood 65774 Neuroblastoma 1165 Other (also 22061 Primates bodymap) 68 bp exon 68 bp exon 241 bp [gt-ag] intron 143 GenBank accessions 150428 RNA-seq supporting reads 28443 UHR pooled cells 20051 Brain 8163 Blood 92129 Neuroblastoma 1642 Other (also 26115 Primates bodymap) 115 bp exon 115 bp exon 2356 bp [gt-ag] intron 139 GenBank accessions 155002 RNA-seq supporting reads 30635 UHR pooled cells 20871 Brain 7065 Blood 94470 Neuroblastoma 1961 Other (also 27234 Primates bodymap) 88 bp exon 88 bp exon 4112 bp [gt-ag] intron 131 GenBank accessions 114981 RNA-seq supporting reads 22650 UHR pooled cells 16114 Brain 6078 Blood 69009 Neuroblastoma 1130 Other (also 18691 Primates bodymap) 62 bp exon 62 bp exon 86 bp [gt-ag] intron 110 GenBank accessions 108744 RNA-seq supporting reads 21677 UHR pooled cells 15461 Brain 4107 Blood 66355 Neuroblastoma 1144 Other (also 20862 Primates bodymap) 124 bp exon 124 bp exon 624 bp [gt-ag] intron 95 GenBank accessions 136800 RNA-seq supporting reads 27359 UHR pooled cells 18942 Brain 6332 Blood 82968 Neuroblastoma 1199 Other (also 26587 Primates bodymap) 62 bp exon 62 bp exon 1822 bp [gt-ag] intron 82 GenBank accessions 113248 RNA-seq supporting reads 23375 UHR pooled cells 16268 Brain 5489 Blood 66904 Neuroblastoma 1212 Other (also 22320 Primates bodymap) 121 bp exon 121 bp exon 128 bp [gt-ag] intron 80 GenBank accessions 147160 RNA-seq supporting reads 29586 UHR pooled cells 20872 Brain 7601 Blood 87861 Neuroblastoma 1240 Other (also 29279 Primates bodymap) 81 bp exon 81 bp exon 2774 bp [gt-ag] intron 77 GenBank accessions 159236 RNA-seq supporting reads 33658 UHR pooled cells 24787 Brain 5292 Blood 94288 Neuroblastoma 1211 Other (also 7272 Primates bodymap) 72 bp exon 72 bp exon 3462 bp [gt-ag] intron 96 GenBank accessions 175685 RNA-seq supporting reads 34741 UHR pooled cells 24505 Brain 6278 Blood 109042 Neuroblastoma 1119 Other (also 7141 Primates bodymap) 1091 bp exon 1091 bp exon 182 accessions, NM_002806.3 some from placenta (seen 16 times) placenta cot 25-normalized (14) lung (8), eye (7), uterus (7) capped 5' end, 19 accessions Validated 3' end, 3 accessions Validated 3' end, 2 accessions Validated 3' end, 1 accession Validated 3' end, 4 accessions Validated 3' end, 26 accessions 1091 bp exon 101 bp exon 101 bp exon 1004 bp [gt-ag] intron 135 GenBank accessions 106027 RNA-seq supporting reads 20569 UHR pooled cells 13891 Brain 4400 Blood 65865 Neuroblastoma 1302 Other (also 23206 Primates bodymap) 80 bp exon 94 bp [gt-ag] intron 146 GenBank accessions 101484 RNA-seq supporting reads 19941 UHR pooled cells 14101 Brain 5951 Blood 60519 Neuroblastoma 972 Other (also 12570 Primates bodymap) 40 bp exon 241 bp [gt-ag] intron 142 GenBank accessions 109059 RNA-seq supporting reads 21369 UHR pooled cells 15094 Brain 6868 Blood 64731 Neuroblastoma 997 Other (also 25460 Primates bodymap) 53 bp exon 2284 bp [gt-ag] intron 133 GenBank accessions 114713 RNA-seq supporting reads 23531 UHR pooled cells 16757 Brain 7486 Blood 65774 Neuroblastoma 1165 Other (also 22061 Primates bodymap) 68 bp exon 241 bp [gt-ag] intron 143 GenBank accessions 150428 RNA-seq supporting reads 28443 UHR pooled cells 20051 Brain 8163 Blood 92129 Neuroblastoma 1642 Other (also 26115 Primates bodymap) 115 bp exon 2356 bp [gt-ag] intron 139 GenBank accessions 155002 RNA-seq supporting reads 30635 UHR pooled cells 20871 Brain 7065 Blood 94470 Neuroblastoma 1961 Other (also 27234 Primates bodymap) 88 bp exon 4112 bp [gt-ag] intron 131 GenBank accessions 114981 RNA-seq supporting reads 22650 UHR pooled cells 16114 Brain 6078 Blood 69009 Neuroblastoma 1130 Other (also 18691 Primates bodymap) 208 bp exon 3 accessions, some from pooled pancreas and spleen (seen once) testis (once) 208 bp exon 90 bp exon 1004 bp [gt-ag] intron 135 GenBank accessions 106027 RNA-seq supporting reads 20569 UHR pooled cells 13891 Brain 4400 Blood 65865 Neuroblastoma 1302 Other (also 23206 Primates bodymap) 80 bp exon 94 bp [gt-ag] intron 146 GenBank accessions 101484 RNA-seq supporting reads 19941 UHR pooled cells 14101 Brain 5951 Blood 60519 Neuroblastoma 972 Other (also 12570 Primates bodymap) 224 bp exon 224 bp exon 2394 bp [gt-ag] intron 3 GenBank accessions 1712 RNA-seq supporting reads 21 UHR pooled cells 154 Brain 1 Blood 1526 Neuroblastoma 10 Other (also 62 Primates bodymap) 68 bp exon 241 bp [gt-ag] intron 143 GenBank accessions 150428 RNA-seq supporting reads 28443 UHR pooled cells 20051 Brain 8163 Blood 92129 Neuroblastoma 1642 Other (also 26115 Primates bodymap) 115 bp exon 2356 bp [gt-ag] intron 139 GenBank accessions 155002 RNA-seq supporting reads 30635 UHR pooled cells 20871 Brain 7065 Blood 94470 Neuroblastoma 1961 Other (also 27234 Primates bodymap) 88 bp exon 4112 bp [gt-ag] intron 131 GenBank accessions 114981 RNA-seq supporting reads 22650 UHR pooled cells 16114 Brain 6078 Blood 69009 Neuroblastoma 1130 Other (also 18691 Primates bodymap) 62 bp exon 86 bp [gt-ag] intron 110 GenBank accessions 108744 RNA-seq supporting reads 21677 UHR pooled cells 15461 Brain 4107 Blood 66355 Neuroblastoma 1144 Other (also 20862 Primates bodymap) 124 bp exon 624 bp [gt-ag] intron 95 GenBank accessions 136800 RNA-seq supporting reads 27359 UHR pooled cells 18942 Brain 6332 Blood 82968 Neuroblastoma 1199 Other (also 26587 Primates bodymap) 62 bp exon 4926 bp [gt-ag] intron 1 GenBank accession 424 RNA-seq supporting reads 56 UHR pooled cells 67 Brain 15 Blood 286 Neuroblastoma (also 81 Primates bodymap) 72 bp exon 72 bp exon 3462 bp [gt-ag] intron 96 GenBank accessions 175685 RNA-seq supporting reads 34741 UHR pooled cells 24505 Brain 6278 Blood 109042 Neuroblastoma 1119 Other (also 7141 Primates bodymap) 4 accessions, some from brain (seen 2 times) hypothalamus (2), adenocarcinoma (once) pancreas (once) 496 bp exon 121 bp exon 121 bp exon 1178 bp [gt-ag] intron 2 GenBank accessions 1048 RNA-seq supporting reads 65 UHR pooled cells 260 Brain 46 Blood 660 Neuroblastoma 17 Other (also 75 Primates bodymap) 40 bp exon 241 bp [gt-ag] intron 142 GenBank accessions 109059 RNA-seq supporting reads 21369 UHR pooled cells 15094 Brain 6868 Blood 64731 Neuroblastoma 997 Other (also 25460 Primates bodymap) 53 bp exon 2284 bp [gt-ag] intron 133 GenBank accessions 114713 RNA-seq supporting reads 23531 UHR pooled cells 16757 Brain 7486 Blood 65774 Neuroblastoma 1165 Other (also 22061 Primates bodymap) 68 bp exon 241 bp [gt-ag] intron 143 GenBank accessions 150428 RNA-seq supporting reads 28443 UHR pooled cells 20051 Brain 8163 Blood 92129 Neuroblastoma 1642 Other (also 26115 Primates bodymap) 115 bp exon 2356 bp [gt-ag] intron 139 GenBank accessions 155002 RNA-seq supporting reads 30635 UHR pooled cells 20871 Brain 7065 Blood 94470 Neuroblastoma 1961 Other (also 27234 Primates bodymap) 88 bp exon 4112 bp [gt-ag] intron 131 GenBank accessions 114981 RNA-seq supporting reads 22650 UHR pooled cells 16114 Brain 6078 Blood 69009 Neuroblastoma 1130 Other (also 18691 Primates bodymap) 2303 bp exon 13 accessions, some from head neck (seen 4 times) uterus (2), breast (once) colon normal (once), leiomyosarcoma (once) capped 5' end, 2 accessions 2303 bp exon 2927 bp exon 2927 bp exon 2927 bp exon 3462 bp [gt-ag] intron 96 GenBank accessions 175685 RNA-seq supporting reads 34741 UHR pooled cells 24505 Brain 6278 Blood 109042 Neuroblastoma 1119 Other (also 7141 Primates bodymap) 19 accessions, some from uterus (seen 3 times) leiomios (2), adenocarcinoma (once) breast (once), head neck (once) Validated 3' end, 2 accessions 498 bp exon 219 bp uORF 330 bp exon 330 bp exon 779 bp [gt-ag] intron 6 GenBank accessions 1773 RNA-seq supporting reads 183 UHR pooled cells 131 Brain 123 Blood 1325 Neuroblastoma 11 Other (also 96 Primates bodymap) 80 bp exon 80 bp exon 80 bp exon 94 bp [gt-ag] intron 146 GenBank accessions 101484 RNA-seq supporting reads 19941 UHR pooled cells 14101 Brain 5951 Blood 60519 Neuroblastoma 972 Other (also 12570 Primates bodymap) 40 bp exon 40 bp exon 241 bp [gt-ag] intron 142 GenBank accessions 109059 RNA-seq supporting reads 21369 UHR pooled cells 15094 Brain 6868 Blood 64731 Neuroblastoma 997 Other (also 25460 Primates bodymap) 53 bp exon 53 bp exon 2284 bp [gt-ag] intron 133 GenBank accessions 114713 RNA-seq supporting reads 23531 UHR pooled cells 16757 Brain 7486 Blood 65774 Neuroblastoma 1165 Other (also 22061 Primates bodymap) 68 bp exon 68 bp exon 241 bp [gt-ag] intron 143 GenBank accessions 150428 RNA-seq supporting reads 28443 UHR pooled cells 20051 Brain 8163 Blood 92129 Neuroblastoma 1642 Other (also 26115 Primates bodymap) 115 bp exon 115 bp exon 2356 bp [gt-ag] intron 139 GenBank accessions 155002 RNA-seq supporting reads 30635 UHR pooled cells 20871 Brain 7065 Blood 94470 Neuroblastoma 1961 Other (also 27234 Primates bodymap) 88 bp exon 88 bp exon 4112 bp [gt-ag] intron 131 GenBank accessions 114981 RNA-seq supporting reads 22650 UHR pooled cells 16114 Brain 6078 Blood 69009 Neuroblastoma 1130 Other (also 18691 Primates bodymap) 138 bp exon 138 bp exon 5 accessions, some from blastocyst (seen once) embryonic stem cells embryoid bodiesderived from H1 H7 and H9 cells (once) human skeletal muscle (once) pluripotent cell line derived fromblastocyst inner cell mass (once) t-lymphocytes (once) 138 bp exon 548 bp exon 548 bp exon 1 accession from uterus capped 5' end, 1 accession 548 bp exon 45 bp exon 45 bp exon 1006 bp [gt-ag] intron 2 GenBank accessions 97 RNA-seq supporting reads 14 UHR pooled cells 9 Brain 6 Blood 68 Neuroblastoma (also 27 Primates bodymap) 80 bp exon 94 bp [gt-ag] intron 146 GenBank accessions 101484 RNA-seq supporting reads 19941 UHR pooled cells 14101 Brain 5951 Blood 60519 Neuroblastoma 972 Other (also 12570 Primates bodymap) 40 bp exon 241 bp [gt-ag] intron 142 GenBank accessions 109059 RNA-seq supporting reads 21369 UHR pooled cells 15094 Brain 6868 Blood 64731 Neuroblastoma 997 Other (also 25460 Primates bodymap) 53 bp exon 2284 bp [gt-ag] intron 133 GenBank accessions 114713 RNA-seq supporting reads 23531 UHR pooled cells 16757 Brain 7486 Blood 65774 Neuroblastoma 1165 Other (also 22061 Primates bodymap) 68 bp exon 241 bp [gt-ag] intron 143 GenBank accessions 150428 RNA-seq supporting reads 28443 UHR pooled cells 20051 Brain 8163 Blood 92129 Neuroblastoma 1642 Other (also 26115 Primates bodymap) 115 bp exon 2356 bp [gt-ag] intron 139 GenBank accessions 155002 RNA-seq supporting reads 30635 UHR pooled cells 20871 Brain 7065 Blood 94470 Neuroblastoma 1961 Other (also 27234 Primates bodymap) 38 bp exon 2 accessions, some from embryonic stem cells embryoid bodiesderived from H1 H7 and H9 cells (seen once) muscle (once), rhabdomyosarcoma (once) 38 bp exon 121 bp exon 121 bp exon 108 bp uORF 121 bp exon 1004 bp [gt-ag] intron 135 GenBank accessions 106027 RNA-seq supporting reads 20569 UHR pooled cells 13891 Brain 4400 Blood 65865 Neuroblastoma 1302 Other (also 23206 Primates bodymap) 108 bp uORF 80 bp exon 80 bp exon 94 bp [gt-ag] intron 146 GenBank accessions 101484 RNA-seq supporting reads 19941 UHR pooled cells 14101 Brain 5951 Blood 60519 Neuroblastoma 972 Other (also 12570 Primates bodymap) 40 bp exon 40 bp exon 241 bp [gt-ag] intron 142 GenBank accessions 109059 RNA-seq supporting reads 21369 UHR pooled cells 15094 Brain 6868 Blood 64731 Neuroblastoma 997 Other (also 25460 Primates bodymap) 326 bp exon 326 bp exon 1 accession from brain capped 5' end, 1 accession 326 bp exon 81 bp exon 81 bp exon 2614 bp [gt-ag] intron 2 GenBank accessions 2096 RNA-seq supporting reads 406 UHR pooled cells 110 Brain 123 Blood 1450 Neuroblastoma 7 Other (also 14 Primates bodymap) 70 bp exon 70 bp exon 90 bp [gt-ag] intron 8 GenBank accessions 5489 RNA-seq supporting reads 1023 UHR pooled cells 217 Brain 297 Blood 3929 Neuroblastoma 23 Other (also 74 Primates bodymap) 72 bp exon 3462 bp [gt-ag] intron 96 GenBank accessions 175685 RNA-seq supporting reads 34741 UHR pooled cells 24505 Brain 6278 Blood 109042 Neuroblastoma 1119 Other (also 7141 Primates bodymap) 7 accessions, some from uterus (seen 4 times) b-cell, chronic lymphotic leukemia (once) lung (once), primary lung epithelial cells (once) Validated 3' end, 3 accessions 493 bp exon 108 bp exon 108 bp exon 1004 bp [gt-ag] intron 135 GenBank accessions 106027 RNA-seq supporting reads 20569 UHR pooled cells 13891 Brain 4400 Blood 65865 Neuroblastoma 1302 Other (also 23206 Primates bodymap) 80 bp exon 94 bp [gt-ag] intron 146 GenBank accessions 101484 RNA-seq supporting reads 19941 UHR pooled cells 14101 Brain 5951 Blood 60519 Neuroblastoma 972 Other (also 12570 Primates bodymap) 40 bp exon 241 bp [gt-ag] intron 142 GenBank accessions 109059 RNA-seq supporting reads 21369 UHR pooled cells 15094 Brain 6868 Blood 64731 Neuroblastoma 997 Other (also 25460 Primates bodymap) 53 bp exon 758 bp [gt-ag] intron 10 GenBank accessions 6664 RNA-seq supporting reads 507 UHR pooled cells 388 Brain 705 Blood 5037 Neuroblastoma 27 Other (also 62 Primates bodymap) 1594 bp exon 1594 bp exon 241 bp [gt-ag] intron 143 GenBank accessions 150428 RNA-seq supporting reads 28443 UHR pooled cells 20051 Brain 8163 Blood 92129 Neuroblastoma 1642 Other (also 26115 Primates bodymap) 115 bp exon 2356 bp [gt-ag] intron 139 GenBank accessions 155002 RNA-seq supporting reads 30635 UHR pooled cells 20871 Brain 7065 Blood 94470 Neuroblastoma 1961 Other (also 27234 Primates bodymap) 21 accessions, some from blood (seen 3 times) germinal center B cell (3) cerebellum (2), hepatocellular carcinoma (2) placenta (2) 141 bp exon 2375 bp exon 2375 bp exon 2375 bp exon 90 bp [gt-ag] intron 8 GenBank accessions 5489 RNA-seq supporting reads 1023 UHR pooled cells 217 Brain 297 Blood 3929 Neuroblastoma 23 Other (also 74 Primates bodymap) 72 bp exon 3462 bp [gt-ag] intron 96 GenBank accessions 175685 RNA-seq supporting reads 34741 UHR pooled cells 24505 Brain 6278 Blood 109042 Neuroblastoma 1119 Other (also 7141 Primates bodymap) 1 accession from thalamus Validated 3' end, 1 accession 492 bp exon 104 bp exon 104 bp exon 1004 bp [gt-ag] intron 135 GenBank accessions 106027 RNA-seq supporting reads 20569 UHR pooled cells 13891 Brain 4400 Blood 65865 Neuroblastoma 1302 Other (also 23206 Primates bodymap) 80 bp exon 94 bp [gt-ag] intron 146 GenBank accessions 101484 RNA-seq supporting reads 19941 UHR pooled cells 14101 Brain 5951 Blood 60519 Neuroblastoma 972 Other (also 12570 Primates bodymap) 417 bp exon 2 accessions, some from cerebellum (seen once) kidney (once) capped 5' end, 1 accession 417 bp exon 299 bp exon 299 bp exon 779 bp [gt-ag] intron 6 GenBank accessions 1773 RNA-seq supporting reads 183 UHR pooled cells 131 Brain 123 Blood 1325 Neuroblastoma 11 Other (also 96 Primates bodymap) 80 bp exon 80 bp exon 94 bp [gt-ag] intron 146 GenBank accessions 101484 RNA-seq supporting reads 19941 UHR pooled cells 14101 Brain 5951 Blood 60519 Neuroblastoma 972 Other (also 12570 Primates bodymap) 224 bp exon 868 bp [gt-ag] intron 1 GenBank accession 9 RNA-seq supporting reads 9 Neuroblastoma (also 1 Primates bodymap) 2 accessions, some from embryonic stem cells embryoid bodiesderived from H1 H7 and H9 cells (seen once) eye (once) 33 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 2178 bp 389 aa 36 bp 972 bp 105 bp 2kb including Promoter 21406 bp 1kb
bAug10 753 bp 206 aa 16 bp 116 bp 2kb probably including promoter 11085 bp 1kb
cAug10 1481 bp 194 aa 346 bp 550 bp 2kb probably including promoter 20780 bp 1kb
dAug10 2788 bp 186 aa 16 bp 2211 bp 2kb including Promoter 13200 bp 1kb
eAug10 912 bp 177 aa 332 bp 46 bp 216 bp 2kb probably including promoter 11019 bp 1kb
fAug10 439 bp 145 aa 2kb 6661 bp 1kb
gAug10 567 bp 97 aa 36 bp 237 bp 105 bp 2kb including Promoter 1906 bp 1kb
hAug10 2131 bp 96 aa 23 bp 1817 bp 2kb probably including promoter 6825 bp 1kb
iAug10 601 bp 70 aa 19 bp 369 bp 2kb including Promoter 1699 bp 1kb
jAug10 3425 bp 58 aa 2573 bp 675 bp 2kb 6887 bp 1kb
kAug10 2939 bp 58 aa 2183 bp 579 bp 2kb 6491 bp 1kb
lAug10 716 bp 33 aa 612 bp 2kb 6882 bp 1kb
mAug10 636 bp 53 aa 174 bp 300 bp 2kb probably including promoter 2377 bp 1kb
nAug10-unspliced 548 bp 32 aa 430 bp 19 bp 2kb including Promoter 548 bp 1kb

Gene neighbors and Navigator on chromosome 14q22.1 back to top
PTGDR D C I R P PTGER2 D C I R P GPR137C C R P PSMC6 C I R P STYX C I R P R C R R C R P TXNDC16 C C I R P ERO1L C R P GNPNAT1 C D C I R P FERMT2 C R P DDHD1 100kb 0 PTGDR, 14 accessions, 3 variants PTGER2, 51 accessions 2 variants GPR137C, 47 accessions 4 variants PSMC6, 264 accessions 14 variants STYX, 179 accessions, 7 variants tawwobo, 29 accessions 3 variants beevoy, 1 accession shobyby, 2 accessions spopu, 5 accessions, 2 variants sparnarby, 1 accession noybyby, 1 accession pabyby, 1 accession pybyby, 1 accession pubyby, 2 accessions sharcherbu, 2 accessions pobyby, 1 accession shawcherbu, 2 accessions chawsar, 19 accessions peebyby, 1 accession sheecherbu, 1 accession shercherbu, 4 accessions shorcherbu, 1 accession shoycherbu, 3 accessions yakuru, 4 accessions perbyby, 1 accession blucherbu, 1 accession porbyby, 1 accession rabyby, 1 accession steevor, 1 accession robyby, 1 accession rarbyby, 1 accession flacherbu, 1 accession flawsley, 1 accession steynarby, 1 accession fleecherbu, 3 accessions beyzer, 2 accessions fleycherbu, 1 accession floysoybo, 2 accessions florcherbu, 2 accessions swarvor, 1 accession nuyami, 2 accessions, 2 variants sobyby, 1 accession sarbyby, 1 accession floycherbu, 1 accession glacherbu, 3 accessions swanarby, 1 accession glycherbu, 3 accessions glucherbu, 3 accessions seebyby, 1 accession swonarby, 2 accessions soybyby, 1 accession deynawby, 1 accession gonawby, 1 accession tarbyby, 1 accession tawbyby, 1 accession terbyby, 2 accessions buvoy, 5 accessions naturu, 1 accession vawbyby, 1 accession dazer, 1 accession veebyby, 1 accession vorbyby, 1 accession voybyby, 1 accession wabyby, 1 accession glorcherbu, 1 accession wybyby, 2 accessions kornawby, 1 accession weybyby, 1 accession woybyby, 1 accession zabyby, 2 accessions zubyby, 2 accessions zeenawby, 1 accession zerbyby, 1 accession cheenawby, 1 accession choynawby, 1 accession sharnawby, 1 accession glernawby, 1 accession chobyby, 1 accession charbyby, 2 accessions chawbyby, 1 accession cheebyby, 1 accession cherbyby, 1 accession plunawby, 1 accession cheybyby, 1 accession spoysley, 2 accessions shabyby, 1 accession shubyby, 5 accessions foyvoy, 1 accession plucherbu, 2 accessions spanawby, 1 accession steenawby, 3 accessions sparpu, 1 accession norbyby, 1 accession cheesar, 9 accessions pawbyby, 1 accession sheycherbu, 2 accessions blycherbu, 1 accession peybyby, 1 accession stawvor, 1 accession blocherbu, 1 accession blarcherbu, 2 accessions hoturu, 1 accession rybyby, 1 accession barzer, 1 accession fleysoybo, 1 accession sternarby, 1 accession rawbyby, 1 accession bleycherbu, 1 accession bloycherbu, 1 accession reebyby, 1 accession niyami, 2 accessions, 2 variants flycherbu, 1 accession flucherbu, 1 accession florsoybo, 1 accession swuvor, 1 accession sybyby, 1 accession sawbyby, 1 accession serbyby, 1 accession glocherbu, 1 accession seybyby, 1 accession borzer, 5 accessions neyami, 5 accessions snopu, 2 accessions tybyby, 2 accessions glarcherbu, 4 accessions tubyby, 2 accessions tobyby, 4 accessions teebyby, 3 accessions skysley, 2 accessions jornawby, 1 accession joynawby, 8 accessions varbyby, 1 accession glasoybo, 1 accession kanawby, 1 accession wubyby, 1 accession spawsley, 1 accession warbyby, 1 accession wawbyby, 1 accession weebyby, 1 accession leynawby, 4 accessions snawpu, 2 accessions, 2 variants vanawby, 1 accession warnawby, 1 accession worbyby, 1 accession zybyby, 1 accession zawnawby, 1 accession noyami, 1 accession zobyby, 1 accession klycherbu, 8 accessions zeybyby, 2 accessions zorbyby, 1 accession zoybyby, 1 accession klucherbu, 1 accession klocherbu, 1 accession chubyby, 1 accession klarcherbu, 2 accessions klanawby, 1 accession kleecherbu, 1 accession tayami, 1 accession chorbyby, 1 accession shybyby, 1 accession speedey, 1 accession tiyami, 1 accession dyvoy, 1 accession klorcherbu, 1 accession sheebyby, 2 accessions kloycherbu, 1 accession pleynawby, 1 accession placherbu, 1 accession jovoy, 1 accession shorbyby, 1 accession shoybyby, 2 accessions plycherbu, 1 accession blabyby, 1 accession spupu, 15 accessions TXNDC16, 158 accessions 10 variants rorbyby, 1 accession ERO1L, 453 accessions 13 variants GNPNAT1, 176 accessions 6 variants snerpu, 1 accession FERMT2, 365 accessions 14 variants DDHD1, 247 accessions 9 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               45 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, .n-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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