Homo sapiens complex locus EIF2C2, encoding eukaryotic translation initiation factor 2C, 2.
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SUMMARY back to top
RefSeq summary
[EIF2C2] This gene encodes a member of the Argonaute family of proteins which play a role in RNA interference. The encoded protein is highly basic, and contains a PAZ domain and a PIWI domain. It may interact with dicer1 and play a role in short-interfering-RNA-mediated gene silencing. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq].

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 10 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, 1.6 times the average gene in this release. The sequence of this gene is defined by 187 GenBank accessions from 165 cDNA clones, some from placenta (seen 9 times), brain (8), eye (8), liver and spleen (7), lymph (7), lung (6), colon (5) and 70 other tissues. We annotate structural defects or features in 16 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 23 distinct introns (22 gt-ag, 1 gc-ag). Transcription produces 12 different mRNAs, 10 alternatively spliced variants and 2 unspliced forms. There are 5 probable alternative promotors, 4 non overlapping alternative last exons and 4 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 3 cassette exons, overlapping exons with different boundaries.
Function: There are 64 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (Breast Neoplasms; Carcinoma, Squamous Cell; Colorectal Neoplasms; Esophageal Neoplasms; Multiple myeloma; Prostatic Neoplasms; Stomach Neoplasms) and proposed to participate in processes (mRNA cleavage involved in gene silencing by miRNA, negative regulation of translation involved in gene silencing by miRNA, negative regulation of translational initiation, pre-microRNA processing, gene silencing by RNA, regulation of transcription). Proteins are expected to have molecular functions (endoribonuclease activity, cleaving siRNA-paired mRNA, protein binding, RNA 7-methylguanosine cap binding, siRNA binding, translation initiation factor activity, endonuclease activity, hydrolase activity, metal ion binding) and to localize in various compartments (micro-ribonucleoprotein complex, mRNA cap binding complex, RNA-induced silencing complex, cytoplasm, cytoplasmic mRNA processing body, nucleus). Putative protein interactors have been described (DCP1A, DCP2, DDX20, DICER1, EIF2C1, GEMIN4, PRKRA, TARBP2, TNRC6A, TNRC6B).
Protein coding potential: 9 spliced mRNAs putatively encode good proteins, altogether 9 different isoforms (3 complete, 2 COOH complete, 4 partial), some containing domains Domain of unknown function (DUF1785), PAZ domain, Piwi domain [Pfam], a second peroximal domain [Psort2]. The remaining 3 mRNA variants (1 spliced, 2 unspliced; 1 partial) appear not to encode good proteins. Finally proteins from this gene may be modulated by acetylation; di-methylation; 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 8, links to other databases and other names
Map: This gene EIF2C2 maps on chromosome 8, at 8q24 according to Entrez Gene. In AceView, it covers 104.48 kb, from 141645724 to 141541242 (NCBI 37, August 2010), on the reverse strand.
Links to: manual annotations from PhosphoSite, the SNP view, gene overviews from Entrez Gene 27161, 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 EIF2C2, Q10, AGO2, MGC3183, LOC27161 or rase, vucheyby. It has been described as protein argonaute-2, PPD, hAgo2, eIF2C 2, eIF-2C 2, argonaute2, argonaute 2, protein slicer, PAZ Piwi domain protein.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Eif2c2 (e=0.0).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes alg-1 (e=0.0), alg-2 (e=0.0), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes AGO1andAT1G48405 (e=0.0), ZLL (e=0.0), AT2G27880 (e= 10-168), 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
EIF2C2 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 9.41 6.65 15.3 5.79 23.2 11.6 30.6 40.3 35.1 24.8 21.6 3.57 4.10 5.79 1.55 1.66 8.19 7.64 28.5 2.52 3.10 5.79 16.4 26.6 30.6 26.6 35.1 35.1 70.2 37.6 13.3 16.4 17.6 11.6 28.5 24.8 1.26 0.96 2.35 65.5 17.6 15.3 14.3 20.2 10.8 10.1 17.6 14.3 57.1 24.8 14.3 3.82 18.8 16.4 21.6 26.6 18.8 16.4 32.8 20.2 12.4 18.8 37.6 30.6 26.6 53.2 14.3 26.6 8.78 21.6 10.8 17.6 20.2 26.6 12.4 12.4 8.78 24.8 21.6 20.2 10.8 10.1 16.4 12.4 24.8 15.3 9.41 11.6 20.2 14.3 24.8 18.8 20.2 8.19 7.13 16.4 11.6 11.6 12.4 30.6 10.1 28.5 21.6 24.8 32.8 24.8 46.3 30.6 37.6 35.1 21.6 17.6 7.13 16.4 21.6 5.79 17.6 30.6 13.3 10.8 16.4 24.8 18.8 10.8 15.3 10.8 10.8 37.6 26.6 17.6 26.6 37.6 18.8 37.6 32.8 30.6 23.2 15.3 35.1 46.3 8.78 11.6 9.41 5.79 17.6 7.64 13.3 28.5 23.2 2.52 92.7 18.8 10.1 23.2 23.2 18.8 40.3 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!.
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          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 EIF2C2 5' 3' encoded on minus strand of chromosome 8 from 141,645,724 to 141,541,242 6077 27561 22843 16157 24706 21330 15781 19889 23104 12220 20248 15167 12345 11456 15742 22744 21135 22613 a [NM] 6077 27561 22843 16157 24706 21330 15781 19889 23104 12220 20248 15167 12345 11456 15742 428 22613 b [NM] 296 22843 16157 24706 21330 15781 19889 23104 12220 20248 15167 12345 11456 15742 22744 21135 22613 c 7 l k-u 23104 i j-u 15742 22744 21135 d 6077 27561 e 22744 f 4114 27561 g 22613 h 5kb 0 141 bp exon 141 bp exon 50173 bp [gt-ag] intron 10 GenBank accessions 6067 RNA-seq supporting reads 507 UHR pooled cells 220 Brain 4101 Blood 1230 Neuroblastoma 9 Other (also 1731 Primates bodymap) 193 bp exon 12186 bp [gt-ag] intron 22 GenBank accessions 27539 RNA-seq supporting reads 2368 UHR pooled cells 1123 Brain 20212 Blood 3756 Neuroblastoma 80 Other (also 9715 Primates bodymap) 121 bp exon 10177 bp [gt-ag] intron 22 GenBank accessions 22821 RNA-seq supporting reads 1813 UHR pooled cells 854 Brain 17367 Blood 2750 Neuroblastoma 37 Other (also 5610 Primates bodymap) 182 bp exon 1942 bp [gt-ag] intron 15 GenBank accessions 16142 RNA-seq supporting reads 1954 UHR pooled cells 928 Brain 10284 Blood 2939 Neuroblastoma 37 Other (also 3854 Primates bodymap) 137 bp exon 844 bp [gt-ag] intron 15 GenBank accessions 24691 RNA-seq supporting reads 2410 UHR pooled cells 1093 Brain 17783 Blood 3330 Neuroblastoma 75 Other (also 6200 Primates bodymap) 135 bp exon 822 bp [gt-ag] intron 15 GenBank accessions 21315 RNA-seq supporting reads 2211 UHR pooled cells 1022 Brain 15003 Blood 3038 Neuroblastoma 41 Other (also 5949 Primates bodymap) 88 bp exon 1248 bp [gt-ag] intron 17 GenBank accessions 15764 RNA-seq supporting reads 2190 UHR pooled cells 1070 Brain 9098 Blood 3366 Neuroblastoma 40 Other (also 5883 Primates bodymap) 148 bp exon 802 bp [gc-ag] intron 17 GenBank accessions 19872 RNA-seq supporting reads 2610 UHR pooled cells 1146 Brain 12502 Blood 3549 Neuroblastoma 65 Other (also 7740 Primates bodymap) 120 bp exon 148 bp [gt-ag] intron 30 GenBank accessions 23074 RNA-seq supporting reads 2453 UHR pooled cells 1111 Brain 15922 Blood 3524 Neuroblastoma 64 Other (also 7052 Primates bodymap) 123 bp exon 4459 bp [gt-ag] intron 30 GenBank accessions 12190 RNA-seq supporting reads 2336 UHR pooled cells 959 Brain 5732 Blood 3118 Neuroblastoma 45 Other (also 5209 Primates bodymap) 134 bp exon 2004 bp [gt-ag] intron 33 GenBank accessions 20215 RNA-seq supporting reads 2585 UHR pooled cells 1134 Brain 12645 Blood 3806 Neuroblastoma 45 Other (also 4971 Primates bodymap) 185 bp exon 1486 bp [gt-ag] intron 30 GenBank accessions 15137 RNA-seq supporting reads 2729 UHR pooled cells 1156 Brain 6851 Blood 4322 Neuroblastoma 79 Other (also 4629 Primates bodymap) 160 bp exon 3164 bp [gt-ag] intron 29 GenBank accessions 12316 RNA-seq supporting reads 2559 UHR pooled cells 1070 Brain 4573 Blood 4032 Neuroblastoma 82 Other (also 4309 Primates bodymap) 91 bp exon 2854 bp [gt-ag] intron 27 GenBank accessions 11429 RNA-seq supporting reads 2198 UHR pooled cells 890 Brain 4906 Blood 3369 Neuroblastoma 66 Other (also 3141 Primates bodymap) 195 bp exon 1709 bp [gt-ag] intron 30 GenBank accessions 15712 RNA-seq supporting reads 2938 UHR pooled cells 1196 Brain 7484 Blood 3999 Neuroblastoma 95 Other (also 4383 Primates bodymap) 135 bp exon 3750 bp [gt-ag] intron 35 GenBank accessions 22709 RNA-seq supporting reads 4801 UHR pooled cells 1723 Brain 10410 Blood 5656 Neuroblastoma 119 Other (also 6837 Primates bodymap) 102 bp exon 2852 bp [gt-ag] intron 34 GenBank accessions 21101 RNA-seq supporting reads 4376 UHR pooled cells 1637 Brain 9348 Blood 5668 Neuroblastoma 72 Other (also 6950 Primates bodymap) 200 bp exon 263 bp [gt-ag] intron 39 GenBank accessions 22574 RNA-seq supporting reads 3902 UHR pooled cells 1811 Brain 11348 Blood 5460 Neuroblastoma 53 Other (also 6892 Primates bodymap) 1010 bp exon 143 accessions, NM_012154.3 some from placenta (seen 9 times) brain (8), eye (7), liver and spleen (7) lymph (7) Validated 3' end, 8 accessions Validated 3' end, 2 accessions 1010 bp exon 63 bp exon 63 bp exon 50173 bp [gt-ag] intron 10 GenBank accessions 6067 RNA-seq supporting reads 507 UHR pooled cells 220 Brain 4101 Blood 1230 Neuroblastoma 9 Other (also 1731 Primates bodymap) 193 bp exon 12186 bp [gt-ag] intron 22 GenBank accessions 27539 RNA-seq supporting reads 2368 UHR pooled cells 1123 Brain 20212 Blood 3756 Neuroblastoma 80 Other (also 9715 Primates bodymap) 121 bp exon 10177 bp [gt-ag] intron 22 GenBank accessions 22821 RNA-seq supporting reads 1813 UHR pooled cells 854 Brain 17367 Blood 2750 Neuroblastoma 37 Other (also 5610 Primates bodymap) 182 bp exon 1942 bp [gt-ag] intron 15 GenBank accessions 16142 RNA-seq supporting reads 1954 UHR pooled cells 928 Brain 10284 Blood 2939 Neuroblastoma 37 Other (also 3854 Primates bodymap) 137 bp exon 844 bp [gt-ag] intron 15 GenBank accessions 24691 RNA-seq supporting reads 2410 UHR pooled cells 1093 Brain 17783 Blood 3330 Neuroblastoma 75 Other (also 6200 Primates bodymap) 135 bp exon 822 bp [gt-ag] intron 15 GenBank accessions 21315 RNA-seq supporting reads 2211 UHR pooled cells 1022 Brain 15003 Blood 3038 Neuroblastoma 41 Other (also 5949 Primates bodymap) 88 bp exon 1248 bp [gt-ag] intron 17 GenBank accessions 15764 RNA-seq supporting reads 2190 UHR pooled cells 1070 Brain 9098 Blood 3366 Neuroblastoma 40 Other (also 5883 Primates bodymap) 148 bp exon 802 bp [gc-ag] intron 17 GenBank accessions 19872 RNA-seq supporting reads 2610 UHR pooled cells 1146 Brain 12502 Blood 3549 Neuroblastoma 65 Other (also 7740 Primates bodymap) 120 bp exon 148 bp [gt-ag] intron 30 GenBank accessions 23074 RNA-seq supporting reads 2453 UHR pooled cells 1111 Brain 15922 Blood 3524 Neuroblastoma 64 Other (also 7052 Primates bodymap) 123 bp exon 4459 bp [gt-ag] intron 30 GenBank accessions 12190 RNA-seq supporting reads 2336 UHR pooled cells 959 Brain 5732 Blood 3118 Neuroblastoma 45 Other (also 5209 Primates bodymap) 134 bp exon 2004 bp [gt-ag] intron 33 GenBank accessions 20215 RNA-seq supporting reads 2585 UHR pooled cells 1134 Brain 12645 Blood 3806 Neuroblastoma 45 Other (also 4971 Primates bodymap) 185 bp exon 1486 bp [gt-ag] intron 30 GenBank accessions 15137 RNA-seq supporting reads 2729 UHR pooled cells 1156 Brain 6851 Blood 4322 Neuroblastoma 79 Other (also 4629 Primates bodymap) 160 bp exon 3164 bp [gt-ag] intron 29 GenBank accessions 12316 RNA-seq supporting reads 2559 UHR pooled cells 1070 Brain 4573 Blood 4032 Neuroblastoma 82 Other (also 4309 Primates bodymap) 91 bp exon 2854 bp [gt-ag] intron 27 GenBank accessions 11429 RNA-seq supporting reads 2198 UHR pooled cells 890 Brain 4906 Blood 3369 Neuroblastoma 66 Other (also 3141 Primates bodymap) 195 bp exon 1709 bp [gt-ag] intron 30 GenBank accessions 15712 RNA-seq supporting reads 2938 UHR pooled cells 1196 Brain 7484 Blood 3999 Neuroblastoma 95 Other (also 4383 Primates bodymap) 135 bp exon 6704 bp [gt-ag] intron 2 GenBank accessions 426 RNA-seq supporting reads 121 UHR pooled cells 49 Brain 103 Blood 151 Neuroblastoma 2 Other (also 81 Primates bodymap) 200 bp exon 263 bp [gt-ag] intron 39 GenBank accessions 22574 RNA-seq supporting reads 3902 UHR pooled cells 1811 Brain 11348 Blood 5460 Neuroblastoma 53 Other (also 6892 Primates bodymap) 987 bp exon 2 accessions, NM_001164623.1 Validated 3' end, 1 accession 987 bp exon 62 bp exon 62552 bp [gt-ag] intron 1 GenBank accession 295 RNA-seq supporting reads 26 UHR pooled cells 15 Brain 199 Blood 55 Neuroblastoma (also 71 Primates bodymap) 121 bp exon 121 bp exon 10177 bp [gt-ag] intron 22 GenBank accessions 22821 RNA-seq supporting reads 1813 UHR pooled cells 854 Brain 17367 Blood 2750 Neuroblastoma 37 Other (also 5610 Primates bodymap) 182 bp exon 1942 bp [gt-ag] intron 15 GenBank accessions 16142 RNA-seq supporting reads 1954 UHR pooled cells 928 Brain 10284 Blood 2939 Neuroblastoma 37 Other (also 3854 Primates bodymap) 137 bp exon 844 bp [gt-ag] intron 15 GenBank accessions 24691 RNA-seq supporting reads 2410 UHR pooled cells 1093 Brain 17783 Blood 3330 Neuroblastoma 75 Other (also 6200 Primates bodymap) 135 bp exon 822 bp [gt-ag] intron 15 GenBank accessions 21315 RNA-seq supporting reads 2211 UHR pooled cells 1022 Brain 15003 Blood 3038 Neuroblastoma 41 Other (also 5949 Primates bodymap) 88 bp exon 1248 bp [gt-ag] intron 17 GenBank accessions 15764 RNA-seq supporting reads 2190 UHR pooled cells 1070 Brain 9098 Blood 3366 Neuroblastoma 40 Other (also 5883 Primates bodymap) 148 bp exon 802 bp [gc-ag] intron 17 GenBank accessions 19872 RNA-seq supporting reads 2610 UHR pooled cells 1146 Brain 12502 Blood 3549 Neuroblastoma 65 Other (also 7740 Primates bodymap) 120 bp exon 148 bp [gt-ag] intron 30 GenBank accessions 23074 RNA-seq supporting reads 2453 UHR pooled cells 1111 Brain 15922 Blood 3524 Neuroblastoma 64 Other (also 7052 Primates bodymap) 123 bp exon 4459 bp [gt-ag] intron 30 GenBank accessions 12190 RNA-seq supporting reads 2336 UHR pooled cells 959 Brain 5732 Blood 3118 Neuroblastoma 45 Other (also 5209 Primates bodymap) 134 bp exon 2004 bp [gt-ag] intron 33 GenBank accessions 20215 RNA-seq supporting reads 2585 UHR pooled cells 1134 Brain 12645 Blood 3806 Neuroblastoma 45 Other (also 4971 Primates bodymap) 185 bp exon 1486 bp [gt-ag] intron 30 GenBank accessions 15137 RNA-seq supporting reads 2729 UHR pooled cells 1156 Brain 6851 Blood 4322 Neuroblastoma 79 Other (also 4629 Primates bodymap) 160 bp exon 3164 bp [gt-ag] intron 29 GenBank accessions 12316 RNA-seq supporting reads 2559 UHR pooled cells 1070 Brain 4573 Blood 4032 Neuroblastoma 82 Other (also 4309 Primates bodymap) 91 bp exon 2854 bp [gt-ag] intron 27 GenBank accessions 11429 RNA-seq supporting reads 2198 UHR pooled cells 890 Brain 4906 Blood 3369 Neuroblastoma 66 Other (also 3141 Primates bodymap) 195 bp exon 1709 bp [gt-ag] intron 30 GenBank accessions 15712 RNA-seq supporting reads 2938 UHR pooled cells 1196 Brain 7484 Blood 3999 Neuroblastoma 95 Other (also 4383 Primates bodymap) 135 bp exon 3750 bp [gt-ag] intron 35 GenBank accessions 22709 RNA-seq supporting reads 4801 UHR pooled cells 1723 Brain 10410 Blood 5656 Neuroblastoma 119 Other (also 6837 Primates bodymap) 102 bp exon 2852 bp [gt-ag] intron 34 GenBank accessions 21101 RNA-seq supporting reads 4376 UHR pooled cells 1637 Brain 9348 Blood 5668 Neuroblastoma 72 Other (also 6950 Primates bodymap) 200 bp exon 263 bp [gt-ag] intron 39 GenBank accessions 22574 RNA-seq supporting reads 3902 UHR pooled cells 1811 Brain 11348 Blood 5460 Neuroblastoma 53 Other (also 6892 Primates bodymap) 732 bp exon 1 accession 732 bp exon 67 bp exon 8641 bp [gt-ag] intron 3 GenBank accessions 4 RNA-seq supporting reads 2 UHR pooled cells 2 Neuroblastoma 428 bp exon 428 bp exon 3 accessions 428 bp exon 670 bp exon 670 bp exon 4 accessions, some from liver (seen once) peripheral nervous system sympathetictrunk (once) sciatic nerve (once) Validated 3' end, 1 accession 670 bp exon 627 bp exon 627 bp exon 30 bp uORF 627 bp exon 627 bp exon 148 bp [gt-ag] intron 30 GenBank accessions 23074 RNA-seq supporting reads 2453 UHR pooled cells 1111 Brain 15922 Blood 3524 Neuroblastoma 64 Other (also 7052 Primates bodymap) 611 bp exon 611 bp exon 2 accessions, some from ascites (seen once) cornea (once), eye (once) stomach (once) 611 bp exon 724 bp exon 724 bp exon 4 accessions, some from kidney (seen once) kidney tumor (once), kidney tumor (once) lung (once), marrow (once) 724 bp exon 294 bp exon 1709 bp [gt-ag] intron 30 GenBank accessions 15712 RNA-seq supporting reads 2938 UHR pooled cells 1196 Brain 7484 Blood 3999 Neuroblastoma 95 Other (also 4383 Primates bodymap) 135 bp exon 3750 bp [gt-ag] intron 35 GenBank accessions 22709 RNA-seq supporting reads 4801 UHR pooled cells 1723 Brain 10410 Blood 5656 Neuroblastoma 119 Other (also 6837 Primates bodymap) 102 bp exon 2852 bp [gt-ag] intron 34 GenBank accessions 21101 RNA-seq supporting reads 4376 UHR pooled cells 1637 Brain 9348 Blood 5668 Neuroblastoma 72 Other (also 6950 Primates bodymap) 83 bp exon 1 accession from embryonal carcinoma cell line from testis 83 bp exon 62 bp exon 62 bp exon 50173 bp [gt-ag] intron 10 GenBank accessions 6067 RNA-seq supporting reads 507 UHR pooled cells 220 Brain 4101 Blood 1230 Neuroblastoma 9 Other (also 1731 Primates bodymap) 193 bp exon 12186 bp [gt-ag] intron 22 GenBank accessions 27539 RNA-seq supporting reads 2368 UHR pooled cells 1123 Brain 20212 Blood 3756 Neuroblastoma 80 Other (also 9715 Primates bodymap) 121 bp exon 208 bp [gt-ag] intron 1 GenBank accession 410 RNA-seq supporting reads 65 UHR pooled cells 2 Brain 307 Blood 35 Neuroblastoma 1 Other 1 accession 46 bp exon 135 bp exon 3750 bp [gt-ag] intron 35 GenBank accessions 22709 RNA-seq supporting reads 4801 UHR pooled cells 1723 Brain 10410 Blood 5656 Neuroblastoma 119 Other (also 6837 Primates bodymap) 179 bp exon 1 accession from colon 179 bp exon 92 bp exon 92 bp exon 20485 bp [gt-ag] intron 1 GenBank accession 4113 RNA-seq supporting reads 52 UHR pooled cells 26 Brain 3896 Blood 134 Neuroblastoma 5 Other (also 118 Primates bodymap) 193 bp exon 12186 bp [gt-ag] intron 22 GenBank accessions 27539 RNA-seq supporting reads 2368 UHR pooled cells 1123 Brain 20212 Blood 3756 Neuroblastoma 80 Other (also 9715 Primates bodymap) 31 bp exon 1 accession 31 bp exon 291 bp exon 291 bp exon 114 bp uORF 291 bp exon 291 bp exon 263 bp [gt-ag] intron 39 GenBank accessions 22574 RNA-seq supporting reads 3902 UHR pooled cells 1811 Brain 11348 Blood 5460 Neuroblastoma 53 Other (also 6892 Primates bodymap) 59 bp exon 59 bp exon 1 accession from cartilage 59 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 3600 bp 898 aa 901 bp 2kb 104483 bp 1kb
bAug10 3397 bp 838 aa 41 bp 878 bp 2kb probably including promoter 104382 bp 1kb
cAug10 3050 bp 782 aa 78 bp 623 bp 2kb probably including promoter 104126 bp 1kb
dAug10 614 bp 204 aa 2kb 8925 bp 1kb
eAug10 422 bp 139 aa 2kb probably including promoter 62989 bp 1kb
fAug10 314 bp 104 aa 2kb 4064 bp 1kb
gAug10 316 bp 104 aa 2kb 32987 bp 1kb
hAug10 350 bp 83 aa 100 bp 111 bp 2kb possibly including promoter 613 bp 1kb
iAug10 1238 bp 83 aa 570 bp 416 bp 27 bp 2kb possibly including promoter 1386 bp 1kb
jAug10-unspliced 724 bp 92 aa 369 bp 76 bp 2kb 724 bp 1kb
kAug10-unspliced 670 bp 60 aa 132 bp 355 bp 2kb 670 bp 1kb
lAug10 495 bp 43 aa 116 bp 247 bp 2kb probably including promoter 9136 bp 1kb

Gene neighbors and Navigator on chromosome 8q24 back to top
C CHRAC1 C I R P C C R C C R D C I R P EIF2C2 D C I R P PTK2 C C 100kb 0 teyzyby, 1 accession CHRAC1, 181 accessions 6 variants leekor, 2 accessions vaforby, 1 accession tareya, 4 accessions, 2 variants faweebu, 1 accession pyzyby, 1 accession porzyby, 2 accessions poyzyby, 4 accessions snyterbo, 1 accession fyweebu, 2 accessions rozyby, 1 accession reezyby, 1 accession rerzyby, 1 accession rorzyby, 1 accession percheyby, 1 accession larskorbu, 1 accession tushoy, 3 accessions gorforby, 2 accessions fuweebu, 1 accession foweebu, 1 accession serzyby, 1 accession feeweebu, 3 accessions jarforby, 2 accessions fawweebu, 1 accession ferweebu, 1 accession tarzyby, 1 accession tawzyby, 1 accession rercheyby, 1 accession gerweebu, 1 accession vazyby, 1 accession vyzyby, 1 accession goyweebu, 1 accession meeskorbu, 2 accessions jerforby, 4 accessions veezyby, 1 accession morskorbu, 1 accession kaforby, 1 accession naskorbu, 1 accession wuzyby, 1 accession warzyby, 1 accession jawweebu, 1 accession lakor, 2 accessions nerskorbu, 1 accession lukor, 1 accession jerweebu, 1 accession noyskorbu, 1 accession jorweebu, 1 accession snarterbo, 3 accessions kerforby, 2 accessions zerzyby, 1 accession zeyzyby, 1 accession zoyzyby, 3 accessions chyzyby, 1 accession parskorbu, 2 accessions lyforby, 1 accession chuzyby, 1 accession snawterbo, 1 accession shyzyby, 5 accessions shozyby, 2 accessions sharzyby, 1 accession sheezyby, 1 accession loykor, 6 accessions makor, 4 accessions peeskorbu, 1 accession porskorbu, 1 accession shoyzyby, 1 accession blyzyby, 1 accession lyweebu, 1 accession blozyby, 4 accessions blarzyby, 5 accessions blawzyby, 3 accessions bleezyby, 4 accessions blerzyby, 1 accession leyweebu, 1 accession raskorbu, 1 accession blorzyby, 2 accessions loyweebu, 1 accession ruskorbu, 1 accession vervyby, 2 accessions 2 variants flazyby, 1 accession flarzyby, 1 accession rawskorbu, 3 accessions myweebu, 1 accession rerskorbu, 1 accession poyblu, 1 accession floyzyby, 1 accession glazyby, 3 accessions paweebu, 1 accession parweebu, 1 accession glawzyby, 4 accessions glorzyby, 3 accessions flawcheyby, 6 accessions roblu, 2 accessions saskorbu, 1 accession syskorbu, 1 accession kluzyby, 4 accessions syweebu, 1 accession klerzyby, 3 accessions seyweebu, 2 accessions poyforby, 1 accession klucheyby, 2 accessions pluzyby, 1 accession toweebu, 1 accession rarblu, 1 accession serskorbu, 1 accession plerzyby, 1 accession plorzyby, 1 accession ployzyby, 2 accessions skuzyby, 1 accession skozyby, 5 accessions slazyby, 2 accessions wyweebu, 1 accession slozyby, 1 accession worweebu, 1 accession slarzyby, 1 accession slawzyby, 1 accession sleezyby, 1 accession slerzyby, 1 accession zerweebu, 1 accession smazyby, 1 accession teeskorbu, 1 accession smozyby, 2 accessions toyforby, 1 accession smeyzyby, 2 accessions chuweebu, 1 accession torskorbu, 1 accession snozyby, 1 accession snarzyby, 2 accessions veyforby, 1 accession woforby, 1 accession charweebu, 1 accession sneyzyby, 1 accession snorzyby, 1 accession cheeweebu, 2 accessions vuskorbu, 1 accession spuzyby, 1 accession rerblu, 2 accessions sparzyby, 1 accession sworvawbu, 1 accession dawlu, 1 accession nehare, 12 accessions pazyby, 1 accession puzyby, 1 accession vagor, 4 accessions pozyby, 1 accession kerskorbu, 1 accession gerberby, 1 accession parzyby, 2 accessions peezyby, 2 accessions peyzyby, 4 accessions farberby, 5 accessions razyby, 5 accessions deylu, 9 accessions lyskorbu, 1 accession ruzyby, 1 accession luskorbu, 1 accession rarzyby, 1 accession rawzyby, 2 accessions loskorbu, 1 accession reyzyby, 1 accession stervawbu, 1 accession sazyby, 1 accession leyskorbu, 2 accessions lawskorbu, 1 accession kawkor, 4 accessions leeskorbu, 6 accessions lorskorbu, 12 accessions suzyby, 1 accession sozyby, 3 accessions sawzyby, 1 accession muskorbu, 1 accession seezyby, 1 accession seyzyby, 1 accession sorzyby, 1 accession soyzyby, 1 accession tazyby, 1 accession stawvawbu, 1 accession foberby, 1 accession faberby, 2 accessions 2 variants gawweebu, 2 accessions tuzyby, 1 accession tozyby, 1 accession rycheyby, 1 accession teezyby, 1 accession torzyby, 1 accession toyzyby, 2 accessions vozyby, 2 accessions vawzyby, 1 accession verzyby, 1 accession vugor, 1 accession snuterbo, 1 accession voyzyby, 1 accession sarcheyby, 12 accessions boyberby, 1 accession wazyby, 1 accession seecheyby, 1 accession wozyby, 1 accession styvawbu, 1 accession peeblu, 2 accessions weezyby, 1 accession werzyby, 1 accession noskorbu, 1 accession charlu, 33 accessions 2 variants nawskorbu, 4 accessions woyzyby, 1 accession rase, 4 accessions neeskorbu, 3 accessions snoterbo, 1 accession zyzyby, 2 accessions zuzyby, 1 accession norskorbu, 1 accession snoyvawbu, 1 accession zeelu, 1 accession zarzyby, 1 accession sanora, 7 accessions zawzyby, 1 accession snorvawbu, 1 accession sneyvawbu, 1 accession snervawbu, 1 accession pyskorbu, 1 accession vucheyby, 6 accessions snawvawbu, 1 accession snarvawbu, 1 accession zorzyby, 3 accessions chazyby, 3 accessions poskorbu, 1 accession chozyby, 1 accession charzyby, 1 accession chawzyby, 1 accession cheyzyby, 7 accessions chorzyby, 2 accessions snovawbu, 1 accession choyzyby, 1 accession smawvawbu, 2 accessions steebeeby, 1 accession shuzyby, 1 accession shawzyby, 3 accessions sherzyby, 2 accessions kyweebu, 1 accession perskorbu, 1 accession koweebu, 11 accessions 2 variants blazyby, 1 accession peyblu, 5 accessions leeweebu, 2 accessions poyskorbu, 1 accession nemaya, 2 accessions porblu, 2 accessions ryskorbu, 2 accessions bloyzyby, 1 accession fluzyby, 2 accessions flozyby, 1 accession flawzyby, 6 accessions pyforby, 1 accession reeskorbu, 1 accession fleyzyby, 1 accession glyzyby, 11 accessions noyweebu, 1 accession glozyby, 1 accession chorfley, 7 accessions puforby, 4 accessions gloyzyby, 3 accessions royskorbu, 3 accessions poforby, 1 accession parforby, 1 accession rawweebu, 1 accession klozyby, 3 accessions suskorbu, 1 accession klawzyby, 1 accession soskorbu, 1 accession saweebu, 1 accession glarcheyby, 1 accession suweebu, 1 accession kleyzyby, 1 accession kloyzyby, 2 accessions plazyby, 2 accessions sorweebu, 1 accession sawskorbu, 2 accessions soyweebu, 1 accession nomaya, 1 accession seeskorbu, 1 accession tyweebu, 2 accessions minora, 10 accessions rerforby, 1 accession plozyby, 1 accession plarzyby, 1 accession plawzyby, 1 accession pleezyby, 1 accession rawblu, 3 accessions kleycheyby, 1 accession royforby, 1 accession skazyby, 1 accession seyskorbu, 2 accessions beelu, 9 accessions sorskorbu, 1 accession skerzyby, 1 accession sunimu, 1 accession serforby, 1 accession skeyzyby, 1 accession vawweebu, 1 accession vorweebu, 2 accessions soyskorbu, 1 accession werweebu, 1 accession toskorbu, 1 accession tarskorbu, 1 accession soyforby, 1 accession taforby, 1 accession tawskorbu, 1 accession tuforby, 1 accession sleyzyby, 1 accession slorzyby, 1 accession zawweebu, 1 accession sloyzyby, 2 accessions tamaya, 1 accession smyzyby, 1 accession smuzyby, 2 accessions zeyweebu, 1 accession smarzyby, 4 accessions smawzyby, 2 accessions terskorbu, 1 accession zoyweebu, 1 accession smerzyby, 1 accession smorzyby, 2 accessions smoyzyby, 5 accessions vawforby, 1 accession snazyby, 3 accessions sloyskobu, 3 accessions snuzyby, 1 accession beylu, 2 accessions wyforby, 1 accession vaskorbu, 2 accessions snerzyby, 1 accession snoyzyby, 4 accessions spazyby, 2 accessions spyzyby, 1 accession spozyby, 1 accession borlu, 2 accessions TRAPPC9, 226 accessions 17 variants dolu, 67 accessions mawskorbu, 1 accession tarshoy, 2 accessions nahemu, 274 accessions 3 variants EIF2C2, 171 accessions 12 variants PTK2, 807 accessions, 76 variants skeezyby, 13 accessions senimu, 3 accessions ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               64 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i, .j-u, .k-u, .l Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

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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