Homo sapiens complex locus RAD51AP1, encoding RAD51 associated protein 1.
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SUMMARY back to top
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 15 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, 2.3 times the average gene in this release. The sequence of this gene is defined by 274 GenBank accessions from 248 cDNA clones, some from brain (seen 12 times), testis (10), liver (9), thymus (9), uterus (9), embryonic stem cells, dmso-treated H9 cellline (7), leiomyosarcoma (6) and 82 other tissues. We annotate structural defects or features in 6 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 24 distinct gt-ag introns. Transcription produces 18 different mRNAs, 15 alternatively spliced variants and 3 unspliced forms. There are 3 probable alternative promotors, 3 non overlapping alternative last exons and 9 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 6 cassette exons, overlapping exons with different boundaries.
Note that mRNA .kAug10 was found in vivo, although it is a predicted target of nonsense mediated mRNA decay (NMD).
Function: There are 6 articles specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in processes (DNA repair, double-strand break repair via homologous recombination). Proteins are expected to have molecular functions (double-stranded DNA binding, protein binding, RNA binding, single-stranded DNA binding) and to localize in nucleus. Putative protein interactors have been described (RAD51, USP12, USP46, WDR48).
Protein coding potential: 11 spliced mRNAs putatively encode good proteins, altogether 10 different isoforms (7 complete, 1 COOH complete, 2 partial). The remaining 7 mRNA variants (4 spliced, 3 unspliced; 3 partial) appear not to encode good proteins. Finally proteins from this gene may be modulated by acetylation; phosphorylation, 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 12, links to other databases and other names
Map: This gene RAD51AP1 maps on chromosome 12, at 12p13.2-p13.1 according to Entrez Gene. In AceView, it covers 21.68 kb, from 4647926 to 4669603 (NCBI 37, August 2010), on the direct strand.
Links to: manual annotations from PhosphoSite, the SNP view, gene overviews from Entrez Gene 10635, 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 RAD51AP1 or PIR51, LOC10635. It has been described as RAD51-associated protein 1, RAD51-interacting protein.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Rad51ap1 (e=3 10-49)
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
RAD51AP1 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 0.19 0.63 0.34 0.36 0.24 0.59 0.32 0.51 0.68 0.32 0.42 0.29 0.72 0.89 0.17 0.34 0.96 0.21 0.34 2.90 0.78 7.64 0.34 3.57 0.27 0.96 17.6 0.72 0.63 0.63 0.32 0.32 0.15 7.64 1.35 1.02 4.39 0.45 0.36 0.24 2.70 3.57 0.48 0.59 0.68 0.26 1.45 0.32 0.32 0.72 4.10 3.82 9.41 0.34 0.42 0.16 10.1 0.34 0.18 10.1 0.51 0.55 0.89 0.48 0.39 0.26 0.07 8.78 5.79 4.39 5.79 11.6 0.83 0.63 0.21 0.18 14.3 1.78 0.59 3.57 7.13 0.32 0.59 0.55 0.89 7.13 0.34 0.55 0.27 1.02 3.57 0.78 3.33 15.3 0.45 0.89 0.63 0.42 0.19 1.55 0.68 1.55 2.05 3.57 0.83 0.89 0.36 1.78 0.83 0.48 0.26 12.4 1.91 4.71 0.63 10.8 0.15 0.96 2.35 4.71 1.02 1.10 5.04 11.6 16.4 0.63 1.18 3.33 4.71 5.04 43.2 0.13 0.22 0.59 0.45 0.36 0.19 0.78 0.26 2.35 15.3 2.35 17.6 3.82 1.91 8.19 3.82 2.70 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 RAD51AP1 5' 3' encoded on plus strand of chromosome 12 from 4,647,926 to 4,669,603 21753 30837 1919 2272 26804 28522 26866 15529 18537 a [NM] 21753 30837 18677 26804 28522 26866 15529 18537 b [NM] 21753 30837 429 569 2272 26804 28522 26866 15529 18537 c 21753 30837 2737 26804 28522 26866 15529 18537 d 30837 18677 26804 28522 26866 220 18537 e 21753 30837 18677 26804 28522 26866 703 f 21753 30837 756 28522 26866 15529 632 g 21753 30837 2833 28522 26866 15529 632 h r-u 18677 26804 28522 26866 i 30837 815 183 26804 28522 j 21753 30837 1919 75 28522 26866 k l-u 21753 30837 815 569 2272 26804 o 23 983 m 21753 30837 2737 26804 28522 26866 n 21753 30837 306 75 28522 p q-u 1 2kb 0 197 bp exon 197 bp exon 2927 bp [gt-ag] intron 139 GenBank accessions 21614 RNA-seq supporting reads 9532 UHR pooled cells 234 Brain 216 Blood 11613 Neuroblastoma 19 Other (also 1572 Primates bodymap) 50 bp exon 1829 bp [gt-ag] intron 150 GenBank accessions 30687 RNA-seq supporting reads 13732 UHR pooled cells 267 Brain 224 Blood 16443 Neuroblastoma 21 Other (also 2746 Primates bodymap) 142 bp exon 1877 bp [gt-ag] intron 24 GenBank accessions 1895 RNA-seq supporting reads 1004 UHR pooled cells 12 Brain 18 Blood 860 Neuroblastoma 1 Other (also 296 Primates bodymap) 51 bp exon 476 bp [gt-ag] intron 28 GenBank accessions 2244 RNA-seq supporting reads 1062 UHR pooled cells 9 Brain 42 Blood 1130 Neuroblastoma 1 Other (also 259 Primates bodymap) 110 bp exon 1673 bp [gt-ag] intron 145 GenBank accessions 26659 RNA-seq supporting reads 12696 UHR pooled cells 230 Brain 240 Blood 13467 Neuroblastoma 26 Other (also 1950 Primates bodymap) 87 bp exon 508 bp [gt-ag] intron 150 GenBank accessions 28372 RNA-seq supporting reads 12933 UHR pooled cells 232 Brain 169 Blood 15018 Neuroblastoma 20 Other (also 1608 Primates bodymap) 150 bp exon 4146 bp [gt-ag] intron 90 GenBank accessions 26776 RNA-seq supporting reads 12044 UHR pooled cells 197 Brain 207 Blood 14310 Neuroblastoma 18 Other (also 1541 Primates bodymap) 165 bp exon 3205 bp [gt-ag] intron 44 GenBank accessions 15485 RNA-seq supporting reads 8012 UHR pooled cells 80 Brain 109 Blood 7274 Neuroblastoma 10 Other (also 846 Primates bodymap) 150 bp exon 2354 bp [gt-ag] intron 33 GenBank accessions 18504 RNA-seq supporting reads 9188 UHR pooled cells 79 Brain 129 Blood 9102 Neuroblastoma 6 Other (also 924 Primates bodymap) 1192 bp exon 53 accessions, NM_001130862.1 some from brain (seen 3 times) liver (3), testis (3) melanotic melanoma, high MDR (2) primitive neuroectoderm (2) Validated 3' end, 1 accession Validated 3' end, 1 accession Validated 3' end, 2 accessions 1192 bp exon 173 bp exon 173 bp exon 2927 bp [gt-ag] intron 139 GenBank accessions 21614 RNA-seq supporting reads 9532 UHR pooled cells 234 Brain 216 Blood 11613 Neuroblastoma 19 Other (also 1572 Primates bodymap) 50 bp exon 1829 bp [gt-ag] intron 150 GenBank accessions 30687 RNA-seq supporting reads 13732 UHR pooled cells 267 Brain 224 Blood 16443 Neuroblastoma 21 Other (also 2746 Primates bodymap) 142 bp exon 2404 bp [gt-ag] intron 103 GenBank accessions 18574 RNA-seq supporting reads 9152 UHR pooled cells 128 Brain 125 Blood 9159 Neuroblastoma 10 Other (also 1146 Primates bodymap) 110 bp exon 1673 bp [gt-ag] intron 145 GenBank accessions 26659 RNA-seq supporting reads 12696 UHR pooled cells 230 Brain 240 Blood 13467 Neuroblastoma 26 Other (also 1950 Primates bodymap) 87 bp exon 508 bp [gt-ag] intron 150 GenBank accessions 28372 RNA-seq supporting reads 12933 UHR pooled cells 232 Brain 169 Blood 15018 Neuroblastoma 20 Other (also 1608 Primates bodymap) 150 bp exon 4146 bp [gt-ag] intron 90 GenBank accessions 26776 RNA-seq supporting reads 12044 UHR pooled cells 197 Brain 207 Blood 14310 Neuroblastoma 18 Other (also 1541 Primates bodymap) 165 bp exon 3205 bp [gt-ag] intron 44 GenBank accessions 15485 RNA-seq supporting reads 8012 UHR pooled cells 80 Brain 109 Blood 7274 Neuroblastoma 10 Other (also 846 Primates bodymap) 150 bp exon 2354 bp [gt-ag] intron 33 GenBank accessions 18504 RNA-seq supporting reads 9188 UHR pooled cells 79 Brain 129 Blood 9102 Neuroblastoma 6 Other (also 924 Primates bodymap) 1193 bp exon 128 accessions, NM_006479.4 some from testis (seen 7 times) brain (6), bladder (5) carcinoma, cell line (5) embryonic stem cells dmso-treated H9 cellline (5) Validated 3' end, 1 accession Validated 3' end, 10 accessions 1193 bp exon 67 bp exon 2927 bp [gt-ag] intron 139 GenBank accessions 21614 RNA-seq supporting reads 9532 UHR pooled cells 234 Brain 216 Blood 11613 Neuroblastoma 19 Other (also 1572 Primates bodymap) 50 bp exon 1829 bp [gt-ag] intron 150 GenBank accessions 30687 RNA-seq supporting reads 13732 UHR pooled cells 267 Brain 224 Blood 16443 Neuroblastoma 21 Other (also 2746 Primates bodymap) 149 bp exon 1307 bp [gt-ag] intron 2 GenBank accessions 427 RNA-seq supporting reads 105 UHR pooled cells 3 Brain 319 Neuroblastoma 94 bp exon 94 bp exon 469 bp [gt-ag] intron 4 GenBank accessions 565 RNA-seq supporting reads 124 UHR pooled cells 2 Brain 4 Blood 435 Neuroblastoma 51 bp exon 476 bp [gt-ag] intron 28 GenBank accessions 2244 RNA-seq supporting reads 1062 UHR pooled cells 9 Brain 42 Blood 1130 Neuroblastoma 1 Other (also 259 Primates bodymap) 110 bp exon 1673 bp [gt-ag] intron 145 GenBank accessions 26659 RNA-seq supporting reads 12696 UHR pooled cells 230 Brain 240 Blood 13467 Neuroblastoma 26 Other (also 1950 Primates bodymap) 87 bp exon 508 bp [gt-ag] intron 150 GenBank accessions 28372 RNA-seq supporting reads 12933 UHR pooled cells 232 Brain 169 Blood 15018 Neuroblastoma 20 Other (also 1608 Primates bodymap) 150 bp exon 4146 bp [gt-ag] intron 90 GenBank accessions 26776 RNA-seq supporting reads 12044 UHR pooled cells 197 Brain 207 Blood 14310 Neuroblastoma 18 Other (also 1541 Primates bodymap) 165 bp exon 3205 bp [gt-ag] intron 44 GenBank accessions 15485 RNA-seq supporting reads 8012 UHR pooled cells 80 Brain 109 Blood 7274 Neuroblastoma 10 Other (also 846 Primates bodymap) 150 bp exon 2354 bp [gt-ag] intron 33 GenBank accessions 18504 RNA-seq supporting reads 9188 UHR pooled cells 79 Brain 129 Blood 9102 Neuroblastoma 6 Other (also 924 Primates bodymap) 1577 bp exon 24 accessions, some from uterus (seen 3 times) colon (2), liver (2) placenta cot 25-normalized (2) 2 pooled tumors (clear cell type) (once) Validated 3' end, 1 accession Validated 3' end, 7 accessions 1577 bp exon 159 bp exon 2927 bp [gt-ag] intron 139 GenBank accessions 21614 RNA-seq supporting reads 9532 UHR pooled cells 234 Brain 216 Blood 11613 Neuroblastoma 19 Other (also 1572 Primates bodymap) 50 bp exon 1829 bp [gt-ag] intron 150 GenBank accessions 30687 RNA-seq supporting reads 13732 UHR pooled cells 267 Brain 224 Blood 16443 Neuroblastoma 21 Other (also 2746 Primates bodymap) 149 bp exon 2397 bp [gt-ag] intron 14 GenBank accessions 2723 RNA-seq supporting reads 1110 UHR pooled cells 27 Brain 24 Blood 1560 Neuroblastoma 2 Other (also 109 Primates bodymap) 110 bp exon 110 bp exon 1673 bp [gt-ag] intron 145 GenBank accessions 26659 RNA-seq supporting reads 12696 UHR pooled cells 230 Brain 240 Blood 13467 Neuroblastoma 26 Other (also 1950 Primates bodymap) 87 bp exon 508 bp [gt-ag] intron 150 GenBank accessions 28372 RNA-seq supporting reads 12933 UHR pooled cells 232 Brain 169 Blood 15018 Neuroblastoma 20 Other (also 1608 Primates bodymap) 150 bp exon 4146 bp [gt-ag] intron 90 GenBank accessions 26776 RNA-seq supporting reads 12044 UHR pooled cells 197 Brain 207 Blood 14310 Neuroblastoma 18 Other (also 1541 Primates bodymap) 165 bp exon 3205 bp [gt-ag] intron 44 GenBank accessions 15485 RNA-seq supporting reads 8012 UHR pooled cells 80 Brain 109 Blood 7274 Neuroblastoma 10 Other (also 846 Primates bodymap) 150 bp exon 2354 bp [gt-ag] intron 33 GenBank accessions 18504 RNA-seq supporting reads 9188 UHR pooled cells 79 Brain 129 Blood 9102 Neuroblastoma 6 Other (also 924 Primates bodymap) 1181 bp exon 6 accessions, some from brain (seen once) embryonic stem cells cell lines H1, H7, andh9 (once) human embryonic stem cells differentiated toan early endodermal cell type (once) T cells (jurkat cell line) (once) 1181 bp exon 50 bp exon 50 bp exon 1829 bp [gt-ag] intron 150 GenBank accessions 30687 RNA-seq supporting reads 13732 UHR pooled cells 267 Brain 224 Blood 16443 Neuroblastoma 21 Other (also 2746 Primates bodymap) 142 bp exon 2404 bp [gt-ag] intron 103 GenBank accessions 18574 RNA-seq supporting reads 9152 UHR pooled cells 128 Brain 125 Blood 9159 Neuroblastoma 10 Other (also 1146 Primates bodymap) 110 bp exon 1673 bp [gt-ag] intron 145 GenBank accessions 26659 RNA-seq supporting reads 12696 UHR pooled cells 230 Brain 240 Blood 13467 Neuroblastoma 26 Other (also 1950 Primates bodymap) 87 bp exon 508 bp [gt-ag] intron 150 GenBank accessions 28372 RNA-seq supporting reads 12933 UHR pooled cells 232 Brain 169 Blood 15018 Neuroblastoma 20 Other (also 1608 Primates bodymap) 150 bp exon 4146 bp [gt-ag] intron 90 GenBank accessions 26776 RNA-seq supporting reads 12044 UHR pooled cells 197 Brain 207 Blood 14310 Neuroblastoma 18 Other (also 1541 Primates bodymap) 165 bp exon 3283 bp [gt-ag] intron 1 GenBank accession 219 RNA-seq supporting reads 165 UHR pooled cells 2 Brain 1 Blood 51 Neuroblastoma (also 5 Primates bodymap) 72 bp exon 2354 bp [gt-ag] intron 33 GenBank accessions 18504 RNA-seq supporting reads 9188 UHR pooled cells 79 Brain 129 Blood 9102 Neuroblastoma 6 Other (also 924 Primates bodymap) 18 bp exon 1 accession from blastocyst from pluripotent cell line derived fromblastocyst inner cell mass 18 bp exon 26 bp exon 26 bp exon 2927 bp [gt-ag] intron 139 GenBank accessions 21614 RNA-seq supporting reads 9532 UHR pooled cells 234 Brain 216 Blood 11613 Neuroblastoma 19 Other (also 1572 Primates bodymap) 50 bp exon 1829 bp [gt-ag] intron 150 GenBank accessions 30687 RNA-seq supporting reads 13732 UHR pooled cells 267 Brain 224 Blood 16443 Neuroblastoma 21 Other (also 2746 Primates bodymap) 142 bp exon 2404 bp [gt-ag] intron 103 GenBank accessions 18574 RNA-seq supporting reads 9152 UHR pooled cells 128 Brain 125 Blood 9159 Neuroblastoma 10 Other (also 1146 Primates bodymap) 110 bp exon 1673 bp [gt-ag] intron 145 GenBank accessions 26659 RNA-seq supporting reads 12696 UHR pooled cells 230 Brain 240 Blood 13467 Neuroblastoma 26 Other (also 1950 Primates bodymap) 87 bp exon 508 bp [gt-ag] intron 150 GenBank accessions 28372 RNA-seq supporting reads 12933 UHR pooled cells 232 Brain 169 Blood 15018 Neuroblastoma 20 Other (also 1608 Primates bodymap) 150 bp exon 4146 bp [gt-ag] intron 90 GenBank accessions 26776 RNA-seq supporting reads 12044 UHR pooled cells 197 Brain 207 Blood 14310 Neuroblastoma 18 Other (also 1541 Primates bodymap) 107 bp exon 5767 bp [gt-ag] intron 1 GenBank accession 702 RNA-seq supporting reads 369 UHR pooled cells 9 Brain 5 Blood 319 Neuroblastoma (also 15 Primates bodymap) 114 bp exon 1 accession capped 5' end, 1 accession 114 bp exon 69 bp exon 69 bp exon 213 bp uORF 2927 bp [gt-ag] intron 139 GenBank accessions 21614 RNA-seq supporting reads 9532 UHR pooled cells 234 Brain 216 Blood 11613 Neuroblastoma 19 Other (also 1572 Primates bodymap) 50 bp exon 213 bp uORF 1829 bp [gt-ag] intron 150 GenBank accessions 30687 RNA-seq supporting reads 13732 UHR pooled cells 267 Brain 224 Blood 16443 Neuroblastoma 21 Other (also 2746 Primates bodymap) 213 bp uORF 149 bp exon 149 bp exon 4180 bp [gt-ag] intron 2 GenBank accessions 754 RNA-seq supporting reads 155 UHR pooled cells 19 Brain 5 Blood 575 Neuroblastoma (also 38 Primates bodymap) 87 bp exon 87 bp exon 87 bp exon 508 bp [gt-ag] intron 150 GenBank accessions 28372 RNA-seq supporting reads 12933 UHR pooled cells 232 Brain 169 Blood 15018 Neuroblastoma 20 Other (also 1608 Primates bodymap) 150 bp exon 150 bp exon 4146 bp [gt-ag] intron 90 GenBank accessions 26776 RNA-seq supporting reads 12044 UHR pooled cells 197 Brain 207 Blood 14310 Neuroblastoma 18 Other (also 1541 Primates bodymap) 165 bp exon 165 bp exon 3205 bp [gt-ag] intron 44 GenBank accessions 15485 RNA-seq supporting reads 8012 UHR pooled cells 80 Brain 109 Blood 7274 Neuroblastoma 10 Other (also 846 Primates bodymap) 198 bp exon 198 bp exon 2306 bp [gt-ag] intron 2 GenBank accessions 630 RNA-seq supporting reads 436 UHR pooled cells 6 Brain 188 Neuroblastoma 163 bp exon 163 bp exon 2 accessions, some from esophageal tumor tissue (seen once) esophagus, tumor tissue (once) 163 bp exon 106 bp exon 106 bp exon 216 bp uORF 2927 bp [gt-ag] intron 139 GenBank accessions 21614 RNA-seq supporting reads 9532 UHR pooled cells 234 Brain 216 Blood 11613 Neuroblastoma 19 Other (also 1572 Primates bodymap) 50 bp exon 216 bp uORF 1829 bp [gt-ag] intron 150 GenBank accessions 30687 RNA-seq supporting reads 13732 UHR pooled cells 267 Brain 224 Blood 16443 Neuroblastoma 21 Other (also 2746 Primates bodymap) 142 bp exon 216 bp uORF 4187 bp [gt-ag] intron 9 GenBank accessions 2824 RNA-seq supporting reads 740 UHR pooled cells 45 Brain 9 Blood 2029 Neuroblastoma 1 Other (also 69 Primates bodymap) 216 bp uORF 87 bp exon 87 bp exon 87 bp exon 508 bp [gt-ag] intron 150 GenBank accessions 28372 RNA-seq supporting reads 12933 UHR pooled cells 232 Brain 169 Blood 15018 Neuroblastoma 20 Other (also 1608 Primates bodymap) 150 bp exon 150 bp exon 4146 bp [gt-ag] intron 90 GenBank accessions 26776 RNA-seq supporting reads 12044 UHR pooled cells 197 Brain 207 Blood 14310 Neuroblastoma 18 Other (also 1541 Primates bodymap) 165 bp exon 165 bp exon 3205 bp [gt-ag] intron 44 GenBank accessions 15485 RNA-seq supporting reads 8012 UHR pooled cells 80 Brain 109 Blood 7274 Neuroblastoma 10 Other (also 846 Primates bodymap) 198 bp exon 198 bp exon 2306 bp [gt-ag] intron 2 GenBank accessions 630 RNA-seq supporting reads 436 UHR pooled cells 6 Brain 188 Neuroblastoma 474 bp exon 474 bp exon 8 accessions, some from neuroblastoma (seen 2 times) thymus (2), pericardium (once) 474 bp exon 121 bp exon 121 bp exon 1 accession from liver 121 bp exon 121 bp exon 121 bp exon 2404 bp [gt-ag] intron 103 GenBank accessions 18574 RNA-seq supporting reads 9152 UHR pooled cells 128 Brain 125 Blood 9159 Neuroblastoma 10 Other (also 1146 Primates bodymap) 110 bp exon 1673 bp [gt-ag] intron 145 GenBank accessions 26659 RNA-seq supporting reads 12696 UHR pooled cells 230 Brain 240 Blood 13467 Neuroblastoma 26 Other (also 1950 Primates bodymap) 87 bp exon 508 bp [gt-ag] intron 150 GenBank accessions 28372 RNA-seq supporting reads 12933 UHR pooled cells 232 Brain 169 Blood 15018 Neuroblastoma 20 Other (also 1608 Primates bodymap) 150 bp exon 4146 bp [gt-ag] intron 90 GenBank accessions 26776 RNA-seq supporting reads 12044 UHR pooled cells 197 Brain 207 Blood 14310 Neuroblastoma 18 Other (also 1541 Primates bodymap) 283 bp exon 2 accessions 283 bp exon 48 bp exon 48 bp exon 33 bp uORF 1829 bp [gt-ag] intron 150 GenBank accessions 30687 RNA-seq supporting reads 13732 UHR pooled cells 267 Brain 224 Blood 16443 Neuroblastoma 21 Other (also 2746 Primates bodymap) 33 bp uORF 142 bp exon 142 bp exon 1314 bp [gt-ag] intron 3 GenBank accessions 812 RNA-seq supporting reads 188 UHR pooled cells 10 Brain 614 Neuroblastoma 94 bp exon 94 bp exon 94 bp exon 996 bp [gt-ag] intron 1 GenBank accession 182 RNA-seq supporting reads 18 UHR pooled cells 1 Brain 163 Neuroblastoma 110 bp exon 110 bp exon 1673 bp [gt-ag] intron 145 GenBank accessions 26659 RNA-seq supporting reads 12696 UHR pooled cells 230 Brain 240 Blood 13467 Neuroblastoma 26 Other (also 1950 Primates bodymap) 87 bp exon 87 bp exon 508 bp [gt-ag] intron 150 GenBank accessions 28372 RNA-seq supporting reads 12933 UHR pooled cells 232 Brain 169 Blood 15018 Neuroblastoma 20 Other (also 1608 Primates bodymap) 84 bp exon 84 bp exon 1 accession capped 5' end, 1 accession 84 bp exon 79 bp exon 79 bp exon 2927 bp [gt-ag] intron 139 GenBank accessions 21614 RNA-seq supporting reads 9532 UHR pooled cells 234 Brain 216 Blood 11613 Neuroblastoma 19 Other (also 1572 Primates bodymap) 50 bp exon 1829 bp [gt-ag] intron 150 GenBank accessions 30687 RNA-seq supporting reads 13732 UHR pooled cells 267 Brain 224 Blood 16443 Neuroblastoma 21 Other (also 2746 Primates bodymap) 142 bp exon 1877 bp [gt-ag] intron 24 GenBank accessions 1895 RNA-seq supporting reads 1004 UHR pooled cells 12 Brain 18 Blood 860 Neuroblastoma 1 Other (also 296 Primates bodymap) 51 bp exon 2259 bp [gt-ag] intron 2 GenBank accessions 73 RNA-seq supporting reads 37 UHR pooled cells 2 Brain 33 Neuroblastoma 1 Other (also 1 Primates bodymap) 87 bp exon 87 bp exon 508 bp [gt-ag] intron 150 GenBank accessions 28372 RNA-seq supporting reads 12933 UHR pooled cells 232 Brain 169 Blood 15018 Neuroblastoma 20 Other (also 1608 Primates bodymap) 150 bp exon 4146 bp [gt-ag] intron 90 GenBank accessions 26776 RNA-seq supporting reads 12044 UHR pooled cells 197 Brain 207 Blood 14310 Neuroblastoma 18 Other (also 1541 Primates bodymap) 1 accession from eye from fetal eyes 140 bp exon 2437 bp exon 2437 bp exon 6 accessions, some from eye (seen 2 times) liver and spleen (2) embryonic stem cells dmso-treated H9 cellline (once) fetal eye (once), retinoblastoma (once) Validated 3' end, 1 accession 2437 bp exon 44 bp exon 2927 bp [gt-ag] intron 139 GenBank accessions 21614 RNA-seq supporting reads 9532 UHR pooled cells 234 Brain 216 Blood 11613 Neuroblastoma 19 Other (also 1572 Primates bodymap) 50 bp exon 1829 bp [gt-ag] intron 150 GenBank accessions 30687 RNA-seq supporting reads 13732 UHR pooled cells 267 Brain 224 Blood 16443 Neuroblastoma 21 Other (also 2746 Primates bodymap) 142 bp exon 1314 bp [gt-ag] intron 3 GenBank accessions 812 RNA-seq supporting reads 188 UHR pooled cells 10 Brain 614 Neuroblastoma 94 bp exon 94 bp exon 469 bp [gt-ag] intron 4 GenBank accessions 565 RNA-seq supporting reads 124 UHR pooled cells 2 Brain 4 Blood 435 Neuroblastoma 51 bp exon 476 bp [gt-ag] intron 28 GenBank accessions 2244 RNA-seq supporting reads 1062 UHR pooled cells 9 Brain 42 Blood 1130 Neuroblastoma 1 Other (also 259 Primates bodymap) 110 bp exon 1673 bp [gt-ag] intron 145 GenBank accessions 26659 RNA-seq supporting reads 12696 UHR pooled cells 230 Brain 240 Blood 13467 Neuroblastoma 26 Other (also 1950 Primates bodymap) 84 bp exon 2 accessions capped 5' end, 2 accessions 84 bp exon 32 bp exon 2435 bp [gt-ag] intron 2 GenBank accessions 21 RNA-seq supporting reads 5 UHR pooled cells 16 Neuroblastoma 165 bp exon 165 bp exon 5709 bp [gt-ag] intron 2 GenBank accessions 981 RNA-seq supporting reads 594 UHR pooled cells 17 Brain 1 Blood 366 Neuroblastoma 3 Other (also 12 Primates bodymap) 826 bp exon 2 accessions capped 5' end, 1 accession 826 bp exon 70 bp exon 70 bp exon 2927 bp [gt-ag] intron 139 GenBank accessions 21614 RNA-seq supporting reads 9532 UHR pooled cells 234 Brain 216 Blood 11613 Neuroblastoma 19 Other (also 1572 Primates bodymap) 50 bp exon 1829 bp [gt-ag] intron 150 GenBank accessions 30687 RNA-seq supporting reads 13732 UHR pooled cells 267 Brain 224 Blood 16443 Neuroblastoma 21 Other (also 2746 Primates bodymap) 149 bp exon 149 bp exon 2397 bp [gt-ag] intron 14 GenBank accessions 2723 RNA-seq supporting reads 1110 UHR pooled cells 27 Brain 24 Blood 1560 Neuroblastoma 2 Other (also 109 Primates bodymap) 110 bp exon 1673 bp [gt-ag] intron 145 GenBank accessions 26659 RNA-seq supporting reads 12696 UHR pooled cells 230 Brain 240 Blood 13467 Neuroblastoma 26 Other (also 1950 Primates bodymap) 87 bp exon 508 bp [gt-ag] intron 150 GenBank accessions 28372 RNA-seq supporting reads 12933 UHR pooled cells 232 Brain 169 Blood 15018 Neuroblastoma 20 Other (also 1608 Primates bodymap) 150 bp exon 4146 bp [gt-ag] intron 90 GenBank accessions 26776 RNA-seq supporting reads 12044 UHR pooled cells 197 Brain 207 Blood 14310 Neuroblastoma 18 Other (also 1541 Primates bodymap) 9 accessions, some from bone marrow (seen once) brain (once), cervical carcinoma cell line (once) cervix (once), esophageal tumor tissue (once) Validated 3' end, 1 accession 147 bp exon 67 bp exon 67 bp exon 2927 bp [gt-ag] intron 139 GenBank accessions 21614 RNA-seq supporting reads 9532 UHR pooled cells 234 Brain 216 Blood 11613 Neuroblastoma 19 Other (also 1572 Primates bodymap) 50 bp exon 1829 bp [gt-ag] intron 150 GenBank accessions 30687 RNA-seq supporting reads 13732 UHR pooled cells 267 Brain 224 Blood 16443 Neuroblastoma 21 Other (also 2746 Primates bodymap) 149 bp exon 149 bp exon 1870 bp [gt-ag] intron 1 GenBank accession 305 RNA-seq supporting reads 134 UHR pooled cells 171 Neuroblastoma (also 34 Primates bodymap) 51 bp exon 2259 bp [gt-ag] intron 2 GenBank accessions 73 RNA-seq supporting reads 37 UHR pooled cells 2 Brain 33 Neuroblastoma 1 Other (also 1 Primates bodymap) 87 bp exon 508 bp [gt-ag] intron 150 GenBank accessions 28372 RNA-seq supporting reads 12933 UHR pooled cells 232 Brain 169 Blood 15018 Neuroblastoma 20 Other (also 1608 Primates bodymap) 1 accession from normal nasopharynx 142 bp exon 430 bp exon 430 bp exon 1 accession 430 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 2294 bp 352 aa 180 bp 1055 bp 2kb possibly including promoter 21289 bp 1kb
bAug10 2220 bp 335 aa 156 bp 1056 bp 2kb possibly including promoter 21266 bp 1kb
cAug10 2650 bp 298 aa 313 bp 1440 bp 2kb probably including promoter 21544 bp 1kb
dAug10 2201 bp 265 aa 359 bp 1044 bp 2kb possibly including promoter 21240 bp 1kb
eAug10 794 bp 264 aa 2kb 16991 bp 1kb
fAug10 786 bp 235 aa 9 bp 69 bp 2kb including Promoter 20040 bp 1kb
gAug10 1031 bp 233 aa 303 bp 26 bp 210 bp 2kb probably including promoter 20132 bp 1kb
hAug10 1372 bp 233 aa 333 bp 337 bp 213 bp 2kb probably including promoter 20480 bp 1kb
iAug10 751 bp 220 aa 86 bp 2kb 9482 bp 1kb
jAug10 565 bp 109 aa 237 bp 30 bp 2kb including Promoter 6885 bp 1kb
kAug10 699 bp 88 aa 62 bp 370 bp 2kb probably including promoter 14245 bp 1kb
lAug10-unspliced 2437 bp 39 aa 1829 bp 488 bp 2kb 2437 bp 1kb
mAug10 1023 bp 79 aa 94 bp 689 bp 2kb including Promoter 9167 bp 1kb
nAug10 763 bp 70 aa 53 bp 497 bp 2kb probably including promoter 14243 bp 1kb
oAug10 575 bp 97 aa 283 bp 2kb including Promoter 9263 bp 1kb
pAug10 546 bp 70 aa 50 bp 283 bp 2kb probably including promoter 9939 bp 1kb
qAug10-unspliced 430 bp 70 aa 215 bp 2kb 430 bp 1kb
rAug10-unspliced 121 bp 19 aa 62 bp 2kb probably including promoter 121 bp 1kb

Gene neighbors and Navigator on chromosome 12p13.2-p13.1 back to top
G D C P CCND2 D C I R P C12orf5 D C R P RAD51AP1 C I R P DYRK4_ D C I R P R KCNA1 D C I R P D C I R P RPL18P9 RPS15P7 R D C I P FGF23 D C I R P FGF6 C R P C12orf4 D C I R P AKAP3 100kb 0 LOC399988, 10 accessions CCND2, 485 accessions 6 variants C12orf5, 172 accessions 5 variants RAD51AP1, 253 accessions 18 variants DYRK4_, 680 accessions 57 variants nernee, 13 accessions KCNA1, 92 accessions, 5 variants peynee, 20 accessions 3 variants darblaw, 2 accessions chogerby, 2 accessions borbloby, 1 accession chargerby, 1 accession varfu, 3 accessions chawgerby, 1 accession dybloby, 1 accession chergerby, 1 accession dobloby, 2 accessions dawbloby, 2 accessions chorgerby, 2 accessions choygerby, 1 accession shagerby, 3 accessions deybloby, 1 accession yosure, 1 accession shawgerby, 1 accession sheygerby, 3 accessions forbloby, 1 accession jyblawbu, 1 accession shorgerby, 3 accessions joblawbu, 1 accession menimi, 2 accessions, 2 variants jabloby, 1 accession blergerby, 1 accession blorgerby, 2 accessions jeyblawbu, 1 accession jublaw, 1 accession flygerby, 1 accession jeeblaw, 1 accession flugerby, 2 accessions kawbloby, 1 accession flawgerby, 2 accessions lublaw, 1 accession kerbloby, 2 accessions kyblawbu, 2 accessions kublawbu, 1 accession nablaw, 1 accession monimi, 1 accession koblawbu, 1 accession porbloby, 1 accession sarbloby, 1 accession werbloby, 1 accession glagerby, 1 accession hanimi, 2 accessions torcho, 7 accessions misure, 1 accession glogerby, 1 accession musure, 1 accession blorbloby, 1 accession korblawbu, 1 accession koyblawbu, 1 accession woyfu, 2 accessions lyblawbu, 1 accession glergerby, 1 accession hehere, 1 accession vycho, 4 accessions klygerby, 1 accession hinimi, 2 accessions, 2 variants mesure, 1 accession klargerby, 2 accessions vucho, 2 accessions kleegerby, 1 accession klergerby, 4 accessions kleygerby, 6 accessions loblawbu, 1 accession skerbloby, 1 accession dorblaw, 1 accession RPL18P9, 1 accession bawbloby, 1 accession beybloby, 2 accessions munimi, 1 accession gablaw, 1 accession cheegerby, 1 accession cheygerby, 1 accession shargerby, 1 accession derbloby, 3 accessions RPS15P7, 1 accession fubloby, 1 accession tarcho, 1 accession shergerby, 3 accessions gabloby, 3 accessions shoygerby, 1 accession jablaw, 1 accession blawgerby, 1 accession bleegerby, 1 accession bleygerby, 1 accession karbloby, 1 accession flagerby, 2 accessions jerblawbu, 1 accession jorblawbu, 1 accession narnee, 2 accessions kyblaw, 1 accession jeetybo, 13 accessions fleegerby, 1 accession loybloby, 1 accession flotybo, 1 accession pobloby, 1 accession parblaw, 1 accession florgerby, 1 accession kawblawbu, 1 accession rawblaw, 1 accession neynee, 8 accessions glygerby, 1 accession glugerby, 1 accession keyblawbu, 1 accession lablawbu, 1 accession glawgerby, 1 accession nornee, 2 accessions gleegerby, 3 accessions glorgerby, 1 accession gloygerby, 2 accessions plabloby, 1 accession rerblaw, 1 accession klawgerby, 1 accession vocho, 1 accession moynee, 2 accessions, 2 variants FGF23, 11 accessions, 2 variants FGF6, 7 accessions, 3 variants C12orf4, 296 accessions 14 variants AKAP3, 132 accessions 7 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               6 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i, .j, .k, .l-u, .m, .n, .o, .p, .q-u, .r-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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