Homo sapiens complex locus BOP1, encoding block of proliferation 1.
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SUMMARY back to top
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 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 very high level, 4.3 times the average gene in this release. The sequence of this gene is defined by 494 GenBank accessions from 453 cDNA clones, some from brain (seen 60 times), skin (50), lung (31), melanotic melanoma, cell line (31), pancreas (21), eye (20), adenocarcinoma, cell line (17) and 134 other tissues. We annotate structural defects or features in 6 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 21 distinct gt-ag introns. Transcription produces 11 different mRNAs, 10 alternatively spliced variants and 1 unspliced form. There are 6 probable alternative promotors and 3 non overlapping alternative last exons (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, splicing versus retention of 6 introns. 117 bp of this gene are antisense to spliced gene muhemu, 965 to SCXA, raising the possibility of regulated alternate expression.
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 eAug10).
Function: There are 17 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (Colorectal Neoplasms; Pancreatic Neoplasms) and proposed to participate in processes (cell proliferation, maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA), regulation of cell cycle, ribosome biogenesis, rRNA processing). Proteins are expected to have molecular function (protein binding) and to localize in various compartments (PeBoW complex, ribonucleoprotein complex, membrane, nucleolus, nucleoplasm, nucleus). Putative protein interactors have been described (ARRB1, ARRB2, PES1, WDR48).
Protein coding potential: 10 spliced mRNAs putatively encode good proteins, altogether 10 different isoforms (4 complete, 2 COOH complete, 4 partial), some containing domains BOP1NT (NUC169) domain, WD domain, G-beta repeat [Pfam], some transmembrane domains [Psort2]. The remaining mRNA variant (unspliced; partial) appears not to encode a good protein.
3 isoforms are annotated using as Met a Kozak-compatible non-AUG start, thereby gaining a minimum of 91 amino acids N-terminal to the first AUG. 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 8, links to other databases and other names
Map: This gene BOP1 maps on chromosome 8, at 8q24.3 according to Entrez Gene. In AceView, it covers 29.30 kb, from 145515081 to 145485780 (NCBI 37, August 2010), on the reverse strand.
Links to: manual annotations from PhosphoSite, the SNP view, gene overviews from Entrez Gene 23246, 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 BOP1, KIAA0124 or LOC23246, HLH.1. It has been described as ribosome biogenesis protein BOP1, block of proliferation 1 protein.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Bop1 (e=0.0).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene 2O442 (e= 10-164).
The closest A.thaliana gene, according to BlastP, is the AceView gene AT2G40360 (e= 10-151)
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
BOP1 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 5.79 0.78 3.33 2.19 2.05 7.13 2.90 2.05 2.05 10.8 2.52 4.10 6.21 3.10 4.71 4.71 1.91 5.04 32.8 7.13 11.6 3.33 2.19 0.48 0.63 0.48 0.63 1.02 1.18 1.10 1.66 2.90 3.10 1.45 1.55 5.40 9.41 8.19 12.4 11.6 10.1 6.65 4.71 4.71 5.40 7.13 5.79 5.40 3.10 2.70 1.78 2.52 3.33 1.78 2.52 4.39 2.70 1.45 3.10 6.21 3.33 5.04 3.33 2.52 3.57 7.13 8.78 8.78 2.70 6.21 5.04 8.78 10.8 7.13 7.64 7.13 5.79 8.19 3.82 6.65 6.21 7.64 5.40 7.13 5.79 7.13 6.21 4.10 5.79 5.04 7.64 4.71 5.04 5.04 3.33 8.19 8.78 4.71 8.78 1.45 1.10 1.35 0.78 0.89 1.66 1.18 1.78 0.89 0.72 1.18 3.10 4.39 5.04 4.10 3.10 4.39 6.21 3.82 4.39 7.64 7.13 3.82 5.40 3.57 3.82 4.10 15.3 5.04 3.82 10.1 7.64 3.33 5.40 4.39 5.04 1.35 0.32 0.21 0.63 1.91 1.55 1.45 1.10 1.66 2.52 1.66 1.91 2.35 1.66 3.57 3.82 4.39 0.59 2.52 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 BOP1 5' 3' encoded on minus strand of chromosome 8 from 145,515,081 to 145,485,780 79480 108486 117830 77630 87482 93753 86564 91274 95796 a [NM] 793 117830 77630 87482 93753 86564 91274 95796 b 117830 77630 87482 93753 1160 91274 95796 c 79480 6 95796 d 406 77630 87482 93753 1160 91274 e 79480 108486 117830 f 86564 91274 g 77630 87482 h 72 77630 87482 j 14 i k-u 1 2kb 0 128 bp exon 128 bp exon 1968 bp [gt-ag] intron 156 GenBank accessions 79324 RNA-seq supporting reads 12057 UHR pooled cells 4585 Brain 1215 Blood 61233 Neuroblastoma 234 Other (also 1416 Primates bodymap) 210 bp exon 12483 bp [gt-ag] intron 210 GenBank accessions 108276 RNA-seq supporting reads 20314 UHR pooled cells 7674 Brain 2261 Blood 77586 Neuroblastoma 441 Other (also 548 Primates bodymap) 81 bp exon 11151 bp [gt-ag] intron 219 GenBank accessions 117611 RNA-seq supporting reads 20798 UHR pooled cells 7797 Brain 2404 Blood 85986 Neuroblastoma 626 Other (also 3845 Primates bodymap) 155 bp exon 85 bp [gt-ag] intron 200 GenBank accessions 98003 RNA-seq supporting reads 18112 UHR pooled cells 6253 Brain 1776 Blood 71344 Neuroblastoma 518 Other (also 3630 Primates bodymap) 118 bp exon 97 bp [gt-ag] intron 180 GenBank accessions 77450 RNA-seq supporting reads 14334 UHR pooled cells 5138 Brain 1492 Blood 56081 Neuroblastoma 405 Other (also 2692 Primates bodymap) 102 bp exon 77 bp [gt-ag] intron 136 GenBank accessions 87346 RNA-seq supporting reads 15711 UHR pooled cells 6134 Brain 1551 Blood 63485 Neuroblastoma 465 Other (also 3902 Primates bodymap) 213 bp exon 82 bp [gt-ag] intron 90 GenBank accessions 93663 RNA-seq supporting reads 15664 UHR pooled cells 6193 Brain 1607 Blood 69697 Neuroblastoma 502 Other (also 2238 Primates bodymap) 162 bp exon 69 bp [gt-ag] intron 82 GenBank accessions 102812 RNA-seq supporting reads 18131 UHR pooled cells 7241 Brain 1714 Blood 75285 Neuroblastoma 441 Other (also 4188 Primates bodymap) 81 bp exon 69 bp [gt-ag] intron 84 GenBank accessions 86480 RNA-seq supporting reads 15381 UHR pooled cells 5952 Brain 1547 Blood 63271 Neuroblastoma 329 Other (also 3181 Primates bodymap) 70 bp exon 81 bp [gt-ag] intron 94 GenBank accessions 91180 RNA-seq supporting reads 16151 UHR pooled cells 6231 Brain 1318 Blood 67170 Neuroblastoma 310 Other (also 2869 Primates bodymap) 133 bp exon 76 bp [gt-ag] intron 106 GenBank accessions 99752 RNA-seq supporting reads 16818 UHR pooled cells 6436 Brain 823 Blood 75280 Neuroblastoma 395 Other (also 1158 Primates bodymap) 181 bp exon 79 bp [gt-ag] intron 102 GenBank accessions 81561 RNA-seq supporting reads 13090 UHR pooled cells 4832 Brain 504 Blood 62875 Neuroblastoma 260 Other (also 623 Primates bodymap) 289 bp exon 213 bp [gt-ag] intron 127 GenBank accessions 95669 RNA-seq supporting reads 18146 UHR pooled cells 6782 Brain 1125 Blood 69431 Neuroblastoma 185 Other (also 2192 Primates bodymap) 85 bp exon 84 bp [gt-ag] intron 125 GenBank accessions 100298 RNA-seq supporting reads 18917 UHR pooled cells 7477 Brain 1941 Blood 71748 Neuroblastoma 215 Other (also 4097 Primates bodymap) 108 bp exon 78 bp [gt-ag] intron 125 GenBank accessions 131222 RNA-seq supporting reads 24790 UHR pooled cells 10029 Brain 2093 Blood 94168 Neuroblastoma 142 Other (also 3885 Primates bodymap) 494 bp exon 432 accessions, NM_015201.3 some from brain (seen 56 times) skin (50), melanotic melanoma cell line (31), lung (30) eye (19) capped 5' end, 19 accessions Validated 3' end, 1 accession 494 bp exon 102 bp exon 102 bp exon 14661 bp [gt-ag] intron 2 GenBank accessions 791 RNA-seq supporting reads 81 UHR pooled cells 62 Brain 12 Blood 630 Neuroblastoma 6 Other (also 9 Primates bodymap) 81 bp exon 11151 bp [gt-ag] intron 219 GenBank accessions 117611 RNA-seq supporting reads 20798 UHR pooled cells 7797 Brain 2404 Blood 85986 Neuroblastoma 626 Other (also 3845 Primates bodymap) 155 bp exon 85 bp [gt-ag] intron 200 GenBank accessions 98003 RNA-seq supporting reads 18112 UHR pooled cells 6253 Brain 1776 Blood 71344 Neuroblastoma 518 Other (also 3630 Primates bodymap) 118 bp exon 97 bp [gt-ag] intron 180 GenBank accessions 77450 RNA-seq supporting reads 14334 UHR pooled cells 5138 Brain 1492 Blood 56081 Neuroblastoma 405 Other (also 2692 Primates bodymap) 102 bp exon 77 bp [gt-ag] intron 136 GenBank accessions 87346 RNA-seq supporting reads 15711 UHR pooled cells 6134 Brain 1551 Blood 63485 Neuroblastoma 465 Other (also 3902 Primates bodymap) 213 bp exon 82 bp [gt-ag] intron 90 GenBank accessions 93663 RNA-seq supporting reads 15664 UHR pooled cells 6193 Brain 1607 Blood 69697 Neuroblastoma 502 Other (also 2238 Primates bodymap) 162 bp exon 69 bp [gt-ag] intron 82 GenBank accessions 102812 RNA-seq supporting reads 18131 UHR pooled cells 7241 Brain 1714 Blood 75285 Neuroblastoma 441 Other (also 4188 Primates bodymap) 81 bp exon 69 bp [gt-ag] intron 84 GenBank accessions 86480 RNA-seq supporting reads 15381 UHR pooled cells 5952 Brain 1547 Blood 63271 Neuroblastoma 329 Other (also 3181 Primates bodymap) 70 bp exon 81 bp [gt-ag] intron 94 GenBank accessions 91180 RNA-seq supporting reads 16151 UHR pooled cells 6231 Brain 1318 Blood 67170 Neuroblastoma 310 Other (also 2869 Primates bodymap) 133 bp exon 76 bp [gt-ag] intron 106 GenBank accessions 99752 RNA-seq supporting reads 16818 UHR pooled cells 6436 Brain 823 Blood 75280 Neuroblastoma 395 Other (also 1158 Primates bodymap) 181 bp exon 79 bp [gt-ag] intron 102 GenBank accessions 81561 RNA-seq supporting reads 13090 UHR pooled cells 4832 Brain 504 Blood 62875 Neuroblastoma 260 Other (also 623 Primates bodymap) 289 bp exon 213 bp [gt-ag] intron 127 GenBank accessions 95669 RNA-seq supporting reads 18146 UHR pooled cells 6782 Brain 1125 Blood 69431 Neuroblastoma 185 Other (also 2192 Primates bodymap) 85 bp exon 84 bp [gt-ag] intron 125 GenBank accessions 100298 RNA-seq supporting reads 18917 UHR pooled cells 7477 Brain 1941 Blood 71748 Neuroblastoma 215 Other (also 4097 Primates bodymap) 108 bp exon 78 bp [gt-ag] intron 125 GenBank accessions 131222 RNA-seq supporting reads 24790 UHR pooled cells 10029 Brain 2093 Blood 94168 Neuroblastoma 142 Other (also 3885 Primates bodymap) 2 accessions, some from alzheimer cortex (seen once) brain (once), fetal liver (once) liver (once), neuroblastoma cells (once) 154 bp exon 42 bp exon 11151 bp [gt-ag] intron 219 GenBank accessions 117611 RNA-seq supporting reads 20798 UHR pooled cells 7797 Brain 2404 Blood 85986 Neuroblastoma 626 Other (also 3845 Primates bodymap) 155 bp exon 85 bp [gt-ag] intron 200 GenBank accessions 98003 RNA-seq supporting reads 18112 UHR pooled cells 6253 Brain 1776 Blood 71344 Neuroblastoma 518 Other (also 3630 Primates bodymap) 118 bp exon 97 bp [gt-ag] intron 180 GenBank accessions 77450 RNA-seq supporting reads 14334 UHR pooled cells 5138 Brain 1492 Blood 56081 Neuroblastoma 405 Other (also 2692 Primates bodymap) 102 bp exon 77 bp [gt-ag] intron 136 GenBank accessions 87346 RNA-seq supporting reads 15711 UHR pooled cells 6134 Brain 1551 Blood 63485 Neuroblastoma 465 Other (also 3902 Primates bodymap) 213 bp exon 82 bp [gt-ag] intron 90 GenBank accessions 93663 RNA-seq supporting reads 15664 UHR pooled cells 6193 Brain 1607 Blood 69697 Neuroblastoma 502 Other (also 2238 Primates bodymap) 162 bp exon 219 bp [gt-ag] intron 3 GenBank accessions 1157 RNA-seq supporting reads 210 UHR pooled cells 69 Brain 4 Blood 873 Neuroblastoma 1 Other (also 1 Primates bodymap) 70 bp exon 81 bp [gt-ag] intron 94 GenBank accessions 91180 RNA-seq supporting reads 16151 UHR pooled cells 6231 Brain 1318 Blood 67170 Neuroblastoma 310 Other (also 2869 Primates bodymap) 133 bp exon 76 bp [gt-ag] intron 106 GenBank accessions 99752 RNA-seq supporting reads 16818 UHR pooled cells 6436 Brain 823 Blood 75280 Neuroblastoma 395 Other (also 1158 Primates bodymap) 181 bp exon 79 bp [gt-ag] intron 102 GenBank accessions 81561 RNA-seq supporting reads 13090 UHR pooled cells 4832 Brain 504 Blood 62875 Neuroblastoma 260 Other (also 623 Primates bodymap) 289 bp exon 213 bp [gt-ag] intron 127 GenBank accessions 95669 RNA-seq supporting reads 18146 UHR pooled cells 6782 Brain 1125 Blood 69431 Neuroblastoma 185 Other (also 2192 Primates bodymap) 85 bp exon 84 bp [gt-ag] intron 125 GenBank accessions 100298 RNA-seq supporting reads 18917 UHR pooled cells 7477 Brain 1941 Blood 71748 Neuroblastoma 215 Other (also 4097 Primates bodymap) 108 bp exon 78 bp [gt-ag] intron 125 GenBank accessions 131222 RNA-seq supporting reads 24790 UHR pooled cells 10029 Brain 2093 Blood 94168 Neuroblastoma 142 Other (also 3885 Primates bodymap) 214 bp exon 2 accessions, some from astrocytoma grade IV cell line (seen once) brain (once), eye (once) human retina (once) 214 bp exon 96 bp exon 1968 bp [gt-ag] intron 156 GenBank accessions 79324 RNA-seq supporting reads 12057 UHR pooled cells 4585 Brain 1215 Blood 61233 Neuroblastoma 234 Other (also 1416 Primates bodymap) 210 bp exon 7078 bp [gt-ag] intron 1 GenBank accession 5 RNA-seq supporting reads 1 Blood 4 Neuroblastoma 553 bp exon 553 bp exon Sequence gap 18166 bp 137 bp exon 213 bp [gt-ag] intron 127 GenBank accessions 95669 RNA-seq supporting reads 18146 UHR pooled cells 6782 Brain 1125 Blood 69431 Neuroblastoma 185 Other (also 2192 Primates bodymap) 85 bp exon 84 bp [gt-ag] intron 125 GenBank accessions 100298 RNA-seq supporting reads 18917 UHR pooled cells 7477 Brain 1941 Blood 71748 Neuroblastoma 215 Other (also 4097 Primates bodymap) 108 bp exon 78 bp [gt-ag] intron 125 GenBank accessions 131222 RNA-seq supporting reads 24790 UHR pooled cells 10029 Brain 2093 Blood 94168 Neuroblastoma 142 Other (also 3885 Primates bodymap) 213 bp exon 2 accessions, some from leiomyosarcoma (seen once) testis (once), uterus (once) 213 bp exon 504 bp exon 504 bp exon 63 bp uORF 504 bp exon 504 bp exon 511 bp [gt-ag] intron 2 GenBank accessions 404 RNA-seq supporting reads 22 UHR pooled cells 38 Brain 3 Blood 340 Neuroblastoma 1 Other (also 1 Primates bodymap) 155 bp exon 155 bp exon 85 bp [gt-ag] intron 200 GenBank accessions 98003 RNA-seq supporting reads 18112 UHR pooled cells 6253 Brain 1776 Blood 71344 Neuroblastoma 518 Other (also 3630 Primates bodymap) 118 bp exon 118 bp exon 97 bp [gt-ag] intron 180 GenBank accessions 77450 RNA-seq supporting reads 14334 UHR pooled cells 5138 Brain 1492 Blood 56081 Neuroblastoma 405 Other (also 2692 Primates bodymap) 102 bp exon 102 bp exon 77 bp [gt-ag] intron 136 GenBank accessions 87346 RNA-seq supporting reads 15711 UHR pooled cells 6134 Brain 1551 Blood 63485 Neuroblastoma 465 Other (also 3902 Primates bodymap) 213 bp exon 213 bp exon 82 bp [gt-ag] intron 90 GenBank accessions 93663 RNA-seq supporting reads 15664 UHR pooled cells 6193 Brain 1607 Blood 69697 Neuroblastoma 502 Other (also 2238 Primates bodymap) 162 bp exon 162 bp exon 219 bp [gt-ag] intron 3 GenBank accessions 1157 RNA-seq supporting reads 210 UHR pooled cells 69 Brain 4 Blood 873 Neuroblastoma 1 Other (also 1 Primates bodymap) 70 bp exon 70 bp exon 81 bp [gt-ag] intron 94 GenBank accessions 91180 RNA-seq supporting reads 16151 UHR pooled cells 6231 Brain 1318 Blood 67170 Neuroblastoma 310 Other (also 2869 Primates bodymap) 96 bp exon 96 bp exon 4 accessions, some from anaplastic oligodendroglioma (seen once) brain (once), lung (once) small cell carcinoma (once) 96 bp exon 126 bp exon 126 bp exon 1968 bp [gt-ag] intron 156 GenBank accessions 79324 RNA-seq supporting reads 12057 UHR pooled cells 4585 Brain 1215 Blood 61233 Neuroblastoma 234 Other (also 1416 Primates bodymap) 210 bp exon 12483 bp [gt-ag] intron 210 GenBank accessions 108276 RNA-seq supporting reads 20314 UHR pooled cells 7674 Brain 2261 Blood 77586 Neuroblastoma 441 Other (also 548 Primates bodymap) 81 bp exon 11151 bp [gt-ag] intron 219 GenBank accessions 117611 RNA-seq supporting reads 20798 UHR pooled cells 7797 Brain 2404 Blood 85986 Neuroblastoma 626 Other (also 3845 Primates bodymap) 424 bp exon 2 accessions, some from brain (seen once) human embryonic stem cells differentiated toan early endodermal cell type (once) hypothalamus (once) 424 bp exon 200 bp exon 200 bp exon 69 bp [gt-ag] intron 84 GenBank accessions 86480 RNA-seq supporting reads 15381 UHR pooled cells 5952 Brain 1547 Blood 63271 Neuroblastoma 329 Other (also 3181 Primates bodymap) 70 bp exon 81 bp [gt-ag] intron 94 GenBank accessions 91180 RNA-seq supporting reads 16151 UHR pooled cells 6231 Brain 1318 Blood 67170 Neuroblastoma 310 Other (also 2869 Primates bodymap) 133 bp exon 76 bp [gt-ag] intron 106 GenBank accessions 99752 RNA-seq supporting reads 16818 UHR pooled cells 6436 Brain 823 Blood 75280 Neuroblastoma 395 Other (also 1158 Primates bodymap) 181 bp exon 79 bp [gt-ag] intron 102 GenBank accessions 81561 RNA-seq supporting reads 13090 UHR pooled cells 4832 Brain 504 Blood 62875 Neuroblastoma 260 Other (also 623 Primates bodymap) 1 accession from b-cells from primary b-cells from tonsils (cell line) 165 bp exon 561 bp exon 561 bp exon 85 bp [gt-ag] intron 200 GenBank accessions 98003 RNA-seq supporting reads 18112 UHR pooled cells 6253 Brain 1776 Blood 71344 Neuroblastoma 518 Other (also 3630 Primates bodymap) 118 bp exon 97 bp [gt-ag] intron 180 GenBank accessions 77450 RNA-seq supporting reads 14334 UHR pooled cells 5138 Brain 1492 Blood 56081 Neuroblastoma 405 Other (also 2692 Primates bodymap) 102 bp exon 77 bp [gt-ag] intron 136 GenBank accessions 87346 RNA-seq supporting reads 15711 UHR pooled cells 6134 Brain 1551 Blood 63485 Neuroblastoma 465 Other (also 3902 Primates bodymap) 32 bp exon 3 accessions 32 bp exon 156 bp exon 8819 bp [gt-ag] intron 1 GenBank accession 71 RNA-seq supporting reads 14 UHR pooled cells 4 Brain 1 Blood 52 Neuroblastoma 155 bp exon 155 bp exon 85 bp [gt-ag] intron 200 GenBank accessions 98003 RNA-seq supporting reads 18112 UHR pooled cells 6253 Brain 1776 Blood 71344 Neuroblastoma 518 Other (also 3630 Primates bodymap) 118 bp exon 97 bp [gt-ag] intron 180 GenBank accessions 77450 RNA-seq supporting reads 14334 UHR pooled cells 5138 Brain 1492 Blood 56081 Neuroblastoma 405 Other (also 2692 Primates bodymap) 102 bp exon 77 bp [gt-ag] intron 136 GenBank accessions 87346 RNA-seq supporting reads 15711 UHR pooled cells 6134 Brain 1551 Blood 63485 Neuroblastoma 465 Other (also 3902 Primates bodymap) 37 bp exon 1 accession from thymus 37 bp exon 809 bp exon 809 bp exon 97 bp [gt-ag] intron 2 GenBank accessions 12 RNA-seq supporting reads 4 Brain 2 Blood 6 Neuroblastoma (also 2 Primates bodymap) 730 bp exon 9 accessions, some from placenta (seen 6 times) epidermis (2) 730 bp exon 99 bp exon 3 accessions, some from prostate (seen 3 times) 99 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 2610 bp 746 aa 29 bp 340 bp 2kb including Promoter 29302 bp 1kb
bAug10 2034 bp 676 aa 2kb probably including promoter 28936 bp 1kb
cAug10 1872 bp 603 aa 60 bp 2kb 14194 bp 1kb
dAug10 2125 bp 476 aa 635 bp 59 bp 2kb possibly including promoter 28989 bp 1kb
eAug10 1420 bp 434 aa 117 bp 60 bp 2kb possibly including promoter 2572 bp 1kb
fAug10 841 bp 213 aa 198 bp 2kb probably including promoter 26443 bp 1kb
gAug10 749 bp 199 aa 152 bp 2kb possibly including promoter 1054 bp 1kb
hAug10 813 bp 180 aa 271 bp 2kb possibly including promoter 1072 bp 1kb
iAug10 1539 bp 142 aa 397 bp 713 bp 2kb possibly including promoter 1636 bp 1kb
jAug10 568 bp 92 aa 291 bp 2kb possibly including promoter 9646 bp 1kb
kAug10-unspliced 99 bp 31 aa 3 bp 2kb 99 bp 1kb

Gene neighbors and Navigator on chromosome 8q24.3 back to top
R GRINA D C R P SPATC1 C I R P R EXOSC4 C I R P GPAA1 D C I R P CYC1 C I R P MAF1 C I R P KIAA1875 C I R P C8orf30A C I R P HEATR7A C R P SCXB C R P C R C R SCXA C R P HSF1 D C I R P GPR172A C R P ADCK5 C R P G C R KIFC2 C I R P PPP1R16A C I R P GPT D C I R P MFSD3 C I R R LRRC14 C I R P C R R C I R P PARP10 C R P OPLAH R C I R P SHARPIN R C R R D C I R P BOP1 C R D C I R P DGAT1 D C R P SCRT1 C R C8ORFK29 C I R P FBXL6 C I R P CPSF1 D C R P SLC39A4 C I R P VPS28 C I R P NFKBIL2 C I R P CYHR1 C I R P FOXH1 R D C I R P RECQL4 C R P C8orf82andLRRC24 C R P ARHGAP39 C R ZNF251 100kb 0 moroya, 1 accession GRINA, 224 accessions 8 variants SPATC1, 28 accessions 2 variants glyblu, 2 accessions EXOSC4, 164 accessions 4 variants GPAA1, 377 accessions 15 variants CYC1, 542 accessions, 6 variants MAF1, 548 accessions, 7 variants KIAA1875, 32 accessions 7 variants C8orf30A, 133 accessions 6 variants HEATR7A, 176 accessions 24 variants SCXB, 28 accessions, 2 variants mihemu, 117 accessions 4 variants muhemu, 90 accessions 10 variants SCXA, 27 accessions, 2 variants HSF1, 390 accessions, 13 variants GPR172A, 415 accessions 18 variants ADCK5, 157 accessions 14 variants LOC100287098, 14 accessions 4 variants KIFC2, 125 accessions 8 variants PPP1R16A, 404 accessions 14 variants GPT, 85 accessions, 7 variants MFSD3, 166 accessions 6 variants sholy, 5 accessions, 2 variants LRRC14, 218 accessions 8 variants swygeyby, 1 accession suslarbu, 27 accessions 4 variants nuzarby, 7 accessions noroya, 1 accession plawslubu, 5 accessions swarforby, 1 accession glawblu, 2 accessions sawwoyby, 2 accessions plerslubu, 1 accession byfoyby, 1 accession plorslubu, 1 accession derzarbu, 1 accession soywoyby, 1 accession veyvawbu, 1 accession tawoyby, 1 accession tuwoyby, 1 accession skaslubu, 1 accession towoyby, 1 accession teewoyby, 2 accessions skawslubu, 22 accessions foyzarby, 1 accession vawoyby, 2 accessions vywoyby, 1 accession jozarbu, 1 accession jawzarbu, 1 accession jeezarbu, 1 accession veewoyby, 2 accessions woyblaby, 1 accession veywoyby, 3 accessions jerzarbu, 1 accession joyzarbu, 1 accession slaslubu, 3 accessions kumoya, 4 accessions geyzarby, 1 accession weyvyby, 22 accessions kimoya, 1 accession teywoyby, 1 accession temeya, 4 accessions glageyby, 1 accession slyzyby, 3 accessions narslawbu, 1 accession noslawbu, 2 accessions nozeeby, 3 accessions shyzoybu, 1 accession naslawbu, 2 accessions moyslawbu, 1 accession loyblorby, 2 accessions wyteybo, 3 accessions morzeeby, 1 accession flawgor, 1 accession fleygor, 7 accessions jyzarby, 2 accessions perslarbu, 3 accessions steyzerbu, 1 accession poyslarbu, 1 accession juzarby, 1 accession dubleeby, 8 accessions 2 variants komoya, 1 accession skeygeyby, 1 accession jawzarby, 1 accession swoyzerbu, 1 accession jeyzarby, 1 accession joyzarby, 2 accessions jeebleeby, 1 accession kozarby, 1 accession karzarby, 1 accession kawzarby, 1 accession joblu, 3 accessions zyvyby, 2 accessions byzeybu, 8 accessions buzeybu, 1 accession slogeyby, 1 accession smugeyby, 1 accession lyzarby, 1 accession larzarby, 1 accession ruslarbu, 1 accession leyzarby, 1 accession bozeybu, 1 accession rawslarbu, 1 accession barzeybu, 1 accession loyzarby, 1 accession reyslarbu, 2 accessions mozarby, 1 accession meezarby, 1 accession meyzarby, 1 accession nazarby, 5 accessions jeyblu, 2 accessions bawgorby, 2 accessions sorslarbu, 1 accession joyblu, 3 accessions gleeblu, 4 accessions suwoyby, 2 accessions glarblu, 4 accessions weeblaby, 2 accessions rateybo, 1 accession dawzarbu, 1 accession serwoyby, 2 accessions pleyslubu, 1 accession seywoyby, 1 accession sorwoyby, 1 accession ployslubu, 1 accession fuzarbu, 1 accession tywoyby, 1 accession barfoyby, 1 accession skoslubu, 4 accessions weyblaby, 2 accessions glablu, 6 accessions glerblu, 1 accession feyzarbu, 4 accessions guzarbu, 1 accession garzarbu, 2 accessions nerslarbu, 1 accession goyzarbu, 1 accession torwoyby, 2 accessions toywoyby, 1 accession skerslubu, 1 accession jazarbu, 1 accession jarzarbu, 3 accessions vawwoyby, 1 accession verwoyby, 2 accessions peygor, 1 accession vorwoyby, 2 accessions voywoyby, 2 accessions sawgee, 3 accessions jeyzarbu, 5 accessions skorslubu, 1 accession skoyslubu, 1 accession wawoyby, 7 accessions kazarbu, 1 accession boyfoyby, 1 accession glorblu, 10 accessions kyzarbu, 1 accession wowoyby, 2 accessions neeslarbu, 1 accession smoyzerbu, 4 accessions snazerbu, 1 accession snyzerbu, 2 accessions skeeslubu, 1 accession snerzerbu, 1 accession snorzerbu, 1 accession florgeyby, 1 accession gyzarby, 10 accessions snoyzerbu, 1 accession gerzarby, 1 accession kemoya, 1 accession gleygeyby, 1 accession neezeeby, 3 accessions spuzerbu, 1 accession nuzeeby, 1 accession puslarbu, 2 accessions merslawbu, 1 accession pleegeyby, 1 accession pleygeyby, 1 accession mawslawbu, 1 accession worzoybu, 1 accession plorgeyby, 1 accession peeslarbu, 4 accessions woyvyby, 3 accessions peyslarbu, 1 accession dybleeby, 6 accessions jorzarby, 1 accession kazarby, 4 accessions kyzarby, 1 accession kuzarby, 3 accessions 2 variants tonomu, 1 accession skoygeyby, 1 accession keyzarby, 1 accession koyzarby, 1 accession lazarby, 1 accession ryslarbu, 3 accessions jeeblu, 2 accessions luzarby, 1 accession lozarby, 5 accessions roslarbu, 1 accession rarslarbu, 1 accession reeslarbu, 4 accessions florgor, 3 accessions lorzarby, 1 accession rerslarbu, 1 accession bawzeybu, 1 accession muzarby, 1 accession sanomu, 1 accession boyzeybu, 1 accession marzarby, 1 accession dazeybu, 1 accession darzeybu, 1 accession royslarbu, 1 accession saslarbu, 2 accessions merzarby, 2 accessions syslarbu, 1 accession blaly, 10 accessions klerlu, 2 accessions nozarby, 1 accession soslarbu, 1 accession narzarby, 1 accession nawzarby, 1 accession neezarby, 1 accession serslarbu, 5 accessions jorblu, 16 accessions boygorby, 1 accession doygorby, 2 accessions soyslarbu, 29 accessions PLEC, 292 accessions, 15 variants PARP10, 418 accessions 30 variants OPLAH, 68 accessions, 7 variants tarwoyby, 9 accessions 3 variants SHARPIN, 335 accessions 15 variants guzarby, 6 accessions 2 variants rahemu, 266 accessions 7 variants zoyly, 6 accessions, 2 variants BOP1, 466 accessions, 11 variants tenomu, 3 accessions flargor, 2 accessions DGAT1, 270 accessions 8 variants SCRT1, 62 accessions C8ORFK29, 24 accessions 5 variants FBXL6, 140 accessions 9 variants CPSF1, 519 accessions 15 variants SLC39A4, 170 accessions 10 variants VPS28, 595 accessions 33 variants NFKBIL2, 91 accessions 4 variants CYHR1, 351 accessions 14 variants FOXH1, 45 accessions, 2 variants raslarbu, 32 accessions 6 variants RECQL4, 128 accessions 9 variants C8orf82andLRRC24, 173 accessions 10 variants ARHGAP39, 96 accessions 9 variants ZNF251, 156 accessions 10 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               17 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i, .j, .k-u 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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