Homo sapiens complex locus ABCB5, encoding ATP-binding cassette, sub-family B (MDR/TAP), member 5.
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SUMMARY back to top
RefSeq summary
[ABCB5] ABCB5 belongs to the ATP-binding cassette (ABC) transporter superfamily of integral membrane proteins. These proteins participate in ATP-dependent transmembrane transport of structurally diverse molecules ranging from small ions, sugars, and peptides to more complex organic molecules (Chen et al., 2005 [PubMed 15760339]).[supplied by OMIM].

RefSeq annotates 4 representative transcripts (NM included in AceView variants .a, .b, .h and .i), 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 9 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 well expressed, 0.8 times the average gene in this release. The sequence of this gene is defined by 105 GenBank accessions from 91 cDNA clones, some from melanocyte (seen 18 times), pooled human melanocyte, fetal heart, andpregnant uterus (9), adult brain (4), brain (4), breast (4), caudate nucleus (4), mammary adenocarcinoma, cell line (4) and 20 other tissues. We annotate structural defects or features in 6 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 35 distinct introns (34 gt-ag, 1 other). Transcription produces 11 different mRNAs, 9 alternatively spliced variants and 2 unspliced forms. There are 4 probable alternative promotors, 6 non overlapping alternative last exons and 8 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of a cassette exon, overlapping exons with different boundaries, splicing versus retention of 2 introns.
Note that mRNA .cAug10 was found in vivo, although it is a predicted target of nonsense mediated mRNA decay (NMD).
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant bAug10).
Function: There are 11 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to a disease (Melanoma), proposed to participate in pathway (ABC transporters) and a process (transmembrane transport). Proteins are expected to have molecular functions (ATP binding, ATPase activity, ATPase activity, coupled to transmembrane movement of substances, nucleotide binding) and to localize in various compartments (cytoplasm, extracellular space, membrane, plasma membrane, integral to membrane). A putative protein interactor has been described (PSMB5).
Protein coding potential: 7 spliced and the unspliced mRNAs putatively encode good proteins, altogether 8 different isoforms (6 complete, 2 COOH complete), some containing domains ABC transporter transmembrane region, ABC transporter [Pfam], some transmembrane domains [Psort2]; 1 of the 6 complete proteins appears to be secreted. The remaining 3 mRNA variants (2 spliced, 1 unspliced) appear not to encode good proteins.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 7, links to other databases and other names
Map: This gene ABCB5 maps on chromosome 7, at 7p21.1 according to Entrez Gene. In AceView, it covers 161.41 kb, from 20655245 to 20816658 (NCBI 37, August 2010), on the direct strand.
Links to: manual annotations from KEGG_02010, the SNP view, gene overviews from Entrez Gene 340273, 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 ABCB5, ABCB5beta, EST422562, ABCB5alpha or LOC340273, jarja. It has been described as ATP-binding cassette sub-family B member 5, ABCB5 P-gp, P-glycoprotein ABCB5, ATP-binding cassette protein.
Closest AceView homologs in other species ?
The closest mouse genes, according to BlastP, are the AceView genes Abcb1a (e=2 10-43), Abcb1b (e=2 10-43), Abcb4 (e=2 10-41).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes pgp-9 (e=2 10-37), pgp-8 (e=2 10-35), pgp-6 (e=3 10-34), pgp-7 (e=4 10-34), haf-6 (e=10-33), pgp-3 (e=4 10-33), pgp-1 (e=5 10-33), pgp-2 (e=10-32), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes PGP10 (e=5 10-35), PGP13 (e=4 10-33), PGP9 (e=4 10-33), ATPGP1 (e=7 10-33), PGP2 (e=2 10-32), 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
ABCB5 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 1.02 0.07 0.07 0.06 0.18 0.45 0.34 0.10 2.90 0.17 0.17 0.19 0.12 0.10 0.08 0.08 0.05 0.07 0.09 0.11 0.14 0.10 0.14 0.10 0.08 0.08 0.06 0.08 0.08 0.08 1.02 0.06 0.07 0.08 0.07 0.09 0.06 0.08 0.08 0.05 0.10 0.07 0.13 0.04 0.07 0.07 0.08 0.08 0.08 0.07 0.07 0.07 0.09 0.06 0.08 0.05 0.07 0.04 0.08 0.10 0.24 0.10 0.08 0.08 0.36 0.14 0.11 0.11 0.11 0.09 0.06 0.09 0.10 0.04 0.04 0.09 0.08 0.09 0.13 0.06 0.04 0.06 0.04 0.07 0.06 0.08 0.08 0.08 0.09 0.05 0.09 0.10 0.08 0.10 0.13 0.06 0.14 0.16 0.13 0.34 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 ABCB5 5' 3' encoded on plus strand of chromosome 7 from 20,655,245 to 20,816,658 3 3 4 9 8 9 6 5 5 726 795 976 789 109 125 99 157 124 115 102 217 211 100 141 157 125 159 a [NM] 726 795 976 789 109 125 99 157 124 115 102 217 211 100 141 157 125 159 b [NM] 726 795 976 789 696 h [NM] 217 211 100 141 157 1 1 c 726 795 976 d j-u 217 211 e 726 795 976 k f-u 1 16 211 g 726 795 976 789 36 i [NM] 10kb 0 216 bp exon 7427 bp [gt-ag] intron 3 GenBank accessions 74 bp exon 74 bp exon 3218 bp [gt-ag] intron 3 GenBank accessions 55 bp exon 2076 bp [gt-ag] intron 4 GenBank accessions (also 1 Primates bodymap) 151 bp exon 3220 bp [gt-ag] intron 7 GenBank accessions 2 RNA-seq supporting reads 2 Neuroblastoma (also 10 Primates bodymap) 55 bp exon 11070 bp [gt-ag] intron 7 GenBank accessions 1 RNA-seq supporting reads 1 Neuroblastoma (also 5 Primates bodymap) 192 bp exon 85 bp [gt-ag] intron 9 GenBank accessions (also 3 Primates bodymap) 172 bp exon 2123 bp [gt-ag] intron 6 GenBank accessions 125 bp exon 80 bp [gt-ag] intron 5 GenBank accessions (also 6 Primates bodymap) 178 bp exon 1396 bp [gt-ag] intron 5 GenBank accessions (also 1 Primates bodymap) 114 bp exon 319 bp [gt-ag] intron 31 GenBank accessions 695 RNA-seq supporting reads 676 UHR pooled cells 1 Brain 1 Blood 17 Neuroblastoma (also 2 Primates bodymap) 111 bp exon 1943 bp [gt-ag] intron 31 GenBank accessions 764 RNA-seq supporting reads 751 UHR pooled cells 11 Neuroblastoma 2 Other (also 1 Primates bodymap) 126 bp exon 1272 bp [gt-ag] intron 34 GenBank accessions 942 RNA-seq supporting reads 931 UHR pooled cells 11 Neuroblastoma (also 3 Primates bodymap) 204 bp exon 6882 bp [gt-ag] intron 27 GenBank accessions 762 RNA-seq supporting reads 751 UHR pooled cells 11 Neuroblastoma 171 bp exon 22828 bp [gt-ag] intron 12 GenBank accessions 97 RNA-seq supporting reads 83 UHR pooled cells 2 Blood 11 Neuroblastoma 1 Other (also 6 Primates bodymap) 162 bp exon 4029 bp [gt-ag] intron 14 GenBank accessions 111 RNA-seq supporting reads 103 UHR pooled cells 1 Blood 7 Neuroblastoma (also 5 Primates bodymap) 141 bp exon 12570 bp [gt-ag] intron 14 GenBank accessions 85 RNA-seq supporting reads 78 UHR pooled cells 1 Brain 2 Blood 4 Neuroblastoma (also 8 Primates bodymap) 144 bp exon 1274 bp [gt-ag] intron 14 GenBank accessions 143 RNA-seq supporting reads 120 UHR pooled cells 10 Blood 13 Neuroblastoma (also 14 Primates bodymap) 105 bp exon 128 bp [gt-ag] intron 14 GenBank accessions 110 RNA-seq supporting reads 83 UHR pooled cells 22 Blood 5 Neuroblastoma (also 18 Primates bodymap) 78 bp exon 4588 bp [gt-ag] intron 14 GenBank accessions 101 RNA-seq supporting reads 79 UHR pooled cells 11 Blood 11 Neuroblastoma (also 18 Primates bodymap) 84 bp exon 18208 bp [gt-ag] intron 13 GenBank accessions 89 RNA-seq supporting reads 77 UHR pooled cells 4 Blood 8 Neuroblastoma (also 4 Primates bodymap) 204 bp exon 3820 bp [gt-ag] intron 16 GenBank accessions 201 RNA-seq supporting reads 135 UHR pooled cells 42 Blood 24 Neuroblastoma (also 8 Primates bodymap) 101 bp exon 1174 bp [gt-ag] intron 19 GenBank accessions 192 RNA-seq supporting reads 129 UHR pooled cells 46 Blood 17 Neuroblastoma (also 12 Primates bodymap) 141 bp exon 10527 bp [gt-ag] intron 17 GenBank accessions 83 RNA-seq supporting reads 66 UHR pooled cells 12 Blood 5 Neuroblastoma (also 7 Primates bodymap) 157 bp exon 3737 bp [gt-ag] intron 16 GenBank accessions 125 RNA-seq supporting reads 69 UHR pooled cells 38 Blood 18 Neuroblastoma (also 9 Primates bodymap) 198 bp exon 2157 bp [gt-ag] intron 14 GenBank accessions 143 RNA-seq supporting reads 77 UHR pooled cells 39 Blood 27 Neuroblastoma (also 6 Primates bodymap) 207 bp exon 7921 bp [gt-ag] intron 12 GenBank accessions 113 RNA-seq supporting reads 72 UHR pooled cells 7 Blood 34 Neuroblastoma (also 4 Primates bodymap) 147 bp exon 1920 bp [gt-ag] intron 12 GenBank accessions 147 RNA-seq supporting reads 92 UHR pooled cells 2 Brain 21 Blood 32 Neuroblastoma (also 7 Primates bodymap) 1588 bp exon 28 accessions, NM_001163941.1 some from melanocyte (seen 4 times) brain, cerebral cortex and lung PCR rescuedclones (2) breast (once), caudate nucleus (once) mammary adenocarcinoma cell line (once) Validated 3' end, 1 accession Validated 3' end, 1 accession 1588 bp exon 306 bp exon 319 bp [gt-ag] intron 31 GenBank accessions 695 RNA-seq supporting reads 676 UHR pooled cells 1 Brain 1 Blood 17 Neuroblastoma (also 2 Primates bodymap) 111 bp exon 111 bp exon 45 bp uORF 1943 bp [gt-ag] intron 31 GenBank accessions 764 RNA-seq supporting reads 751 UHR pooled cells 11 Neuroblastoma 2 Other (also 1 Primates bodymap) 45 bp uORF 126 bp exon 126 bp exon 1272 bp [gt-ag] intron 34 GenBank accessions 942 RNA-seq supporting reads 931 UHR pooled cells 11 Neuroblastoma (also 3 Primates bodymap) 204 bp exon 204 bp exon 204 bp exon 6882 bp [gt-ag] intron 27 GenBank accessions 762 RNA-seq supporting reads 751 UHR pooled cells 11 Neuroblastoma 171 bp exon 171 bp exon 22828 bp [gt-ag] intron 12 GenBank accessions 97 RNA-seq supporting reads 83 UHR pooled cells 2 Blood 11 Neuroblastoma 1 Other (also 6 Primates bodymap) 162 bp exon 162 bp exon 4029 bp [gt-ag] intron 14 GenBank accessions 111 RNA-seq supporting reads 103 UHR pooled cells 1 Blood 7 Neuroblastoma (also 5 Primates bodymap) 141 bp exon 141 bp exon 12570 bp [gt-ag] intron 14 GenBank accessions 85 RNA-seq supporting reads 78 UHR pooled cells 1 Brain 2 Blood 4 Neuroblastoma (also 8 Primates bodymap) 144 bp exon 144 bp exon 1274 bp [gt-ag] intron 14 GenBank accessions 143 RNA-seq supporting reads 120 UHR pooled cells 10 Blood 13 Neuroblastoma (also 14 Primates bodymap) 105 bp exon 105 bp exon 128 bp [gt-ag] intron 14 GenBank accessions 110 RNA-seq supporting reads 83 UHR pooled cells 22 Blood 5 Neuroblastoma (also 18 Primates bodymap) 78 bp exon 78 bp exon 4588 bp [gt-ag] intron 14 GenBank accessions 101 RNA-seq supporting reads 79 UHR pooled cells 11 Blood 11 Neuroblastoma (also 18 Primates bodymap) 84 bp exon 84 bp exon 18208 bp [gt-ag] intron 13 GenBank accessions 89 RNA-seq supporting reads 77 UHR pooled cells 4 Blood 8 Neuroblastoma (also 4 Primates bodymap) 204 bp exon 204 bp exon 3820 bp [gt-ag] intron 16 GenBank accessions 201 RNA-seq supporting reads 135 UHR pooled cells 42 Blood 24 Neuroblastoma (also 8 Primates bodymap) 101 bp exon 101 bp exon 1174 bp [gt-ag] intron 19 GenBank accessions 192 RNA-seq supporting reads 129 UHR pooled cells 46 Blood 17 Neuroblastoma (also 12 Primates bodymap) 141 bp exon 141 bp exon 10527 bp [gt-ag] intron 17 GenBank accessions 83 RNA-seq supporting reads 66 UHR pooled cells 12 Blood 5 Neuroblastoma (also 7 Primates bodymap) 157 bp exon 157 bp exon 3737 bp [gt-ag] intron 16 GenBank accessions 125 RNA-seq supporting reads 69 UHR pooled cells 38 Blood 18 Neuroblastoma (also 9 Primates bodymap) 198 bp exon 198 bp exon 2157 bp [gt-ag] intron 14 GenBank accessions 143 RNA-seq supporting reads 77 UHR pooled cells 39 Blood 27 Neuroblastoma (also 6 Primates bodymap) 207 bp exon 207 bp exon 7921 bp [gt-ag] intron 12 GenBank accessions 113 RNA-seq supporting reads 72 UHR pooled cells 7 Blood 34 Neuroblastoma (also 4 Primates bodymap) 147 bp exon 147 bp exon 1920 bp [gt-ag] intron 12 GenBank accessions 147 RNA-seq supporting reads 92 UHR pooled cells 2 Brain 21 Blood 32 Neuroblastoma (also 7 Primates bodymap) 1588 bp exon 1588 bp exon 7 accessions, NM_178559.5 some from melanocyte (seen 2 times) brain (once), small intestine (once) 1588 bp exon 309 bp exon 319 bp [gt-ag] intron 31 GenBank accessions 695 RNA-seq supporting reads 676 UHR pooled cells 1 Brain 1 Blood 17 Neuroblastoma (also 2 Primates bodymap) 111 bp exon 1943 bp [gt-ag] intron 31 GenBank accessions 764 RNA-seq supporting reads 751 UHR pooled cells 11 Neuroblastoma 2 Other (also 1 Primates bodymap) 126 bp exon 1272 bp [gt-ag] intron 34 GenBank accessions 942 RNA-seq supporting reads 931 UHR pooled cells 11 Neuroblastoma (also 3 Primates bodymap) 204 bp exon 204 bp exon 6882 bp [gt-ag] intron 27 GenBank accessions 762 RNA-seq supporting reads 751 UHR pooled cells 11 Neuroblastoma 171 bp exon 389 bp [gt-ag] intron 10 GenBank accessions 686 RNA-seq supporting reads 675 UHR pooled cells 2 Brain 9 Neuroblastoma 1329 bp exon 18 accessions, NM_001163942.1 some from adult brain (seen 4 times) brain (3), melanocyte (3) skin (2), testis (2) Validated 3' end, 1 accession Validated 3' end, 1 accession 1329 bp exon 125 bp exon 125 bp exon 3820 bp [gt-ag] intron 16 GenBank accessions 201 RNA-seq supporting reads 135 UHR pooled cells 42 Blood 24 Neuroblastoma (also 8 Primates bodymap) 101 bp exon 1174 bp [gt-ag] intron 19 GenBank accessions 192 RNA-seq supporting reads 129 UHR pooled cells 46 Blood 17 Neuroblastoma (also 12 Primates bodymap) 141 bp exon 10527 bp [gt-ag] intron 17 GenBank accessions 83 RNA-seq supporting reads 66 UHR pooled cells 12 Blood 5 Neuroblastoma (also 7 Primates bodymap) 157 bp exon 3737 bp [gt-ag] intron 16 GenBank accessions 125 RNA-seq supporting reads 69 UHR pooled cells 38 Blood 18 Neuroblastoma (also 9 Primates bodymap) 198 bp exon 2157 bp [gt-ag] intron 14 GenBank accessions 143 RNA-seq supporting reads 77 UHR pooled cells 39 Blood 27 Neuroblastoma (also 6 Primates bodymap) 207 bp exon 17817 bp [gt-ag] intron 1 GenBank accession 213 bp exon 213 bp exon 12506 bp [gt-ag] intron 1 GenBank accession 1 accession from caudate nucleus Validated 3' end, 1 accession 1061 bp exon 47 bp exon 47 bp exon 160 bp [gt-ag] intron 2 GenBank accessions 65 RNA-seq supporting reads 64 UHR pooled cells 1 Neuroblastoma 114 bp exon 319 bp [gt-ag] intron 31 GenBank accessions 695 RNA-seq supporting reads 676 UHR pooled cells 1 Brain 1 Blood 17 Neuroblastoma (also 2 Primates bodymap) 111 bp exon 1943 bp [gt-ag] intron 31 GenBank accessions 764 RNA-seq supporting reads 751 UHR pooled cells 11 Neuroblastoma 2 Other (also 1 Primates bodymap) 126 bp exon 1272 bp [gt-ag] intron 34 GenBank accessions 942 RNA-seq supporting reads 931 UHR pooled cells 11 Neuroblastoma (also 3 Primates bodymap) 634 bp exon 3 accessions, some from breast (seen once) mammary adenocarcinoma cell line (once), melanocyte (once) 634 bp exon 1388 bp exon 1388 bp exon 5 accessions, some from pooled human melanocyte fetal heart, andpregnant uterus (seen 4 times) pool of melanoma cell lines (once) Validated 3' end, 1 accession 1388 bp exon 217 bp exon 217 bp exon 57 bp uORF 217 bp exon 217 bp exon 3820 bp [gt-ag] intron 16 GenBank accessions 201 RNA-seq supporting reads 135 UHR pooled cells 42 Blood 24 Neuroblastoma (also 8 Primates bodymap) 101 bp exon 101 bp exon 1174 bp [gt-ag] intron 19 GenBank accessions 192 RNA-seq supporting reads 129 UHR pooled cells 46 Blood 17 Neuroblastoma (also 12 Primates bodymap) 175 bp exon 175 bp exon 1 accession from skin 175 bp exon 138 bp exon 114 bp exon 319 bp [gt-ag] intron 31 GenBank accessions 695 RNA-seq supporting reads 676 UHR pooled cells 1 Brain 1 Blood 17 Neuroblastoma (also 2 Primates bodymap) 111 bp exon 1943 bp [gt-ag] intron 31 GenBank accessions 764 RNA-seq supporting reads 751 UHR pooled cells 11 Neuroblastoma 2 Other (also 1 Primates bodymap) 126 bp exon 126 bp exon 1272 bp [gt-ag] intron 34 GenBank accessions 942 RNA-seq supporting reads 931 UHR pooled cells 11 Neuroblastoma (also 3 Primates bodymap) 173 bp exon 3 accessions, some from caudate nucleus (seen once) colon (once), pooled human melanocyte fetal heart, andpregnant uterus (once) capped 5' end, 2 accessions 173 bp exon 1984 bp exon 1984 bp exon 1984 bp exon Sequence gap 481 bp 12 accessions, some from melanocyte (seen 5 times) eye (2), breast (once) eye anterior segment (once) mammary adenocarcinoma cell line (once) capped 5' end, 1 accession 873 bp exon 1188 bp exon 279 bp [gc-ct] intron 1 GenBank accession 565 bp exon 565 bp exon 3824 bp [gt-ag] intron 1 GenBank accession 15 RNA-seq supporting reads 7 UHR pooled cells 6 Blood 2 Neuroblastoma 97 bp exon 97 bp exon 1174 bp [gt-ag] intron 19 GenBank accessions 192 RNA-seq supporting reads 129 UHR pooled cells 46 Blood 17 Neuroblastoma (also 12 Primates bodymap) 1 accession from liver Validated 3' end, 1 accession 928 bp exon 306 bp exon 319 bp [gt-ag] intron 31 GenBank accessions 695 RNA-seq supporting reads 676 UHR pooled cells 1 Brain 1 Blood 17 Neuroblastoma (also 2 Primates bodymap) 111 bp exon 1943 bp [gt-ag] intron 31 GenBank accessions 764 RNA-seq supporting reads 751 UHR pooled cells 11 Neuroblastoma 2 Other (also 1 Primates bodymap) 126 bp exon 1272 bp [gt-ag] intron 34 GenBank accessions 942 RNA-seq supporting reads 931 UHR pooled cells 11 Neuroblastoma (also 3 Primates bodymap) 204 bp exon 204 bp exon 6882 bp [gt-ag] intron 27 GenBank accessions 762 RNA-seq supporting reads 751 UHR pooled cells 11 Neuroblastoma 171 bp exon 8082 bp [gt-ag] intron 2 GenBank accessions 34 RNA-seq supporting reads 34 UHR pooled cells 806 bp exon 4 accessions, NM_001163993.1 some from melanocyte (seen once) pooled human melanocyte fetal heart, andpregnant uterus (once) skin, melanotic melanoma (once) Validated 3' end, 1 accession 806 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 5401 bp 1257 aa 237 bp 1390 bp 2kb possibly including promoter 141393 bp 1kb
bAug10 4375 bp 812 aa 546 bp 1390 bp 42 bp 2kb possibly including promoter 109672 bp 1kb
cAug10 2203 bp 313 aa 1259 bp 2kb 53941 bp 1kb
dAug10 1032 bp 209 aa 400 bp 2kb probably including promoter 4726 bp 1kb
eAug10 493 bp 134 aa 58 bp 30 bp 54 bp 2kb possibly including promoter 5487 bp 1kb
fAug10-unspliced 3337 bp 129 aa 903 bp 2044 bp 2kb including Promoter 3338 bp 1kb
gAug10 2778 bp 63 aa 1594 bp 992 bp 2kb 8055 bp 1kb
hAug10 2250 bp 131 aa 549 bp 1305 bp 2kb probably including promoter 13055 bp 1kb
iAug10 1724 bp 126 aa 546 bp 797 bp 2kb possibly including promoter 20222 bp 1kb
jAug10-unspliced 1388 bp 46 aa 819 bp 428 bp 2kb 1388 bp 1kb
kAug10 662 bp 17 aa 469 bp 139 bp 2kb including Promoter 4286 bp 1kb

Gene neighbors and Navigator on chromosome 7p21.1 back to top
R R ITGB8 D C I R P C ABCB5 D C I R P C RPL23P8 R C R P SP8 100kb 0 roky, 95 accessions, 4 variants tehere, 8 accessions, 3 variants ITGB8, 273 accessions 8 variants glychawby, 4 accessions ABCB5, 93 accessions, 11 variants wulyby, 1 accession deeshobu, 1 accession dershobu, 5 accessions toylyby, 2 accessions fawshobu, 1 accession vulyby, 1 accession fleechawby, 1 accession fawsmabu, 3 accessions flerchawby, 1 accession florchawby, 1 accession jarshobu, 1 accession floychawby, 1 accession jershobu, 1 accession glochawby, 1 accession jablar, 8 accessions glawchawby, 1 accession glerchawby, 3 accessions feysmabu, 2 accessions forsmabu, 1 accession klychawby, 1 accession kluchawby, 1 accession klarchawby, 1 accession kleechawby, 3 accessions taniya, 1 accession klerchawby, 1 accession kleychawby, 1 accession veylyby, 1 accession klorchawby, 1 accession glarglawby, 1 accession plachawby, 1 accession pluchawby, 1 accession joyshobu, 1 accession plochawby, 1 accession foysmabu, 1 accession jyblar, 3 accessions plawchawby, 1 accession kashobu, 1 accession plerchawby, 1 accession pleychawby, 1 accession kushobu, 1 accession kawshobu, 1 accession gersmabu, 1 accession geysmabu, 1 accession pleeglawby, 5 accessions gorsmabu, 1 accession goysmabu, 1 accession skochawby, 1 accession skarchawby, 1 accession skorchawby, 1 accession RPL23P8, 10 accessions 2 variants skoychawby, 1 accession jasmabu, 1 accession jerja, 1 accession jysmabu, 1 accession nychabu, 1 accession keeshobu, 1 accession slarchawby, 1 accession slawchawby, 2 accessions jeeblar, 1 accession flawchawby, 1 accession fysmabu, 1 accession fusmabu, 2 accessions musimu, 1 accession goyblar, 2 accessions farsmabu, 1 accession fleychawby, 1 accession forshobu, 1 accession glachawby, 1 accession fersmabu, 1 accession gluchawby, 1 accession gleechawby, 3 accessions jorshobu, 1 accession volyby, 1 accession klochawby, 3 accessions walyby, 1 accession plychawby, 2 accessions noytorbo, 1 accession pleechawby, 1 accession gysmabu, 1 accession plorchawby, 1 accession jublar, 2 accessions ploychawby, 1 accession skachawby, 1 accession gawsmabu, 1 accession skeechawby, 3 accessions slachawby, 1 accession jawja, 1 accession werjoyby, 2 accessions slychawby, 1 accession sluchawby, 1 accession slochawby, 1 accession MACC1, 184 accessions 16 variants rawky, 33 accessions, 3 variants SP8, 44 accessions, 4 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               11 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f-u, .g, .h, .i, .j-u, .k 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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