Homo sapiens complex locus PSAP, encoding prosaposin.
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SUMMARY back to top
RefSeq summary
[PSAP] This gene encodes a highly conserved glycoprotein which is a precursor for 4 cleavage products: saposins A, B, C, and D. Each domain of the precursor protein is approximately 80 amino acid residues long with nearly identical placement of cysteine residues and glycosylation sites. Saposins A-D localize primarily to the lysosomal compartment where they facilitate the catabolism of glycosphingolipids with short oligosaccharide groups. The precursor protein exists both as a secretory protein and as an integral membrane protein and has neurotrophic activities. Mutations in this gene have been associated with Gaucher disease, Tay-Sachs disease, and metachromatic leukodystrophy. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq].

RefSeq annotates 3 representative transcripts (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 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 expressed at high level, 2.1 times the average gene in this release. The sequence of this gene is defined by 897 GenBank accessions, some from placenta cot 25-normalized (seen 31 times), skin (26), carcinoma, cell line (23), prostate (23), placenta (20), pancreas (13), brain (11) and 68 other tissues.
Alternative mRNA variants and regulation: The gene contains 21 distinct introns (20 gt-ag, 1 gc-ag). Transcription produces 11 different mRNAs, 9 alternatively spliced variants and 2 unspliced forms. There are 5 probable alternative promotors, 3 non overlapping alternative last exons and 6 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 8 cassette exons, overlapping exons with different boundaries, splicing versus retention of one intron. 571 bp of this gene are antisense to spliced gene pymuby, raising the possibility of regulated alternate expression.
Function: There are 72 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (OMIM: combined saposin deficiency; gaucher disease, atypical, due to saposin c deficiency; krabbe disease, atypical, due to saposin a deficiency; metachromatic leukodystrophy due to saposin b deficiency; Other sources: Alzheimer Disease; Combined SAP deficiency; Gaucher disease, atypical; Krabbe disease, atypical; Leukodystrophy, Metachromatic and 7 others), proposed to participate in pathway (Lysosome) and a process (lipid metabolic process). Proteins are expected to localize in various compartments (extracellular space, membrane). Putative protein interactors have been described (BACE1, BRCA1P1, CD1B, CELSR1, COPS6, CTSD, DHRSXANDZBED1, DHRSXANDZBED1.1, GBA, MAFF, PSAP, SGK223, SMAD2, SMAD9).
Protein coding potential: 7 spliced mRNAs putatively encode good proteins, altogether 7 different isoforms (3 complete, 2 COOH complete, 2 partial), some containing domains Saposin A-type domain, Saposin-like type B, region 1, Saposin-like type B, region 2 [Pfam], some transmembrane domains, a vacuolar domain [Psort2]; 1 of the 3 complete proteins appears to be secreted. The remaining 4 mRNA variants (2 spliced, 2 unspliced; 2 partial) 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 10, links to other databases and other names
Map: This gene PSAP maps on chromosome 10, at 10q21-q22 according to Entrez Gene. In AceView, it covers 35.08 kb, from 73611132 to 73576052 (NCBI 37, August 2010), on the reverse strand.
Links to: manual annotations from OMIM_249900, OMIM_610539, OMIM_611721, OMIM_611722, GAD, KEGG_04142, the SNP view, gene overviews from Entrez Gene 5660, 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 PSAP, GLBA, SAP1, FLJ00245, MGC110993 or LOC5660, pymuby. It has been described as proactivator polypeptide, OTTHUMP00000019777, sphingolipid activator protein-1.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Psap (e=3 10-20).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene spp-10 (e=10-04), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes AT5G01800 (e=5 10-10), AT3G51730 (e=9 10-09), 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
PSAP 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 122 281 245 161 213 99.3 281 262 323 245 346 524 371 562 456 301 489 426 426 397 346 1703 301 70.2 24.8 30.6 23.2 24.8 26.6 161 281 245 397 456 562 173 371 323 346 323 397 323 228 245 301 281 397 602 173 213 262 397 185 281 346 92.7 371 173 301 245 262 213 92.7 281 185 213 371 489 346 456 323 323 213 346 397 185 199 426 245 301 281 199 245 489 456 262 245 281 371 346 489 281 245 323 301 397 245 151 456 199 456 346 281 213 213 1384 323 371 262 346 262 456 346 397 426 346 213 562 489 245 397 301 281 397 213 602 301 213 1204 281 281 456 489 741 562 645 161 24.8 65.5 14.3 371 281 397 346 524 173 489 323 151 213 21.6 426 323 301 40.3 426 228 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 PSAP 5' 3' encoded on minus strand of chromosome 10 from 73,611,132 to 73,576,052 630785 1335076 1267184 1472528 1625348 1013039 1892784 1925791 1480825 1350183 1814432 1707344 a [NM] 29 1335076 1267184 1472528 1625348 1013039 3693 1925791 1480825 1350183 1814432 5 b 630785 1335076 1267184 1472528 1625348 621645 635627 1892784 1925791 c 1707344 i 203 1267184 1472528 1625348 1013039 1892784 4 d 630785 1335076 g k-u 1892784 1925791 1480825 1350183 1814432 1707344 e 630785 1335076 424 f h-u 1814432 j 1 2kb 0 194 bp exon 194 bp exon 16676 bp [gt-ag] intron 89 GenBank accessions 630696 RNA-seq supporting reads 61949 UHR pooled cells 83344 Brain 112115 Blood 365653 Neuroblastoma 7635 Other (also 68887 Primates bodymap) 134 bp exon 2451 bp [gt-ag] intron 98 GenBank accessions 1334978 RNA-seq supporting reads 148343 UHR pooled cells 185623 Brain 310988 Blood 675833 Neuroblastoma 14191 Other (also 106061 Primates bodymap) 75 bp exon 594 bp [gt-ag] intron 101 GenBank accessions 1149312 RNA-seq supporting reads 135036 UHR pooled cells 170869 Brain 224234 Blood 605988 Neuroblastoma 13185 Other (also 109984 Primates bodymap) 126 bp exon 2048 bp [gt-ag] intron 100 GenBank accessions 1267084 RNA-seq supporting reads 152489 UHR pooled cells 189223 Brain 259097 Blood 652555 Neuroblastoma 13720 Other (also 121610 Primates bodymap) 201 bp exon 719 bp [gt-ag] intron 102 GenBank accessions 1472426 RNA-seq supporting reads 166656 UHR pooled cells 209804 Brain 319841 Blood 758149 Neuroblastoma 17976 Other (also 154281 Primates bodymap) 144 bp exon 2120 bp [gt-ag] intron 107 GenBank accessions 1625241 RNA-seq supporting reads 188271 UHR pooled cells 226305 Brain 395759 Blood 793952 Neuroblastoma 20954 Other (also 215184 Primates bodymap) 57 bp exon 3829 bp [gt-ag] intron 63 GenBank accessions 1012976 RNA-seq supporting reads 165264 UHR pooled cells 25796 Brain 419393 Blood 399654 Neuroblastoma 2869 Other (also 117921 Primates bodymap) 132 bp exon 1540 bp [gt-ag] intron 78 GenBank accessions 1892706 RNA-seq supporting reads 230582 UHR pooled cells 279810 Brain 407527 Blood 955009 Neuroblastoma 19778 Other (also 208235 Primates bodymap) 96 bp exon 339 bp [gt-ag] intron 67 GenBank accessions 1925724 RNA-seq supporting reads 236682 UHR pooled cells 288482 Brain 344103 Blood 1032850 Neuroblastoma 23607 Other (also 243785 Primates bodymap) 187 bp exon 91 bp [gt-ag] intron 65 GenBank accessions 1480760 RNA-seq supporting reads 178375 UHR pooled cells 225100 Brain 225836 Blood 832193 Neuroblastoma 19256 Other (also 79981 Primates bodymap) 158 bp exon 353 bp [gt-ag] intron 67 GenBank accessions 1350116 RNA-seq supporting reads 169259 UHR pooled cells 204621 Brain 224385 Blood 736235 Neuroblastoma 15616 Other (also 124750 Primates bodymap) 81 bp exon 306 bp [gt-ag] intron 76 GenBank accessions 1814356 RNA-seq supporting reads 233670 UHR pooled cells 281675 Brain 314021 Blood 967072 Neuroblastoma 17918 Other (also 155304 Primates bodymap) 108 bp exon 1140 bp [gt-ag] intron 78 GenBank accessions 1707266 RNA-seq supporting reads 205665 UHR pooled cells 253538 Brain 357729 Blood 871958 Neuroblastoma 18376 Other (also 177817 Primates bodymap) 1179 bp exon 179 accessions, NM_002778.2 NM_001042465.1, NM_001042466.1 some from placenta cot 25-normalized (seen 30 times) carcinoma, cell line (23) prostate (23), skin (22) placenta (19) Validated 3' end, 6 accessions Validated 3' end, 2 accessions Validated 3' end, 18 accessions 1179 bp exon 69 bp exon 69 bp exon 15909 bp [gt-ag] intron 2 GenBank accessions 27 RNA-seq supporting reads 4 UHR pooled cells 4 Blood 17 Neuroblastoma 2 Other (also 8 Primates bodymap) 134 bp exon 2451 bp [gt-ag] intron 98 GenBank accessions 1334978 RNA-seq supporting reads 148343 UHR pooled cells 185623 Brain 310988 Blood 675833 Neuroblastoma 14191 Other (also 106061 Primates bodymap) 75 bp exon 594 bp [gt-ag] intron 101 GenBank accessions 1149312 RNA-seq supporting reads 135036 UHR pooled cells 170869 Brain 224234 Blood 605988 Neuroblastoma 13185 Other (also 109984 Primates bodymap) 126 bp exon 2048 bp [gt-ag] intron 100 GenBank accessions 1267084 RNA-seq supporting reads 152489 UHR pooled cells 189223 Brain 259097 Blood 652555 Neuroblastoma 13720 Other (also 121610 Primates bodymap) 201 bp exon 719 bp [gt-ag] intron 102 GenBank accessions 1472426 RNA-seq supporting reads 166656 UHR pooled cells 209804 Brain 319841 Blood 758149 Neuroblastoma 17976 Other (also 154281 Primates bodymap) 144 bp exon 2120 bp [gt-ag] intron 107 GenBank accessions 1625241 RNA-seq supporting reads 188271 UHR pooled cells 226305 Brain 395759 Blood 793952 Neuroblastoma 20954 Other (also 215184 Primates bodymap) 57 bp exon 3829 bp [gt-ag] intron 63 GenBank accessions 1012976 RNA-seq supporting reads 165264 UHR pooled cells 25796 Brain 419393 Blood 399654 Neuroblastoma 2869 Other (also 117921 Primates bodymap) 132 bp exon 1543 bp [gt-ag] intron 4 GenBank accessions 3689 RNA-seq supporting reads 490 UHR pooled cells 676 Brain 668 Blood 1806 Neuroblastoma 49 Other (also 464 Primates bodymap) 93 bp exon 339 bp [gt-ag] intron 67 GenBank accessions 1925724 RNA-seq supporting reads 236682 UHR pooled cells 288482 Brain 344103 Blood 1032850 Neuroblastoma 23607 Other (also 243785 Primates bodymap) 187 bp exon 91 bp [gt-ag] intron 65 GenBank accessions 1480760 RNA-seq supporting reads 178375 UHR pooled cells 225100 Brain 225836 Blood 832193 Neuroblastoma 19256 Other (also 79981 Primates bodymap) 158 bp exon 353 bp [gt-ag] intron 67 GenBank accessions 1350116 RNA-seq supporting reads 169259 UHR pooled cells 204621 Brain 224385 Blood 736235 Neuroblastoma 15616 Other (also 124750 Primates bodymap) 81 bp exon 306 bp [gt-ag] intron 76 GenBank accessions 1814356 RNA-seq supporting reads 233670 UHR pooled cells 281675 Brain 314021 Blood 967072 Neuroblastoma 17918 Other (also 155304 Primates bodymap) 61 bp exon 1544 bp [gc-ag] intron 5 GenBank accessions 821 bp exon 11 accessions, some from adrenal gland (seen once) embryonic stem cells embryoid bodiesderived from H1 H7 and H9 cells (once) head neck (once), insulinoma (once) melanotic melanoma (once) Validated 3' end, 1 accession 821 bp exon 52 bp exon 52 bp exon 16676 bp [gt-ag] intron 89 GenBank accessions 630696 RNA-seq supporting reads 61949 UHR pooled cells 83344 Brain 112115 Blood 365653 Neuroblastoma 7635 Other (also 68887 Primates bodymap) 134 bp exon 2451 bp [gt-ag] intron 98 GenBank accessions 1334978 RNA-seq supporting reads 148343 UHR pooled cells 185623 Brain 310988 Blood 675833 Neuroblastoma 14191 Other (also 106061 Primates bodymap) 75 bp exon 594 bp [gt-ag] intron 101 GenBank accessions 1149312 RNA-seq supporting reads 135036 UHR pooled cells 170869 Brain 224234 Blood 605988 Neuroblastoma 13185 Other (also 109984 Primates bodymap) 126 bp exon 2048 bp [gt-ag] intron 100 GenBank accessions 1267084 RNA-seq supporting reads 152489 UHR pooled cells 189223 Brain 259097 Blood 652555 Neuroblastoma 13720 Other (also 121610 Primates bodymap) 201 bp exon 719 bp [gt-ag] intron 102 GenBank accessions 1472426 RNA-seq supporting reads 166656 UHR pooled cells 209804 Brain 319841 Blood 758149 Neuroblastoma 17976 Other (also 154281 Primates bodymap) 144 bp exon 2120 bp [gt-ag] intron 107 GenBank accessions 1625241 RNA-seq supporting reads 188271 UHR pooled cells 226305 Brain 395759 Blood 793952 Neuroblastoma 20954 Other (also 215184 Primates bodymap) 57 bp exon 1940 bp [gt-ag] intron 3 GenBank accessions 621642 RNA-seq supporting reads 35207 UHR pooled cells 182186 Brain 10654 Blood 376532 Neuroblastoma 17063 Other (also 59721 Primates bodymap) 9 bp exon 1880 bp [gt-ag] intron 3 GenBank accessions 635624 RNA-seq supporting reads 35864 UHR pooled cells 184792 Brain 11257 Blood 385589 Neuroblastoma 18122 Other (also 59622 Primates bodymap) 132 bp exon 1540 bp [gt-ag] intron 78 GenBank accessions 1892706 RNA-seq supporting reads 230582 UHR pooled cells 279810 Brain 407527 Blood 955009 Neuroblastoma 19778 Other (also 208235 Primates bodymap) 96 bp exon 339 bp [gt-ag] intron 67 GenBank accessions 1925724 RNA-seq supporting reads 236682 UHR pooled cells 288482 Brain 344103 Blood 1032850 Neuroblastoma 23607 Other (also 243785 Primates bodymap) 5 accessions, some from chondrosarcoma lung metastasis cell lines (seen once) colon normal (once), lung (once) melanotic melanoma, cell line (once) nervous normal (once) 78 bp exon 242 bp exon 242 bp exon 1140 bp [gt-ag] intron 78 GenBank accessions 1707266 RNA-seq supporting reads 205665 UHR pooled cells 253538 Brain 357729 Blood 871958 Neuroblastoma 18376 Other (also 177817 Primates bodymap) 220 bp exon 1 accession 220 bp exon 58 bp exon 58 bp exon 19261 bp [gt-ag] intron 2 GenBank accessions 201 RNA-seq supporting reads 43 UHR pooled cells 24 Brain 16 Blood 114 Neuroblastoma 4 Other (also 19 Primates bodymap) 75 bp exon 594 bp [gt-ag] intron 101 GenBank accessions 1149312 RNA-seq supporting reads 135036 UHR pooled cells 170869 Brain 224234 Blood 605988 Neuroblastoma 13185 Other (also 109984 Primates bodymap) 126 bp exon 2048 bp [gt-ag] intron 100 GenBank accessions 1267084 RNA-seq supporting reads 152489 UHR pooled cells 189223 Brain 259097 Blood 652555 Neuroblastoma 13720 Other (also 121610 Primates bodymap) 201 bp exon 719 bp [gt-ag] intron 102 GenBank accessions 1472426 RNA-seq supporting reads 166656 UHR pooled cells 209804 Brain 319841 Blood 758149 Neuroblastoma 17976 Other (also 154281 Primates bodymap) 144 bp exon 2120 bp [gt-ag] intron 107 GenBank accessions 1625241 RNA-seq supporting reads 188271 UHR pooled cells 226305 Brain 395759 Blood 793952 Neuroblastoma 20954 Other (also 215184 Primates bodymap) 57 bp exon 3829 bp [gt-ag] intron 63 GenBank accessions 1012976 RNA-seq supporting reads 165264 UHR pooled cells 25796 Brain 419393 Blood 399654 Neuroblastoma 2869 Other (also 117921 Primates bodymap) 132 bp exon 1540 bp [gt-ag] intron 78 GenBank accessions 1892706 RNA-seq supporting reads 230582 UHR pooled cells 279810 Brain 407527 Blood 955009 Neuroblastoma 19778 Other (also 208235 Primates bodymap) 39 bp exon 3889 bp [gt-ag] intron 2 GenBank accessions 2 RNA-seq supporting reads 2 Brain 109 bp exon 4 accessions, some from epithelioid carcinoma cell line (seen 2 times) pancreas (2), adrenal gland (once) eye (once), fetal eyes (once) Validated 3' end, 2 accessions 109 bp exon 57 bp exon 57 bp exon 16676 bp [gt-ag] intron 89 GenBank accessions 630696 RNA-seq supporting reads 61949 UHR pooled cells 83344 Brain 112115 Blood 365653 Neuroblastoma 7635 Other (also 68887 Primates bodymap) 134 bp exon 2451 bp [gt-ag] intron 98 GenBank accessions 1334978 RNA-seq supporting reads 148343 UHR pooled cells 185623 Brain 310988 Blood 675833 Neuroblastoma 14191 Other (also 106061 Primates bodymap) 786 bp exon 1 accession from placenta 786 bp exon 299 bp exon 1 accession from kidney tumor 299 bp exon 1440 bp exon 1440 bp exon 1540 bp [gt-ag] intron 78 GenBank accessions 1892706 RNA-seq supporting reads 230582 UHR pooled cells 279810 Brain 407527 Blood 955009 Neuroblastoma 19778 Other (also 208235 Primates bodymap) 96 bp exon 339 bp [gt-ag] intron 67 GenBank accessions 1925724 RNA-seq supporting reads 236682 UHR pooled cells 288482 Brain 344103 Blood 1032850 Neuroblastoma 23607 Other (also 243785 Primates bodymap) 187 bp exon 91 bp [gt-ag] intron 65 GenBank accessions 1480760 RNA-seq supporting reads 178375 UHR pooled cells 225100 Brain 225836 Blood 832193 Neuroblastoma 19256 Other (also 79981 Primates bodymap) 158 bp exon 353 bp [gt-ag] intron 67 GenBank accessions 1350116 RNA-seq supporting reads 169259 UHR pooled cells 204621 Brain 224385 Blood 736235 Neuroblastoma 15616 Other (also 124750 Primates bodymap) 81 bp exon 306 bp [gt-ag] intron 76 GenBank accessions 1814356 RNA-seq supporting reads 233670 UHR pooled cells 281675 Brain 314021 Blood 967072 Neuroblastoma 17918 Other (also 155304 Primates bodymap) 108 bp exon 1140 bp [gt-ag] intron 78 GenBank accessions 1707266 RNA-seq supporting reads 205665 UHR pooled cells 253538 Brain 357729 Blood 871958 Neuroblastoma 18376 Other (also 177817 Primates bodymap) 1140 bp exon 12 accessions, some from melanocyte (seen 2 times) skin (2), testis (2) brain (once), embryonic stem (once) Validated 3' end, 1 accession 1140 bp exon 68 bp exon 68 bp exon 16676 bp [gt-ag] intron 89 GenBank accessions 630696 RNA-seq supporting reads 61949 UHR pooled cells 83344 Brain 112115 Blood 365653 Neuroblastoma 7635 Other (also 68887 Primates bodymap) 134 bp exon 2451 bp [gt-ag] intron 98 GenBank accessions 1334978 RNA-seq supporting reads 148343 UHR pooled cells 185623 Brain 310988 Blood 675833 Neuroblastoma 14191 Other (also 106061 Primates bodymap) 75 bp exon 594 bp [gt-ag] intron 101 GenBank accessions 1149312 RNA-seq supporting reads 135036 UHR pooled cells 170869 Brain 224234 Blood 605988 Neuroblastoma 13185 Other (also 109984 Primates bodymap) 126 bp exon 2024 bp [gt-ag] intron 1 GenBank accession 423 RNA-seq supporting reads 11 UHR pooled cells 6 Brain 161 Blood 240 Neuroblastoma 5 Other (also 68 Primates bodymap) 178 bp exon 1 accession from amygdala 178 bp exon 1721 bp exon 1721 bp exon 13 accessions, some from embryonic stem cells cell lines H1, H7, andh9 (seen 2 times) eye (2), adenocarcinoma cell line (once), brain (once) colon ins (once) 1721 bp exon 241 bp exon 241 bp exon 306 bp [gt-ag] intron 76 GenBank accessions 1814356 RNA-seq supporting reads 233670 UHR pooled cells 281675 Brain 314021 Blood 967072 Neuroblastoma 17918 Other (also 155304 Primates bodymap) 103 bp exon 2 accessions, some from placenta normal (seen 2 times) 103 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 Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
aAug10 2872 bp 524 aa 154 bp 1143 bp 2kb possibly including promoter 35078 bp 1kb
bAug10 2339 bp 518 aa 780 bp 2kb 34185 bp 1kb
cAug10 1104 bp 364 aa 12 bp 2kb probably including promoter 31411 bp 1kb
dAug10 941 bp 286 aa 79 bp 2kb probably including promoter 34941 bp 1kb
eAug10 3210 bp 248 aa 1359 bp 1104 bp 2kb possibly including promoter 6979 bp 1kb
fAug10 581 bp 184 aa 28 bp 2kb probably including promoter 22326 bp 1kb
gAug10 977 bp 110 aa 17 bp 642 bp 2kb probably including promoter 20104 bp 1kb
hAug10-unspliced 1721 bp 77 aa 1228 bp 259 bp 2kb 1721 bp 1kb
iAug10 462 bp 52 aa 190 bp 113 bp 2kb 1602 bp 1kb
jAug10 344 bp 42 aa 217 bp 2kb 650 bp 1kb
kAug10-unspliced 299 bp 45 aa 161 bp 2kb 299 bp 1kb

Gene neighbors and Navigator on chromosome 10q21-q22 back to top
P CDH23 D C I R P C R CHST3 D C R P C ANAPC16 C I R P DDIT4 D C I R P C R C10orf105 C I R P C10orf54 D C I R P PSAP C I R P SPOCK2 C C I R P ASCC1 C R 100kb 0 SLC29A3, 186 accessions 11 variants temu, 10 accessions CDH23, 143 accessions 21 variants narswyby, 1 accession pymuby, 1 accession CHST3, 206 accessions monoby, 2 accessions ANAPC16, 538 accessions 17 variants DDIT4, 375 accessions 6 variants doynoby, 2 accessions fanoby, 2 accessions swawglorbu, 3 accessions swerglorbu, 2 accessions fonoby, 1 accession farnoby, 1 accession fernoby, 7 accessions meytarbo, 1 accession loyswyby, 2 accessions gynoby, 1 accession morswyby, 1 accession terfor, 2 accessions gernoby, 1 accession goynoby, 1 accession nyswyby, 1 accession nuswyby, 1 accession jawnoby, 4 accessions nawswyby, 1 accession bogloybu, 1 accession kawnoby, 2 accessions kernoby, 1 accession koynoby, 1 accession nerswyby, 1 accession beegloybu, 2 accessions bergloybu, 1 accession lunoby, 2 accessions lonoby, 2 accessions slarsmey, 1 accession klysha, 2 accessions paswyby, 1 accession plawma, 1 accession dawgloybu, 1 accession dergloybu, 1 accession smosmey, 1 accession peeswyby, 1 accession mynoby, 1 accession munoby, 1 accession meenoby, 2 accessions raswyby, 1 accession fugloybu, 1 accession smersmey, 1 accession mornoby, 1 accession fogloybu, 1 accession nonoby, 1 accession fargloybu, 2 accessions rerimu, 24 accessions kloysha, 3 accessions plasha, 2 accessions nernoby, 1 accession swoglorbu, 1 accession luswyby, 1 accession warimu, 2 accessions, 2 variants sweeglorbu, 1 accession fawnoby, 1 accession gleysha, 2 accessions tarfor, 4 accessions, 2 variants lawswyby, 1 accession feenoby, 4 accessions feynoby, 1 accession fornoby, 1 accession ganoby, 1 accession gloysha, 1 accession gunoby, 1 accession garnoby, 2 accessions geenoby, 2 accessions geynoby, 1 accession sworglorbu, 1 accession klasha, 7 accessions janoby, 1 accession mortarbo, 2 accessions rarimu, 1 accession jarnoby, 1 accession jornoby, 14 accessions joynoby, 2 accessions bugloybu, 7 accessions kanoby, 1 accession kynoby, 1 accession kunoby, 1 accession konoby, 1 accession karnoby, 1 accession keenoby, 2 accessions tehero, 2 accessions, 2 variants keynoby, 1 accession toyfor, 4 accessions bawgloybu, 2 accessions lanoby, 1 accession larnoby, 1 accession tarmuby, 1 accession klusha, 3 accessions slersmey, 1 accession leenoby, 1 accession ririmu, 2 accessions, 2 variants dygloybu, 1 accession dugloybu, 1 accession smysmey, 1 accession dargloybu, 3 accessions pawswyby, 1 accession lornoby, 1 accession dorgloybu, 1 accession loynoby, 1 accession manoby, 3 accessions rurimu, 2 accessions, 2 variants doygloybu, 1 accession wumuby, 3 accessions mawnoby, 1 accession mernoby, 1 accession nanoby, 1 accession nunoby, 1 accession C10orf105, 15 accessions 2 variants C10orf54, 398 accessions 9 variants PSAP, 230 accessions, 11 variants SPOCK2, 423 accessions 10 variants klosha, 8 accessions ASCC1, 418 accessions 19 variants fygloybu, 1 accession cherskaw, 6 accessions 2 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               72 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h-u, .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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