Gene OTOP1TABLE OF CONTENTS / OPEN CLOSE ALL PARAGRAPHS
Compact gene diagram
According to AceView, this gene is expressed at low level
, only 6.5% of the average gene in this release. The sequence
of this gene is defined by 8 GenBank accessions
, some from pooled, cerebellum, kidney, placenta,testis, lung, colon, liver, heart, thyroid, bladder,uterus, PCR rescued clones (seen 2 times).
The gene contains 5 distinct gt-ag introns
. Transcription produces one mRNA.
There is one article
specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in processes
(biomineral formation, detection of gravity, inner ear morphogenesis). Proteins are expected to localize
in various compartments (membrane, extracellular region, extracellular space, integral to membrane).
The spliced mRNA putatively encodes a good protein
, containing Pfam domain
[Pfam], some transmembrane domains, a peroxisomal domain [Psort2]
Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12
8 supporting clones for gene OTOP1
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.
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. Details on tissue of origin for each intron and exon is available from the intron and exons table
Click on any transcript to open the specific mRNA page, to see the exact cDNA clone support and eventual SNPs and to get details on tissues, sequences, mRNA and protein annotations. Proteins supported by a single continuous cDNA sequence lead to underlining the name/ending of the variant. Names not underlined result from cDNA concatenation in the coding region and should be experimentally checked.
are depicted by broken lines; the height of the top of each intron reflects the relative number of clones supporting this intron. ]^[ A pink broken line
denotes an intron with standard boundaries (gt-ag or gc-ag) that is exactly supported (i.e. a cDNA sequence exactly matches the genome over 16 bp, 8 on both sides of the intron). ] ^ ] A blue broken line
denotes non-standard introns, exactly supported, but with non-standard at-ac or any other boundaries. ]-[ Pink
and ] - ] blue
straight lines represent 'fuzzy' introns of the standard and non-standard types respectively, those introns do not follow the 16 bp rule. Black straight lines ]-[denote gaps in the alignments.
Wide filled pink areas represent putative protein coding regions, narrow empty pink boxes represent the 5'UTR (on the left) and 3' UTR (on the right). Flags identify validated endings: cap site on the 5' side, polyadenylation site on the 3' side. Filled flags correspond to frequent events while empty flags have lesser supporting cDNAs (yet all are validated); at the 3' side, black flags are associated to the main AATAAA signal, blue flags
to any single letter variant of the main . More explanations are given in the gene help file
Links to the sequence
most 5' clones
(with AA variation)
relative to genome
|NM_177998.1 || ||.a ||1 to 1869 ||1 to 1869 ||exact ||RefSeq, ||1869/1869 |
| 0 diff|
|BC130430 ||Pooled, cerebellum, kidney, placenta,testis, lung, colon, liver, heart, thyroid, bladder,uterus, PCR rescued clones ||.a ||6 to 1946 ||1 to 1941 ||E40K ||tiling clone, ||1941/1941 |
| 1 diff|
|BC130432 ||Pooled, cerebellum, kidney, placenta,testis, lung, colon, liver, heart, thyroid, bladder,uterus, PCR rescued clones ||.a ||6 to 1946 ||1 to 1941 ||E40K || ||1941/1941 |
| 1 diff|
|TI_1607547033 || ||.a ||6 to 1134 ||40 to 1164 || || ||1125/1263 |
| 12 diff|
|TI_1607547291 || ||.a ||445 to 1537 ||1086 to 7 || || ||1082/1182 |
| 25 diff|
|TI_1607547035 || ||.a ||843 to 1947 ||1165 to 68 || ||tiling clone, ||1098/1247 |
| 14 diff|
|TI_1607547289 || ||.a ||924 to 1949 ||15 to 1034 || || ||1020/1255 |
| 15 diff|
|TI_1607547295 || ||.a ||1298 to 1953 ||11 to 665 || || ||655/1231 |
| 10 diff|