GgaINT0111089 @ galGal4
Intron Retention
Gene
ENSGALG00000010342 | OTOGL
Description
otogelin-like [Source:HGNC Symbol;Acc:HGNC:26901]
Coordinates
chr1:39716774-39718883:+
Coord C1 exon
chr1:39716774-39716898
Coord A exon
chr1:39716899-39718673
Coord C2 exon
chr1:39718674-39718883
Length
1775 bp
Sequences
Splice sites
5' ss Seq
ATAGTATGT
5' ss Score
4.41
3' ss Seq
ACAATGTCACCTTCTCTTAGTTG
3' ss Score
5.81
Exon sequences
Seq C1 exon
TTCTCCAGCAGGGATGATAGAAGGGACCCCGCAACTTCATGCCAATGCATGGAAGGTTTCCTCAGCTTGTTCTGTGCCTATCAATGTTCCTGTAGTCGATCCCTGCAACGTTAATCAGCAAAATA
Seq A exon
GTATGTTTTCATATGGAATTATTTGCATCATTTTCTTATGGGATTTTTTTTTCTCTGTGAATTAGTTTCTCTAGTATTAGTCATTAATTAATATATGCTTGTATTTTAACTTTAGATTTATATGCACGCTCTTTATTTTCTTCTTATATCTTAGTAAAGACAATTTTGTTCCCAGTCATTCGGTGTGGAAACTAAAATAATTTAGGTGAACATTTAATGCTTTGCATGATGGCCTCAAGTCTTACATTTTGCTGTTGAGAATATGTAAAGAATGTTAAGCAGAACACTGTAGTCTTGCAAATTCTTCCAGCTAAGAGGACTGAATACTATTTTTGCTGCATATATCCTGACTGACAAAGAAAGTACATGGGACAAAGTCTCTCCTAGCCAGTGTTCAGATCAAAAGTCCTGTCTCTGTCTTCTCTGTGATTATCTAAACTTTATTTTAATGCTTCTTTGTCCACCATCTATGCTCTTACACATAAACCAAGGCAAACAATAAGATCTGCAGATTCGTTCAAATTCTTCACTAAAGATTTTTTTTTTTTTTGGCTTGTTGACATGCCCAAGTTTTGTTTTCAACTTTCACTGTCTCCCTTTCTCTGCATTGCTATTCTTTTCAGTTAATGAAGACAATGAGCAGAGATTGGTTGCCAATTCTGGCAGAATTTTAATGTTTCAGAAATAAGGATGTGGGATTTGGCCATGCTTAGAGCCTGTGAGAGTGAGCCCAGAATAACTGTAAACCTTTAAGAATCTGGCCCATTATAAGGCTTTTTTTGTCTTCAGCATTGGCTATCTTCTAAAGCAGTACATCTCAGCCAAGTCAGCTCTCTCCAAGATACTTCATGACTTTCCTTCAGATTTGTGTTTCCTCAGTGATGATGGAGTTTGACATATATGTAAGCTGCTTAGAGCAGGAGAATAAGCTAGATGGCCTTCTGGGGTCTCTTCTACCCTTCATTTTCCTGTGATTCTTGAAAAAACATTCCTTGGCTATGTGGTGCTGTTGCATGGTACCACCTGCGCTGAGCCAGAACAATCAAGATTTCAGGCCTGTTGTGATCTGAACCTCACGAAACTAGAAAATAAATCTTTGTTTTTTCACTTATTTTGTCAGGCTATTTTTCAATCAAGTCATGTTTACTCCTTGGATCTTGTTTACTGATAGACTCCTGAAACCCTTGAGTCAGCATGTATATGTGGAAATGAAGAGATATGGGGAGGGCTAGAGACACTTTTTAGCAGCAAAATTGGCTCAAATATGATTCACACTACAGTGTCCCTGAGATATTCCATCAGTGTGGTGGGAGTACACTTCAGTGGTAGAAGGAAGGTCTGTTGGTACTAGAAGGCCTTATGGCCTGCTTGGGGCTTGCACACCCCTGAGCTTCAGTTTGTAATGCCTGCTGAGTTGGCATACCAGTAATAATATGGCCATTACTGATTTCAAAGCTAGATGAAACAGTAAGTAGGAAGAAACAATATTCCAAGCTTTGGAGGACTTTTCCAACTGTTTTGAAATATATTATTTTTCCGTTTATGTTTCCCGTATTACTATAGGAAGGCAAAACTTTTTTTGTTGTTTTTGTTATTTTTATTTTAAATAGAGTTTGTTTTTGAGTGGGTTGCTTACAATAGCAGTTTTAAACTATAAAACTTTCAAGAAATTCTTACTGCACAACTAGTCAATTATATTTGTGTTTATGTCTGTGCTATTCAAGTAGTTGCTGTATTAGCGTGGATCTGTCTAAAACAATGTCACCTTCTCTTAG
Seq C2 exon
TTGGATATGCATCTCACTGTGATATCATCAATGAAGAAGTCTTTGCTCCCTGTCATGCCTACATCAGTCCAGGATTGTACTACCAACTATGTCGCTTTGATGCCTGCAAATGTGGCAGCAGCTGTATGTGTAACTCTCTTGCACACTATGCTTACGTCTGTGGCAAGCATGGCATTGCTGTGGACTTCAGATCTCATATTTCTTACTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010342:ENSGALT00000017091:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009420=VWD=PD(3.2=11.6),PF087426=C8=PU(0.1=0.0)
A:
NA
C2:
PF087426=C8=WD(100=100.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCAGCAGGGATGATAGAAGGG
R:
AAGAAATATGAGATCTGAAGTCCACA
Band lengths:
326-2101
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]