DreINT0083222 @ danRer10
Intron Retention
Gene
ENSDARG00000071863 | itgb1a
Description
integrin, beta 1a [Source:ZFIN;Acc:ZDB-GENE-060803-2]
Coordinates
chr24:1131917-1132854:-
Coord C1 exon
chr24:1132616-1132854
Coord A exon
chr24:1132073-1132615
Coord C2 exon
chr24:1131917-1132072
Length
543 bp
Sequences
Splice sites
5' ss Seq
GGAGTGAGT
5' ss Score
6.05
3' ss Seq
TTTTTTCTTCTCCCTCTCAGGAG
3' ss Score
10.68
Exon sequences
Seq C1 exon
GTTTTGGCTCTTTTGTGGAGAAGACCGTCATGCCGTATATCAGCACGACTCCGGCCAAGCTTCTAAACCCCTGCACTGGAGACCAGAACTGCACCAGCCCCTTCAGCTACAAAAACGTGCTCAAACTGACCAGCAACGGGCAGCGCTTCAACAGCCTGGTGGGACAACAGCAGATTTCTGGAAACCTGGACTCTCCTGAGGGAGGATTCGATGCCATCATGCAAGTGGCCGTCTGTGGA
Seq A exon
GTGAGTATAAAGCTACGTGAAGAGGGTTTGCTCTAGATAAGGACACTTTTTTTGTTATTTTATATATATATATTACAATTTTACAATTTTTTTCATTAACATGTCTTAGTAATGACATTTGCTTGGTTTTATGATCGAGTCTCTATAGTTTTCAAATCTCAATCAATCCATTTGTCAATCTGTTTGTTTACACAAAGAGCAGAAAATCAGATATGTTAATATGTTAAGTGTTTGGTTTTGTCCAATCAGAGTGGAGTGGGCTGCTGCATTGCATATTATGAGAAAAATGATGATGAAGAAAAGTTTTTTTTTCTTATATGGATGTAAATCATCATGTGAGATGAACAAAACTAAACTAGGAACATTTTTAGTAATAAACGGGAGCACTTAAATGTGTGGTTATTTTCAGTAACTTTACCAGTGGAAAATGTACTGTAATGTGGCCTCATTTGTGTGTTTTTGTACTTTCAGCTCATTCCTTGTATCCCTTGGCCTCATTTTTCCCTCTTTCTTCATGTGTGTGTTTTTTCTTCTCCCTCTCAG
Seq C2 exon
GAGCACATTGGCTGGAGAAACGTCACCCGTTTGTTGGTTTTCTCTACTGACGCAGGTTTTCATTTTGCTGGAGATGGGAAACTCGGAGGAATTGTGCTTCCCAATGATGGGAGGTGTCACTTAGAAAATGACATGTACACCATGAGCCATTATTAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000071863:ENSDART00000039700:6
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:
PF0036213=Integrin_beta=FE(18.3=100)
A:
NA
C2:
PF0036213=Integrin_beta=FE(11.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGTGGAGAAGACCGTCATGC
R:
AGTGACACCTCCCATCATTGG
Band lengths:
348-891
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]