DreINT0083212 @ danRer10
Intron Retention
Gene
ENSDARG00000071863 | itgb1a
Description
integrin, beta 1a [Source:ZFIN;Acc:ZDB-GENE-060803-2]
Coordinates
chr24:1127987-1128508:-
Coord C1 exon
chr24:1128368-1128508
Coord A exon
chr24:1128190-1128367
Coord C2 exon
chr24:1127987-1128189
Length
178 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
GTTTTGATTTATATCTCCAGGTG
3' ss Score
9.83
Exon sequences
Seq C1 exon
TCTCTTTCCTCAGAGGTGATCCTGGAGAACAGTAAGCTTCCTGAAGGAGTGACCATCACATATCAGTCGCGCTGTAAGAACGGTGTGGTCAACGAAGGAGAGAGTGGAAGGAAATGCTCCAACATCTCAATCGGAGACGAG
Seq A exon
GTAAGGCCAAATCAACAGCGTTTAGATGCACCAGGGCACAATTGCATATAAGCTCTATGTTTTTCTCCCTCAGCAAAACACCCAAGCCAGATTACATAAGGACTTTCATGCAACCAGGCCCTGACATCAGTAGCCTGTCATTTCTGTACAGTAAGTCTGTTTTGATTTATATCTCCAG
Seq C2 exon
GTGTCGTTCAACATTAACATCACGGCTCAAGGCTGCCCTAAACAAGGCAAGACAGAGACCATAAAGATCAAGCCGCTGGGCTTCACTGAGGAGGTGGAGATAACACTGAGCTTCATCTGCGAATGCGAATGCCACAAACACGCCATGAAGAACAGCCCGCTGTGCCACAACGGCAATGGCTCCTTTGAGTGCGGAGCCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000071863:ENSDART00000039700:10
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(10.7=100)
A:
NA
C2:
PF0036213=Integrin_beta=PD(9.5=60.3)
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:
AGCTTCCTGAAGGAGTGACCA
R:
CGTGTTTGTGGCATTCGCATT
Band lengths:
249-427
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]