DreINT0083220 @ danRer10
Intron Retention
Gene
ENSDARG00000071863 | itgb1a
Description
integrin, beta 1a [Source:ZFIN;Acc:ZDB-GENE-060803-2]
Coordinates
chr24:1133394-1133963:-
Coord C1 exon
chr24:1133744-1133963
Coord A exon
chr24:1133565-1133743
Coord C2 exon
chr24:1133394-1133564
Length
179 bp
Sequences
Splice sites
5' ss Seq
CCGGTGCGT
5' ss Score
9.74
3' ss Seq
CACCTGTGTTATTGCTGTAGGAG
3' ss Score
8.17
Exon sequences
Seq C1 exon
GAGTTTCTGAAGCAGGGAGAGCCGACATCGGCGCGCTGTGATGAGCTGGAGTCGCTCAAGAAAAGAGGCTGCGCAGAAGATAAGATCGAGAACCCGCACGGCAGCCAGAGAATCCTGAAGAATACACCGGTGACCAACCGCAAGAAAGGAGCCGAGAAACTCCGACCCGAGGACATCACGCAGATCCAGCCTCAGAAACTCAGCCTCCAGCTCAGATCCG
Seq A exon
GTGCGTGTGAAAGCAACACCATGCAGTTTATAATGACTGGCATTGCATTTAGAGTTTGTGTTAGCACTGGTATATCTGACTATGTCTTATACAGGTGAAGTCATAATTATTCGCCCTCCTTTTCACACACTTTACTGCTTGTGATTTGGATAATGCTAACACCTGTGTTATTGCTGTAG
Seq C2 exon
GAGAACCTCAGAATATTAAACTGAAGTTCAAGCGGGCTGAGGACTATCCCATAGACCTGTACTACCTGATGGACCTGTCCTACTCCATGAAGGACGACCTGGAGAACGTTAAAAACCTGGGGACGAGTCTGATGAAGGAGATGTCCAAGATCACCTCAGACTTCAGGATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000071863:ENSDART00000039700:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.392 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0036213=Integrin_beta=FE(16.9=100)
A:
NA
C2:
PF0036213=Integrin_beta=FE(13.2=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:
GGCAGCCAGAGAATCCTGAAG
R:
TCAGACTCGTCCCCAGGTTTT
Band lengths:
253-432
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]