DreINT0083260 @ danRer10
Intron Retention
Gene
ENSDARG00000016939 | itgb2
Description
integrin, beta 2 [Source:ZFIN;Acc:ZDB-GENE-110411-4]
Coordinates
chr9:45174032-45174498:-
Coord C1 exon
chr9:45174306-45174498
Coord A exon
chr9:45174203-45174305
Coord C2 exon
chr9:45174032-45174202
Length
103 bp
Sequences
Splice sites
5' ss Seq
CAGGTATTT
5' ss Score
7.51
3' ss Seq
ACTGCTTTTTTTTCTCTCAGGGA
3' ss Score
10.86
Exon sequences
Seq C1 exon
AATTTCACCAAGACTGGAGAGCAGGAAGCAGCACGTTGTGACACTGTCAAGTTGCTTTTAGACAGAGGATGTAGCAAAGAGAACATCATAAATCCTCAAAACATTTTTCAAAATGTTGTGAACAAAGCTCTGGTTGCTGGTAAAGACCCAGTGCAAATCCAACCCCAAGAAATACAACTCAATCTTAGACCAG
Seq A exon
GTATTTTATATCCATATAAATCAACAATATCTCAAACAAACCAGTGGCCTTTACAATATACTGTATGTTTGGACATGGTAATGACTGCTTTTTTTTCTCTCAG
Seq C2 exon
GGATGCCCCAAACTTTTCAACTACGTTTTAAAAGGGCAGAAGGTTATCCTGTAGATCTTTACTACCTGATGGATCTGTCATACTCTATGAAAGACGATTTGGCGAATGTAAAAAACCTGGGAAATGATATACTTGAAAAGCTCAATAGAATCACTGGCAATGCCAGAATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016939:ENSDART00000149704:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.046 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0036213=Integrin_beta=FE(15.3=100)
A:
NA
C2:
PF0036213=Integrin_beta=FE(13.6=100),PF135191=VWA_2=PU(17.3=67.2)
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:
ACCAAGACTGGAGAGCAGGAA
R:
TCTACAGGATAACCTTCTGCCCT
Band lengths:
242-345
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]