DreINT0083253 @ danRer10
Intron Retention
Gene
ENSDARG00000016939 | itgb2
Description
integrin, beta 2 [Source:ZFIN;Acc:ZDB-GENE-110411-4]
Coordinates
chr9:45165330-45166263:-
Coord C1 exon
chr9:45166076-45166263
Coord A exon
chr9:45165563-45166075
Coord C2 exon
chr9:45165330-45165562
Length
513 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGA
5' ss Score
7.61
3' ss Seq
TAACCTTACTGTGTCCACAGGTG
3' ss Score
10.84
Exon sequences
Seq C1 exon
GTGATTTTTGATGTGACGGTGACAGTGGATAGATGCATCAATGATCAGAGCTTCTCCATCGGGCCATTGGGCTTCAATGAAAAGCTGAAGGTGAACGTTCAGACTCTCTGCGAATGTAATTGTGGTGATCCCCCTGGAGTTCATCCTCACTGTAAAGGACAGGGTAAAGTTGTCTGCGGCAGCTGCAA
Seq A exon
GTAAGAGAAATTCATAATTTTATCAAATTTTTTATCACATTTTTCAGATATTTTCTCCTAAGGCCCTGGGTGAATCTGTCTGGGTCATATGCATAATAATAATAATAAGCTATAATAATAAATTAATAATTATATTGAACAGCAAGAAGGCTGCTGGTTTGAGTCCCGACTGGTCCGTTGGCATTTCTTTGTGGAGTTTGTATGTTCTCTCCGTGTCTGCATGAGTGGGGGTGCTCAGATTTCCCCCATAGTCCAAAGATATGCTCTTTAAGTGAACTGAATAAACTAAATTGGCCGTAGTGTATGAGTGTGTGTGTAGTAAGTGTGGGTGTTTCCCCAAAATAATAGGGCATCTGAGAGTATAACATATGCTGGAATAGTTTGGTGGTTCATTCCCCGCTGGCAACCTCTGAAATAGAGACTAAGATGTGGGAAAATTTATGAATGAATTAAAAATTGCAAAAAAAAAAAATTGAAAATAAATGAAATTAAGTAACCTTACTGTGTCCACAG
Seq C2 exon
GTGTAATGATGGCTTCATAGGACAGCTCTGTGAGTGCACAATAGGTAAAAAAGATGAGGCCTCATTTAAAGCCCAGTGCCGGAAAGACAATGGCACTGAATGTGAAGGCAAAGGAGACTGTGTGTGTGGACGGTGTCAGTGCCATTTAACAGAGGGTAACGGACATTTCTATGGCGAACACTGTGAATGCGACGATGAACACTGTGAAAAGTTTGACAATAAACAGTGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016939:ENSDART00000149704:11
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=PD(9.1=60.3)
A:
NA
C2:
PF079748=EGF_2=PU(32.3=12.7)
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:
ATCAGAGCTTCTCCATCGGGC
R:
TTCACAGTGTTCATCGTCGCA
Band lengths:
353-866
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]