DreINT0083254 @ danRer10
Intron Retention
Gene
ENSDARG00000016939 | itgb2
Description
integrin, beta 2 [Source:ZFIN;Acc:ZDB-GENE-110411-4]
Coordinates
chr9:45164646-45165562:-
Coord C1 exon
chr9:45165330-45165562
Coord A exon
chr9:45164863-45165329
Coord C2 exon
chr9:45164646-45164862
Length
467 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAAT
5' ss Score
6.6
3' ss Seq
AAGTGAGTATTTTTTTACAGGTC
3' ss Score
5.59
Exon sequences
Seq C1 exon
GTGTAATGATGGCTTCATAGGACAGCTCTGTGAGTGCACAATAGGTAAAAAAGATGAGGCCTCATTTAAAGCCCAGTGCCGGAAAGACAATGGCACTGAATGTGAAGGCAAAGGAGACTGTGTGTGTGGACGGTGTCAGTGCCATTTAACAGAGGGTAACGGACATTTCTATGGCGAACACTGTGAATGCGACGATGAACACTGTGAAAAGTTTGACAATAAACAGTGTGCAG
Seq A exon
GTGAATTTTTAATACATTTTTTGTCTAATAAGATATTCTTTAAAATACATTTAAATGTACATTTCTTTTTCAAATATTTCTCAAATGATGTTTAACAGAGCAAGGAATTTTTCACAGTATTTCCTATAATATTTTTTCTTTTGGAGAAAGTCTTTGTATTTGTTTAGCTAGAATAAAAGCAGTTTAAAAATTTTTTTTAATCATTTTAAGCTCAAAATTATTAGCTATATATTATTAAACCATCATTTTAGATATACATGACTTGCCTAATTGCCTCTAGTATATTAATAAATATCTAATAAAATACTATTTACTGTCATCAAGGCAAAGATAAAAATAATCAGTCATTAGAAATGAGTAATTAAAACTATTATGTTTAAAAATGTGTTGAAAAATATTTGTAATAATTCAGGAGGGCTAATAATTCTGACTTCAACTGTATGTGTAAAGTGAGTATTTTTTTACAG
Seq C2 exon
GTCATGGCAAGTGCAAATGTGGCAAATGTGAGTGTGATGACGGCTATGAGGGAACAGCTTGTCACTGCGCTAAATCCGACAATGAATGCAAGATTGACAGCCATGTTTGTTATAACCGCGGTAAATGTGTATGTAACCAGTGCGAATGTGAAAGGGGATACAAGGGACCCTACTGCAAAACCTGTCCTACATGTCAACGTCCGTGTCAACAGTCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016939:ENSDART00000149704:12
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:
PF079748=EGF_2=PU(32.3=12.7)
A:
NA
C2:
PF079748=EGF_2=PD(64.5=27.4),PF079748=EGF_2=WD(100=41.1),PF079657=Integrin_B_tail=PU(5.0=5.5)
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:
TTAAAGCCCAGTGCCGGAAAG
R:
AGGTTTTGCAGTAGGGTCCCT
Band lengths:
351-818
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]