DreINT0083261 @ danRer10
Intron Retention
Gene
ENSDARG00000016939 | itgb2
Description
integrin, beta 2 [Source:ZFIN;Acc:ZDB-GENE-110411-4]
Coordinates
chr9:45173017-45174202:-
Coord C1 exon
chr9:45174032-45174202
Coord A exon
chr9:45173259-45174031
Coord C2 exon
chr9:45173017-45173258
Length
773 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGA
5' ss Score
9.14
3' ss Seq
ACCAACCTTTCCTAATACAGGAT
3' ss Score
8.38
Exon sequences
Seq C1 exon
GGATGCCCCAAACTTTTCAACTACGTTTTAAAAGGGCAGAAGGTTATCCTGTAGATCTTTACTACCTGATGGATCTGTCATACTCTATGAAAGACGATTTGGCGAATGTAAAAAACCTGGGAAATGATATACTTGAAAAGCTCAATAGAATCACTGGCAATGCCAGAATAG
Seq A exon
GTAAGAGCATATGCATATATTGGTAACACTTTACTTAAAAAAGATGACAATGTTTGAGATGTGTTTGTTATGACAATTTGATAAACAAATACATTATAACTGACATTTCCAAGACAACAATCTATCAGTGTCTTTGTCATGACAACTTGCATTACCAAGTCAACATAACTTGTCATATATTAGTCTTGTCATACGGCCATTATAATTGTCATTAATATTTTTCTGTTGAAATATTTCAGTGGATTTTTTTTGCTTGCCATTACATTCAAAATTAAAAGTGTCAATACTCTGTCAAATAATTTTATAACATTGTTATTAATATCTAATGACATTTAATTACATTTGAATGACAAATTCAATTTGTACCACTGTAGTTAATTGCAGTTTCAAAATTAATGACAATTCTAATGGCCTCATGACAATTTAAATTACAGTATGACAGATTTACGACAAGTTTTGTTGTCTTGGTAATGTCAAGTTGTCATGACAAAGACAGGTTGTGATGTGTTTGGTTATGTCAAGTTGTCATAACAAGAACATTTGATTCTTACCTTTACATTTAAAATGACATAACTAAGCAAACGACACCTAATGACAGCTGTCATAAGCATGCATGGAATGTCCTTCATATTCATGATGTGATATAAAGGTTTCATGACAGTCTTATGAACACCCCCTTTAAGTAAAGTGCTCCCAATATATTATATTGCACATTTTGGAGTTGCACTTTGAAAAGTTGCAATGGCTTCATTAACCAACCTTTCCTAATACAG
Seq C2 exon
GATTCGGTTCGTTTGTTGACAAAACACTTCTTCCATACACCGACACCAATGAAGCCAAACTTAAACACCCCTGCTCGGATAAAAATGAACCATGTCAGCCAGCATTTGGCTTTCAGCACGTGCTTCCACTCACAGCAAATGGGAACGACTTCAAAGAATTGGTAAAGCAGCAGCATATATCTGGAAACCTGGACCCTCCAGAGGGAAGCCTGGATGCCATCATGCAAGCTGCCGTCTGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016939:ENSDART00000149704:5
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=0.185
Domain overlap (PFAM):
C1:
PF0036213=Integrin_beta=FE(13.6=100),PF135191=VWA_2=PU(17.3=67.2)
A:
NA
C2:
PF0036213=Integrin_beta=FE(19.1=100),PF135191=VWA_2=FE(35.6=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:
AAGGGCAGAAGGTTATCCTGT
R:
CATCCAGGCTTCCCTCTGGAG
Band lengths:
356-1129
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]