DreINT0083237 @ danRer10
Intron Retention
Gene
ENSDARG00000053232 | itgb1b.1
Description
integrin, beta 1b.1 [Source:ZFIN;Acc:ZDB-GENE-060803-3]
Coordinates
chr2:43752781-43753281:+
Coord C1 exon
chr2:43752781-43753001
Coord A exon
chr2:43753002-43753114
Coord C2 exon
chr2:43753115-43753281
Length
113 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAAT
5' ss Score
4.46
3' ss Seq
CTTTGTTTCTGTGTTGACAGAGT
3' ss Score
6.69
Exon sequences
Seq C1 exon
GGATTGTGTGGAGTGCAGACATTTTGGTACAGGCAGCAAGCAAAAGACATGTGAGGAGGACTGCAAATCTTACAGCATAAAGAAGGTGAAGACTAAGGAGGATCTTCCTCCGCCTAACATTAATCACTGCAAAGAGCGAGATGTTGATGACTGCTGGATCTTTTTTACTTCTTCTATCGAGAAAGATGGCAGCATTCAGGTCTATGTGGCTGAAAACAGGG
Seq A exon
GTAAATAAACAAGGGACATTAGCAATTAGCAAACAATCCTACATTTTGTCTTGTTTGATTTCTTTCAGTCAGACATATTAGTTTGAAATTATTCTTTGTTTCTGTGTTGACAG
Seq C2 exon
AGTGTCCCTCTGGCCCTGACATCATCCCCATTGTAGCAGGTGTGGTTGCAGGAATCGTACTGATTGGCTTAGCCCTTCTGCTCATCTGGAAGCTGCTCATGGTAATTCATGACCGCAGAGAGTTTGACAAATTTGAGAAAGAGAAAAATAATGCCAAGTGGGATACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000053232:ENSDART00000148633:13
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=0.054
Domain overlap (PFAM):
C1:
PF079657=Integrin_B_tail=FE(87.1=100)
A:
NA
C2:
PF079657=Integrin_B_tail=PD(7.1=10.7),PF087256=Integrin_b_cyt=PU(53.2=44.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGATTGTGTGGAGTGCAGACA
R:
CAATGGGGATGATGTCAGGGC
Band lengths:
254-367
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]