DreINT0083265 @ danRer10
Intron Retention
Gene
ENSDARG00000016939 | itgb2
Description
integrin, beta 2 [Source:ZFIN;Acc:ZDB-GENE-110411-4]
Coordinates
chr9:45166401-45168097:-
Coord C1 exon
chr9:45168008-45168097
Coord A exon
chr9:45166536-45168007
Coord C2 exon
chr9:45166401-45166535
Length
1472 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGT
5' ss Score
8.62
3' ss Seq
TTCTTTTGGGGTTTGAACAGAAC
3' ss Score
5.66
Exon sequences
Seq C1 exon
GAGCTGAGCAAACTAATCCCCAAATCTGCAGTCGGAGTCCTTTCTGAAGACTCCAACAATGTTGTCAACCTAATTGTGGAAGCATACAAT
Seq A exon
GTAAGTGCATGTGATTTCTAACTTGCCTTTTAAAGGAACACTCCACTATTTTAGAAAATAGGCTCATTTTACAACACTCCTTTAGAGTAAAACAGTTAAGTTCAGACAATTTCTGGGTCTGGTCAGAGCACTTTCAGCTTAATTAATATAATAATAATTCCTTACATTTATATAGCGCTTTTCTGGACACTCAAAGCACATTTACACATTGGTGGATCACCTTATCCACCACCATTAATCCACCACTAAGCTTAGCTTAGCATAGATAAAACCATTAGCATCTCGTTCAAAATCTACCAAACGTTTGGATAATTTTCCTATTTAAAGCTTGACTCCTCTACAGTTACATTGTGTACTAAGACAGATGATAAATGAAAACCTGCTATTTTCCAGGCCAATATAGCTAGCAACTATACTCTCATTTTGGCAATCAAGGAATTTTGCTGCTGTAACATAGCTGCAGCATGCACAATGATATTGTGCAGCACCTAAAAATCTTTCAACCGTGAATACATTGATGTATCTAAAGATTATCTAAAGATTCAGAACAGGCACTGCATAATATCATTGCGGCAGCGATAGTACAGCAGTAAAATTCCTTGAACATTACACTGGAATTAAATTAGTTCCTATAGCCTTATTGGCCTAGAAAATTTTAACTTTCATTTTCTGCCTGTCACAATCACCAGCAATCATAACTCCATAGATCGCTGGATCTCACTCACCATAACCTATGGACTACAATTCCGCCATTTCTGGACTACATATTCATACATGCACTTCGCCCAGACACACATGCTTCCTCATCTAGACTGATTACACTCACACCACCTGAGGATTGTCAGAGACTGATTGCACACACTATTTAAGCTACACACTCACTCATTTAGTTTGCAGAGTCTTGTTATCTGCCACAGTGACATTACAACGCTTTTTCCTAGCCCTGTTTTCCCCTGTACCTATCTTAGCCTTGTTTATCCAGTTCTCCTGTTTAGATGCCTGCCTTCGGACCTCTTGCCTGTTACTTCGACTACGATTCTGGACTGTCTGCATATATCTGTTTCCACCTGTATTGACCTTTGCTTGCCTGACCACTGATTAAACCTGCATTCGGATCCAAACTCAGTTGTTTGTGTCACTCCTTGCGTAACACTACTAGTCTTAGTACACTATATAGGTACAGTACAGAAGAGTCAAGAGTCTTTAAATTTTAAAATGATCAAAACTATTAGCTCATTTTTAAAGCGAGATGCTAATGATCTAATCCGATTGATCAATGCTAAGCTAAGATAAAATTACTCTTGCAAGACCCAAGGATTGGCTGAATGGGTTCAAAAATGGTGAAACTAATGGTAAAACTCTAGGGGAGAATGTAAAATGAGCTTATTTTTTTAAAAAAGTGGAGTATTTCTTTAATAGTAAAGGGCTGAAACACAATGATTTGTTTTAATGTTCTTTTGGGGTTTGAACAG
Seq C2 exon
AACTTAACCTCTGAAGTGATCATGGCCCATGATGCCCTCCCGAACTTTATATCTGTGAAATATTCATCAAAATGTACCGGTGGAAAAACCTTCAGTGACAATGGGAAGTGTGATAATGTGAACATTGGACTAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016939:ENSDART00000149704:9
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=FE(6.9=100),PF135191=VWA_2=PD(8.9=66.7)
A:
NA
C2:
PF0036213=Integrin_beta=FE(10.5=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:
GAGCTGAGCAAACTAATCCCCA
R:
TAGTCCAATGTTCACATTATCACACT
Band lengths:
222-1694
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]