DreINT0083046 @ danRer10
Intron Retention
Gene
ENSDARG00000042282 | itga6a
Description
integrin, alpha 6a [Source:ZFIN;Acc:ZDB-GENE-050309-23]
Coordinates
chr9:3503511-3505226:+
Coord C1 exon
chr9:3503511-3503687
Coord A exon
chr9:3503688-3505127
Coord C2 exon
chr9:3505128-3505226
Length
1440 bp
Sequences
Splice sites
5' ss Seq
GAGGTACCA
5' ss Score
6.43
3' ss Seq
GAGACCTGTGACACTTTCAGGAT
3' ss Score
5.94
Exon sequences
Seq C1 exon
GTGATTAATTTAGGAAAGCCTCTGAAGTCTTTTGGAACCGCTTCGCTAAACATCCAGTGGCCCAAAGAAAGTTCTGTGGGGAAATGGCTGCTGTATCTGATGAAGATCAACACCAGAGACCTGCAGTTGGTGACCTGTTCACCCGAGAGAGAGATTAACCCTCTAAAGCTTAGAGAG
Seq A exon
GTACCAGATAAATCCTAGTTTGCATGTTCTCGGCCATTGTTTTTTTACAGTTGAATTACAGTTGAAGTAATTATTGTGAAATTTTAATTATTGTGATCAAATTATTGTGAAATTTTCATTCTTTTAAAATATTTTCCCAAGTGCTGTTCAACAAAGCAAGGGCATTTTATTAACAGTATTCCCTTTTAAGGTTTAATTCTGGAAAAATTAAGTTAAGGTCAATATTATTAGACCTTTAAGAAATGATGTTTTCCGATTGGCTAAAGAACCAAACACTGTTGTCCAATGACTTGCCTAACCTGCCTAGTAACTAATTTAGCCTTTAAAATACACTTTAAGCTTATTACTAGCATCTTACAATATAACTTTGTAAAATATTGTGTACTGTCATGACAAAATAAATTATTATTATAATTAGTTATTATTATTATTAGTAGTAGTAGTATTAGTTATTATAAATTAGTGTGTAAAAATGTGTACATTTTAGGAAATATTAGTAAAAATAGTAAACATTTCGTAGAAGCGCTAATACATTTGTCTTTAAATTTATACAAACCTGCTGAAAAAATCAGCTTAAACCAGTCTAGGCCAGTCAGCCATTTCCAGCCTAGTTTCCAGCCATTTCCAGCCTGGTCTTAGCTGGTCAGACTGGAAAATGACCTGCTAAAACAAGCTTGACCAGCCTGGTTTTAGCTGGACATAGCTGGTTTTGGCTGGGCTCCCGGTCTGCCCAGACTGTTCAAGCTGGTTTTAGTTGGTCATCTCCAGCTAAGACCAGGCTGGAAATGGCTGGAAACCTGTTTGGAAATGGCCAAAACCCCTATAAAAACTACACTGGTTGACCAGCTAAAACCAGTCAACCACCTTAGGCTTGTTTAAGCTGTTTTTTTCAGCTGCCTCTTAATATGCTGTTTCAAAGTTTTACTTATTTTGTTTCGGATATCTCCTACAATAACAGTCTGCTTTAAGAATCCAGCCTTTTAAATCCCGCCCTTCTGAGAGTCTGCTATGATTGGTCAGATAATTTGTTGTGATTGGTTGTGAGCATGGCATTAGTGAAGCCAAGCATGTGTGTCTTGAAAACAAGAACCGTTATGTGTAGCTTTAATGCTATTTTACATAAAAGCATCTACCAAATATGTAAATCTACAGTGTTATCGTTCAGCTGAAATAGTACCTTTTCTATTTATTGTGACGTATTGTGAATATCTGAGTTAAATTAGTCAAAAATGTTGGGTGGAGCTTGATGTTGTCCTTTGAGAATTGATTGTATCACTTTTAGCTTAGCATAGGTCATTGACTTGAAGTAGACCATTAGCATCTCCCTCAAATCTGAGCAGAGTTTTGACTAAAGAGTGTTCTATTAAGAGCATTAATTGTCATTTTTAAGAAACCTATCTTGCTAAAACATGCTAAAAATGAGACCTGTGACACTTTCAG
Seq C2 exon
GATTCGTCAATCAGGAAAAAGCGGGAGCTGGAGGAGAGAAGACCGTCTGAGGGGAATAAAATATCCCTTTTCACTGACAAACGCAAACATAAGATCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000042282:ENSDART00000114168:20
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=0.212
Domain overlap (PFAM):
C1:
PF084417=Integrin_alpha2=FE(12.4=100)
A:
NA
C2:
PF084417=Integrin_alpha2=FE(6.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATTTAGGAAAGCCTCTGAAGTCT
R:
CAGGATCTTATGTTTGCGTTTGTCA
Band lengths:
270-1710
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]