DreINT0083041 @ danRer10
Intron Retention
Gene
ENSDARG00000042282 | itga6a
Description
integrin, alpha 6a [Source:ZFIN;Acc:ZDB-GENE-050309-23]
Coordinates
chr9:3499442-3501544:+
Coord C1 exon
chr9:3499442-3499601
Coord A exon
chr9:3499602-3501460
Coord C2 exon
chr9:3501461-3501544
Length
1859 bp
Sequences
Splice sites
5' ss Seq
AACGTAAGT
5' ss Score
10.74
3' ss Seq
CCACCTTTTTTATCCTGTAGGAC
3' ss Score
11.31
Exon sequences
Seq C1 exon
GGAGAACGGTGTGCCGGTAATTTCTCTGAGTGATCAGAAGGACATTGCTCTGGAGGTCACGGTGAGGAACAGGAATGGAGATGACGCTCACGAAGCCAAACTCGTCAGCCATTTTGATGATTCTCTCTCGTACTCTGGATTCAGATCTCTGAGAACTAAC
Seq A exon
GTAAGTGTTTTTTATTTAAAAGCTTTCTTTTACAGAAAACAATACGTTTTCCAGGATGGAGCCTTGTTTGGAAGCGCAACTCTCACGTTATTTAAAAACTGTTCATTTAACAAAAACGTTGCTGCTATAAACTTTTTTCTAGGTTTTTTTTTTTTTTTTTTTTTTTGGTGGTGGTTTCAGTAGATTAAATTGATCAATTTTACATCGATTGGCCAGAGTGTCATGAAATTTCGTGAATTTTCTGGATTTTAAAAAGGTCTATTCTAGATATTAAAAGTCATGAATTTTTAATATATTTTTGCACTGGTCATGGAATTTCAGAAATTTTTGTTTGTCACTTTAAATTGTCAATTTTTACTATATTTTGTATGTTCTAGTATGTTCTAAGGCAAACAATATCTAAGATATTCTATATTTTAAGGGCTTTGGCTCCAAAATTACCATTTTAAAGACGGAGTGTTACAAAGTAGATGACAGAAAGCTGCATCTAAAGTTGGTCAAATCACTATTGAGCTAGCAAATATGTATGGGAACATTTGAATGTAAGTACCTCAGATTTAGTTTTTTGTTTTTAAAATCTGAGGGCTGTACTGTATCCATTGATGTCCTGCAAAGTCATGCAAAATGATATTAAATCTAAAACCCATTGTTAGTATTCTAACATTATTTTACTGTTATGTTATTAATATAGATGACAACAGTGGTCTGCTTTTTTGTTTAATAAATGTCATGGAAATTCAGCGTTTTAAATCAGTGAAATTCAGGGAATTTTATATTTAAAGTGAGAACCGTGAAAGGGATAGTTCACCCAAAAATGAATGTTTTCTCACCATTTCCTCCCAAGTGGTTCTAAACTTATGCGTTTTTTGTTTTGTTTTTTAAATACTATGAAAGTGCTATGAAAGTACTATGACATTCAAAAGCTAACATTCTTTAGTAAATCTTTGTGTTCAACAGAAACTCAAACAGGTTTGAAACAAGGTCAGTAAATGATGACAGAATGAAACATTTTAGGGTGAACTATACCCTTAAATTACATTTTCTTTTGTTTTTGCAGTCAATCACTCATGATAATCCATGTTTTCACTGAAGTTTTAACAGTAGTAGACTCTAAATGTAAAGGTCTTTAAGGCCGTACTCACACTAGGTACAGTTGCCTCGAACCGGGCCAAAGCACGCTTGTCCCTCCTCCCGTCTCCCCCGACGGCCCGCACTCACACCACAATCGGGCCTCGGCACGCTTACGTCATTGCTGCTGCGCTGTTCAGTGAGAAGCGCTCTCTCACTCAGCAGCACAGTGGAGATTTCTCTATTTATATCGTTTCAATCGTTTGATATGCAGTGACATGCAGTCAAAAATTTCACCAAACAGTCCTTAGGGATGCGGGGACACGCAGTCAGATATTTTGCCGAACAGATGCGCCACTTTTAGCGCTCAAAAACAATCATAAAGCCCTCGTGCTGCTGCTGCAGGAATGAGGAGGTCTGCTGAAGGCGCGCAGCTGTCGTGCAGTGAGGAGTTCTCGTCTTTAATAAACCACGGCAGTTTGCGTTCACTGAACAGTAAGAATGATTAATAAATCCAGATGAAACAGACCCTTAAATGTCACGTCTCGCTTTCAGTTTCGGGCTTTGGCGCGTTTTGCACTCGCACACAAGCGTACCACGCCAGGCACACCTCTTCCAACCGGGCCAGGGCCGGCCAAGTGAACCGTGCTTGAGCCCGATTCAGCGCACTTACACTTCTCAAACGATCCGGGAAACGGGCCTGGGCACGGTACGGATGGCATAGTGTGAGTAGGCCCTAAGAGTAACCCAGCAGTACAACTAACCGACAATCCACCTTTTTTATCCTGTAG
Seq C2 exon
GACAAACATGTGATCTGTGCAGCCAATCAGAATGGTTCCCTGGCAGACTGTGAACTGGGAAACCCTTTTAAACGGGATTCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000042282:ENSDART00000114168:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.037 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF084417=Integrin_alpha2=FE(11.3=100)
A:
NA
C2:
PF084417=Integrin_alpha2=FE(5.8=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:
GGTGTGCCGGTAATTTCTCTGA
R:
TCCCGTTTAAAAGGGTTTCCC
Band lengths:
230-2089
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]