DreINT0083045 @ danRer10
Intron Retention
Gene
ENSDARG00000042282 | itga6a
Description
integrin, alpha 6a [Source:ZFIN;Acc:ZDB-GENE-050309-23]
Coordinates
chr9:3503324-3503687:+
Coord C1 exon
chr9:3503324-3503426
Coord A exon
chr9:3503427-3503510
Coord C2 exon
chr9:3503511-3503687
Length
84 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAAT
5' ss Score
1.19
3' ss Seq
GATTTTTATCTTTTTCGCAGGTG
3' ss Score
9.9
Exon sequences
Seq C1 exon
GGTTGCCAAGCCCTCTCAGGTCTATTTTGGAGGTGAAGTCAAAGGCATGAGCGCTATGAAGAAGGAGGAGGAAGTCGGCAGCTTGATTGAATATGAATTCAGA
Seq A exon
GTAAATGCTACAAACATTTTCAATATGCCTTTTTAGAAATCACTTTAGTTGTTTTTTTAAATCTGATTTTTATCTTTTTCGCAG
Seq C2 exon
GTGATTAATTTAGGAAAGCCTCTGAAGTCTTTTGGAACCGCTTCGCTAAACATCCAGTGGCCCAAAGAAAGTTCTGTGGGGAAATGGCTGCTGTATCTGATGAAGATCAACACCAGAGACCTGCAGTTGGTGACCTGTTCACCCGAGAGAGAGATTAACCCTCTAAAGCTTAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000042282:ENSDART00000114168:19
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:
PF084417=Integrin_alpha2=FE(7.3=100)
A:
NA
C2:
PF084417=Integrin_alpha2=FE(12.4=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:
AGGAAGTCGGCAGCTTGATTG
R:
GTCACCAACTGCAGGTCTCTG
Band lengths:
169-253
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]