DreINT0083056 @ danRer10
Intron Retention
Gene
ENSDARG00000069946 | itga6b
Description
integrin, alpha 6b [Source:ZFIN;Acc:ZDB-GENE-050320-5]
Coordinates
chr1:30239472-30239799:+
Coord C1 exon
chr1:30239472-30239533
Coord A exon
chr1:30239534-30239635
Coord C2 exon
chr1:30239636-30239799
Length
102 bp
Sequences
Splice sites
5' ss Seq
TGAGTAAGT
5' ss Score
8.82
3' ss Seq
TTTTTCCTCATCTTCTTTAGAGG
3' ss Score
8.55
Exon sequences
Seq C1 exon
CCTTGATGTGAAAGCCTGCTTCAAATTTTCTGTCAAACCCAAAACCTACAATCCAACTCTGA
Seq A exon
GTAAGTACATGTCTAACTTACTTATCAGTAAATTAATCAGCGGTTGTTCATCTCTGTCGAGCAGAAGATCATCTCCATATTATTTTTCCTCATCTTCTTTAG
Seq C2 exon
AGGTGGCATACACCATCAGGGTTGAATCTGAAAGGAAAAAACTAAATCTTCCTTCTAGAGTCATTTTTAATCCACGCTCAAACAATGATTATGAAAGCACTGGGATTGTGGAGCTCAAGGGTCAAGGCACAGAAAGCTGCATCTACAGAAATCTCATGCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000069946:ENSDART00000102210:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.055
Domain overlap (PFAM):
C1:
PF084417=Integrin_alpha2=FE(4.5=100)
A:
NA
C2:
PF084417=Integrin_alpha2=FE(11.6=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:
CCTTGATGTGAAAGCCTGCTT
R:
CTGCAGCATGAGATTTCTGTAGA
Band lengths:
226-328
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]