DreINT0083076 @ danRer10
Intron Retention
Gene
ENSDARG00000069946 | itga6b
Description
integrin, alpha 6b [Source:ZFIN;Acc:ZDB-GENE-050320-5]
Coordinates
chr1:30238446-30238750:+
Coord C1 exon
chr1:30238446-30238534
Coord A exon
chr1:30238535-30238622
Coord C2 exon
chr1:30238623-30238750
Length
88 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCAG
5' ss Score
4.95
3' ss Seq
TGGTTCTTTGATAATTTAAGGTT
3' ss Score
5.87
Exon sequences
Seq C1 exon
ATGTTGCTGTTAGCGCCCCATATGACAGCAATGGAGCTGGAAACGTGATTATCTTCCACGGTTCACCACAAGGACTGAAAAAATCCCAG
Seq A exon
GTGCAGCCATATATCCACTTTACTTTCTGTTTACTTATTGACACATTTTCCATACACTTTTTTATGAATGGTTCTTTGATAATTTAAG
Seq C2 exon
GTTCTTGGAGGAAAAGATCACAATGTGAAACTCTTTGGATACTCTCTTGCTGGGAACATGGATCTGGACAGAAATAATTACCCTGATCTGGCCATTGGATCTCTTTCTGATTCAGTGTTTGTGTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000069946:ENSDART00000102210:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.033 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF135171=VCBS=PD(3.3=10.0)
A:
NA
C2:
PF0183918=FG-GAP=WD(100=72.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTAGCGCCCCATATGACAGC
R:
ATCCAATGGCCAGATCAGGGT
Band lengths:
181-269
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]