HsaINT0082501 @ hg19
Intron Retention
Gene
ENSG00000091409 | ITGA6
Description
integrin, alpha 6 [Source:HGNC Symbol;Acc:6142]
Coordinates
chr2:173349510-173349992:+
Coord C1 exon
chr2:173349510-173349670
Coord A exon
chr2:173349671-173349848
Coord C2 exon
chr2:173349849-173349992
Length
178 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
ACTGCATGCTTTTCATGCAGGAT
3' ss Score
8.58
Exon sequences
Seq C1 exon
CAATTGTGGGCACACTTGAAGCTGAAAAAGAAAGAAGAAAATCTGGGCTATCCTCAAGAGTTCAGTTTCGAAACCAAGGTTCTGAGCCCAAATATACTCAAGAACTAACTCTGAAGAGGCAGAAACAGAAAGTGTGCATGGAGGAAACCCTGTGGCTACAG
Seq A exon
GTGAGGGCTGCAGATGGTCACATCTGTTTTATGAAGAGGACAGAAAAAGGTTATATGGTGATATACAGATTTCTGAAATTTATTCTGGCAACCTCTTAATCAATACAAAATCATTGTTTTGGAATTCCCCAATAGCATGTACACCCCACTTAACTCTGACTGCATGCTTTTCATGCAG
Seq C2 exon
GATAATATCAGAGATAAACTGCGTCCCATTCCCATAACTGCCTCAGTGGAGATCCAAGAGCCAAGCTCTCGTAGGCGAGTGAATTCACTTCCAGAAGTTCTTCCAATTCTGAATTCAGATGAACCCAAGACAGCTCATATTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000091409-ITGA6:NM_000210:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.278 A=NA C2=0.375
Domain overlap (PFAM):
C1:
PF084417=Integrin_alpha2=FE(11.1=100)
A:
NA
C2:
PF084417=Integrin_alpha2=FE(9.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGGCTATCCTCAAGAGTTCAGT
R:
TGAGCTGTCTTGGGTTCATCTG
Band lengths:
255-433
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)