HsaINT0082936 @ hg19
Intron Retention
Gene
ENSG00000115221 | ITGB6
Description
integrin, beta 6 [Source:HGNC Symbol;Acc:6161]
Coordinates
chr2:160993945-160994710:-
Coord C1 exon
chr2:160994576-160994710
Coord A exon
chr2:160994363-160994575
Coord C2 exon
chr2:160993945-160994362
Length
213 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
ATTAGTATTTTCTTTTCCAGGCT
3' ss Score
8.09
Exon sequences
Seq C1 exon
GAACTGCGGTCTGAGGTGGAACTGGAAGTATTAGGAGACACTGAAGGACTCAACTTGTCATTTACAGCCATCTGTAACAACGGTACCCTCTTCCAACACCAAAAGAAATGCTCTCACATGAAAGTGGGAGACACA
Seq A exon
GTAAGTAGCTGGCCAGTAGATAGTCTGAATAAATACCTGGATGGGTCAGAAATTAGCTGAGCTCACTGAAGCTGGATTTCTTTCAAGAATTTTAAAAGCAATTTTCAAAGATTTTCTAGTAAATGCTTTTGGCAAAGCTGATTTCCGTGAAGCCTTGTTTCACCTCGTGCATTTTGGTGGATGGAGGGAGATAATTAGTATTTTCTTTTCCAG
Seq C2 exon
GCTTCCTTCAGCGTGACTGTGAATATCCCACACTGCGAGAGAAGAAGCAGGCACATTATCATAAAGCCTGTGGGGCTGGGGGATGCCCTGGAATTACTTGTCAGCCCAGAATGCAACTGCGACTGTCAGAAAGAAGTGGAAGTGAACAGCTCCAAATGTCACCACGGGAACGGCTCTTTCCAGTGTGGGGTGTGTGCCTGCCACCCTGGCCACATGGGGCCTCGCTGTGAGTGTGGCGAGGACATGCTGAGCACAGATTCCTGCAAGGAGGCCCCAGATCATCCCTCCTGCAGCGGAAGGGGTGACTGCTACTGTGGGCAGTGTATCTGCCACTTGTCTCCCTATGGAAACATTTATGGGCCTTATTGCCAGTGTGACAATTTCTCCTGCGTGAGACACAAAGGGCTGCTCTGCGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000115221-ITGB6:NM_000888:9
Average complexity
IR-S
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:
PF0036213=Integrin_beta=FE(10.3=100)
A:
NA
C2:
PF0036213=Integrin_beta=PD(9.6=29.3),PF079748=EGF_2=WD(100=25.7),PF079748=EGF_2=PU(32.3=7.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGTCTGAGGTGGAACTGGAA
R:
CGTGGTGACATTTGGAGCTGT
Band lengths:
295-508
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)