HsaINT0082939 @ hg19
Intron Retention
Gene
ENSG00000139626 | ITGB7
Description
integrin, beta 7 [Source:HGNC Symbol;Acc:6162]
Coordinates
chr12:53586924-53587685:-
Coord C1 exon
chr12:53587492-53587685
Coord A exon
chr12:53587148-53587491
Coord C2 exon
chr12:53586924-53587147
Length
344 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CCTTTGCCTTCCCCTTCCAGCTG
3' ss Score
12.35
Exon sequences
Seq C1 exon
GTGACTTTCTGGGTTTCTCTCCAAGCCACCCACTGCCTCCCAGAGCCCCATCTCCTGAGGCTCCGGGCCCTTGGCTTCTCAGAGGAGCTGATTGTGGAGTTGCACACGCTGTGTGACTGTAATTGCAGTGACACCCAGCCCCAGGCTCCCCACTGCAGTGATGGCCAGGGACACCTACAATGTGGTGTATGCAG
Seq A exon
GTGAGGGCCTCCTCTTCCCTTCAACCACCTGGCTCCCAACAACCAACCAACCCTGGCCCGTATTCCTCCGCTGCTTTCCATCCCCCCCACAGGAGTCTCCTCGACATCCCGACTCCCCACTCAGTTTCATCCCTTGAAGCTTCCCATGTATGTCCAGGCCCTCCCCCTGACTGGGGCTCCCTCCACTCTCTCACCCCTCAGTGTTTCACTATACTTAACATCCTTTCAGCTGTTTGTCTGTCTCCAACTCTTTTGAGAACTTGGGTTTAGAGGTTCCTGGGAGAGACAAGTCAGGGGTGATCAAACCCTCTGACCTACTTCTCTCCTTTGCCTTCCCCTTCCAG
Seq C2 exon
CTGTGCCCCTGGCCGCCTAGGTCGGCTCTGTGAGTGCTCTGTGGCAGAGCTGTCCTCCCCAGACCTGGAATCTGGGTGCCGGGCTCCCAATGGCACAGGGCCCCTGTGCAGTGGAAAGGGTCACTGTCAATGTGGACGCTGCAGCTGCAGTGGACAGAGCTCTGGGCATCTGTGCGAGTGTGACGATGCCAGCTGTGAGCGACATGAGGGCATCCTCTGCGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139626-ITGB7:NM_000889:11
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=PD(9.1=60.0),PF079657=Integrin_B_tail=PU(5.0=6.2)
A:
NA
C2:
PF079748=EGF_2=PU(32.3=13.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTTCTCTCCAAGCCACCCAC
R:
ACAGATGCCCAGAGCTCTGT
Band lengths:
355-699
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)