HsaINT0082938 @ hg19
Intron Retention
Gene
ENSG00000139626 | ITGB7
Description
integrin, beta 7 [Source:HGNC Symbol;Acc:6162]
Coordinates
chr12:53587492-53588128:-
Coord C1 exon
chr12:53587982-53588128
Coord A exon
chr12:53587686-53587981
Coord C2 exon
chr12:53587492-53587685
Length
296 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGA
5' ss Score
8.94
3' ss Seq
TGATTCCTGCCTCTTCTCAGGTG
3' ss Score
9.69
Exon sequences
Seq C1 exon
AGCCTGTCTTCCACCGTGACCCTTGAACACTCTTCACTCCCTCCTGGGGTCCACATTTCTTACGAATCCCAGTGTGAGGGTCCTGAGAAGAGGGAGGGTAAGGCTGAGGATCGAGGACAGTGCAACCACGTCCGAATCAACCAGACG
Seq A exon
GTGAGAGCCAGCAAGCACAGGCAGAAGGCGGGCAGGGGGAGGTGGGAGTGGGAAATTAAGCAGGCAGGAAAAGATGGGTGGCAGGTACAGGGAGTGACATGAGAGCCTGAGGTAGTCCTCCATCCATCCTTCCTGGAGCAGTCTGAGTGGCTTCCTCAGGCATGTTTCTAGGAGTTGGGTGTTAACATGACCCCATCCCTTCATTTACTAAGGGGTGAGGTTCTGGATGATTGGTGAGTTTGGGGTATGTGTGTGTGCATGTGTATAACCATGGCCTGATTCCTGCCTCTTCTCAG
Seq C2 exon
GTGACTTTCTGGGTTTCTCTCCAAGCCACCCACTGCCTCCCAGAGCCCCATCTCCTGAGGCTCCGGGCCCTTGGCTTCTCAGAGGAGCTGATTGTGGAGTTGCACACGCTGTGTGACTGTAATTGCAGTGACACCCAGCCCCAGGCTCCCCACTGCAGTGATGGCCAGGGACACCTACAATGTGGTGTATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139626-ITGB7:NM_000889:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.265 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0036213=Integrin_beta=FE(11.2=100)
A:
NA
C2:
PF0036213=Integrin_beta=PD(9.1=60.0),PF079657=Integrin_B_tail=PU(5.0=6.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACACTCTTCACTCCCTCCTGG
R:
CACATTGTAGGTGTCCCTGGC
Band lengths:
305-601
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)