HsaINT0082943 @ hg19
Intron Retention
Gene
ENSG00000139626 | ITGB7
Description
integrin, beta 7 [Source:HGNC Symbol;Acc:6162]
Coordinates
chr12:53585107-53585803:-
Coord C1 exon
chr12:53585643-53585803
Coord A exon
chr12:53585421-53585642
Coord C2 exon
chr12:53585107-53585420
Length
222 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TCTGCAACATCTTTCTCCAGGAC
3' ss Score
7.97
Exon sequences
Seq C1 exon
AGGGAGCAGACCACACGCAGGCCATTGTGCTGGGCTGCGTAGGGGGCATCGTGGCAGTGGGGCTGGGGCTGGTCCTGGCTTACCGGCTCTCGGTGGAAATCTATGACCGCCGGGAATACAGTCGCTTTGAGAAGGAGCAGCAACAACTCAACTGGAAGCAG
Seq A exon
GTGAGGAGACTTCCTGGTTAGGCCCCTTTTTAGCTGTTCCCCCACCACAAGACCAGCCCTGATTCCTCCCACTGGGTTCCCCCAGCCCCTGGCACATGTAACCAACCCCTCTGCTAACTTCCATCAGCTCCTAGGATTCGGCTCAAGGCTGGCCTCTTAGGTCTAGAAAGGGGACGAGGAATCCTGGGATTTTTGCTTATAATCTGCAACATCTTTCTCCAG
Seq C2 exon
GACAGTAATCCTCTCTACAAAAGTGCCATCACGACCACCATCAATCCTCGCTTTCAAGAGGCAGACAGTCCCACTCTCTGAAGGAGGGAGGGACACTTACCCAAGGCTCTTCTCCTTGGAGGACAGTGGGAACTGGAGGGTGAGAGGAAGGGTGGGTCTGTAAGACCTTGGTAGGGGACTAATTCACTGGCGAGGTGCGGCCACCACCCTACTTCATTTTCAGAGTGACACCCAAGAGGGCTGCTTCCCATGCCTGCAACCTTGCATCCATCTGGGCTACCCCACCCAAGTATACAATAAAGTCTTACCTCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139626-ITGB7:NM_000889:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.115
Domain overlap (PFAM):
C1:
PF079657=Integrin_B_tail=PD(8.5=9.3),PF0268716=FtsX=PU(90.7=90.7),PF087256=Integrin_b_cyt=PU(92.6=46.3)
A:
NA
C2:
PF0268716=FtsX=PD(7.4=33.3),PF087256=Integrin_b_cyt=PD(3.7=8.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCAGCAACAACTCAACTGGA
R:
GTAGCCCAGATGGATGCAAGG
Band lengths:
306-528
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)