HsaINT0082788 @ hg19
Intron Retention
Gene
ENSG00000150093 | ITGB1
Description
integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12) [Source:HGNC Symbol;Acc:6153]
Coordinates
chr10:33208813-33209313:-
Coord C1 exon
chr10:33209173-33209313
Coord A exon
chr10:33209013-33209172
Coord C2 exon
chr10:33208813-33209012
Length
160 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGT
5' ss Score
9.81
3' ss Seq
ATCTTTTTTTTCCCTTCAAGGTT
3' ss Score
10.83
Exon sequences
Seq C1 exon
TCCCTTTCCTCAGAAGTCATTTTGGAAAACGGCAAATTGTCAGAAGGCGTAACAATAAGTTACAAATCTTACTGCAAGAACGGGGTGAATGGAACAGGGGAAAATGGAAGAAAATGTTCCAATATTTCCATTGGAGATGAG
Seq A exon
GTATGTTGTATAAAGCATTTTCTGTAGAAAACATTGGTTATTTATAAGCAAATTTAGTTTATAGTTTGAGAAACATTAAAATAAGTGAGCAACTTTTTGAAATATTTTTTAGTAGATTTAAATTGTTTAGTTGGTTGTTAATCTTTTTTTTCCCTTCAAG
Seq C2 exon
GTTCAATTTGAAATTAGCATAACTTCAAATAAGTGTCCAAAAAAGGATTCTGACAGCTTTAAAATTAGGCCTCTGGGCTTTACGGAGGAAGTAGAGGTTATTCTTCAGTACATCTGTGAATGTGAATGCCAAAGCGAAGGCATCCCTGAAAGTCCCAAGTGTCATGAAGGAAATGGGACATTTGAGTGTGGCGCGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000150093-ITGB1:NM_002211:10
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(10.7=100)
A:
NA
C2:
PF0036213=Integrin_beta=PD(9.3=59.7)
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:
AACGGCAAATTGTCAGAAGGC
R:
CCTTCGCTTTGGCATTCACAT
Band lengths:
254-414
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)