HsaALTA0004397-2/2 @ hg19
Alternative 3'ss
Gene
ENSG00000150093 | ITGB1
Description
integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12) [Source:HGNC Symbol;Acc:6153]
Coordinates
chr10:33195393-33197462:-
Coord C1 exon
chr10:33197296-33197462
Coord A exon
chr10:33195491-33195508
Coord C2 exon
chr10:33195393-33195490
Length
18 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGT
5' ss Score
11.81
3' ss Seq
ATTTATTTATTTTGAGACAGTCT
3' ss Score
0.24
Exon sequences
Seq C1 exon
AGTGTCCCACTGGTCCAGACATCATTCCAATTGTAGCTGGTGTGGTTGCTGGAATTGTTCTTATTGGCCTTGCATTACTGCTGATATGGAAGCTTTTAATGATAATTCATGACAGAAGGGAGTTTGCTAAATTTGAAAAGGAGAAAATGAATGCCAAATGGGACACG
Seq A exon
TCTCTCTCTGTCGCCCAG
Seq C2 exon
CCTGGAGTGCAGTGGTGTGATATCAGCTCACTGCAACCTCTGACTTCCAGATTCCAGCAATTCTCCTGCCTCAGCCTCCCGAGTACCTGGGATTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000150093-50-51,50-50-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF079657=Integrin_B_tail=PD(6.7=10.7),PF087256=Integrin_b_cyt=PU(53.2=44.6)
A:
NA
C2:
PF087256=Integrin_b_cyt=PD(3.6=2.6),PF139001=GVQW=PU(92.1=89.7)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCATGACAGAAGGGAGTTTGCT
R:
GTCAGAGGTTGCAGTGAGCTG
Band lengths:
105-123
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)