HsaALTD0003350-2/2 @ hg19
Alternative 5'ss
Gene
ENSG00000115221 | ITGB6
Description
integrin, beta 6 [Source:HGNC Symbol;Acc:6161]
Coordinates
chr2:161051880-161052931:-
Coord C1 exon
chr2:161052900-161052931
Coord A exon
chr2:161052727-161052899
Coord C2 exon
chr2:161051880-161052126
Length
173 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
TTTCCTGTTGGGCTTTGCAGGTG
3' ss Score
9.99
Exon sequences
Seq C1 exon
AATTTTACTCATCCATCTGGAGTTGGCGAAAG
Seq A exon
GTGTGATACCCCAGCAAACCTTTTAGCTAAAGGATGTCAATTAAACTTCATCGAAAACCCTGTCTCCCAAGTAGAAATACTTAAAAATAAGCCTCTCAGTGTAGGCAGACAGAAAAATAGTTCTGACATTGTTCAGATTGCGCCTCAAAGCTTGATCCTTAAGTTGAGACCAG
Seq C2 exon
GTGGTGCGCAGACTCTGCAGGTGCATGTCCGCCAGACTGAGGACTACCCGGTGGATTTGTATTACCTCATGGACCTCTCCGCCTCCATGGATGACGACCTCAACACAATAAAGGAGCTGGGCTCCCGGCTTTCCAAAGAGATGTCTAAATTAACCAGCAACTTTAGACTGGGCTTCGGATCTTTTGTGGAAAAACCTGTATCCCCTTTTGTGAAAACAACACCAGAAGAAATTGCCAACCCTTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000115221-11-13,12-13-2/2
Average complexity
Alt5
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=0.018
Domain overlap (PFAM):
C1:
PF0036213=Integrin_beta=FE(26.3=100)
A:
NA
C2:
PF0036213=Integrin_beta=PD(23.7=64.3)
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCATCTGGAGTTGGCGAAAG
R:
TGGTGTTGTTTTCACAAAAGGGG
Band lengths:
245-418
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Autistic and control brains
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)