HsaINT0082797 @ 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
chr10:33214799-33217192:-
Coord C1 exon
chr10:33217022-33217192
Coord A exon
chr10:33215038-33217021
Coord C2 exon
chr10:33214799-33215037
Length
1984 bp
Sequences
Splice sites
5' ss Seq
TTGGTAGGA
5' ss Score
5
3' ss Seq
TACCATTTTTTTCTTGGCAGGAT
3' ss Score
9.14
Exon sequences
Seq C1 exon
GGGAGCCACAGACATTTACATTAAAATTCAAGAGAGCTGAAGACTATCCCATTGACCTCTACTACCTTATGGACCTGTCTTACTCAATGAAAGACGATTTGGAGAATGTAAAAAGTCTTGGAACAGATCTGATGAATGAAATGAGGAGGATTACTTCGGACTTCAGAATTG
Seq A exon
GTAGGAATGTTGGGAACATTGACCATTTTCATTATAAAGTCTTGGCAATTCTCAAATGTTGTTTTATATTTTATTCCTTTGTTACTCACAACATACTTGTGAGATAAACAAGCCAGTTTTTTAGCCTTTTCTGAGTGGAAGTTGATATTCCAGTCACACGTTTAATAATCTTTTCTGCCACCTTGTTCCTCTGTCACTGGATGCTACTGTTTGACACAGATTGTACCTCATAGATAATGACTTGCATGCTTATTTTCATACTAACTTGATCATTTATCTTATGACTTACTTTATTTTATTTTTAAGAGTTTCACTCTTGTCGCCCAGACTGGAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTCCGCTTCCCGGGTTCAAGTGATTTTCCTGCCACAGCCTCCCGAGTAGCTGGGATTACAGGCATCTGCCACCACCCCCAACTAATTTTTTGTATTTTTAGTAGAGATGGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTAATCCAGCTGCCTTGGCCTCCCAGAGTATTGGGACTACAGGCGTGAGCCACCATGCCTGGCCCTTATGACTTATTTTATAAACATGTGTTGAATACCCAGATTTTATCTAATTGCTAATTAGTATGTCTGCACCTGCCCGTACAGCCTGATCTCATCTTAGACCTGGATTTTTCATATGATGATGATCTGCTTTCCAAACCTTATTTTTCCCATTTCATGCATCCCCAGCTTAACCTCTTTTTTGCCTGCTTCTCTCCACTCCTGTTGCTCTAGAGGTTTAGCAACAGAATATTAGAAAGATTTGACAGTTATGAGGCCTAAGAGCTGCCTTTCAAAAATTAGCCCTATTTTAGTGGAAACATTTAAAAATAGCACTTGCTTAAAATGTTCTTTTATTCTGTAAGCATAATTCAAGGACCATGGCATTAGGGAGCTCCTATCAAATTAGTGTTTTTTAAAATGGCCAGAATTCTAGAATATTTGTTTATTCATTTGTTCAGCATGTCATTATTGAGAGCTGGTGTGCCAAGAAAATGAATGTGAGTTATTTTTAAAGTAGGGAGGCAAAATAAAAAGATTGTCTTAGGTCTTAGTCCATTTGTGCTGCTTTAAGAAAATACTATAAACTGGGTGGCTTATGAACAACAGAAATTTATTTCTCACAGCTCTGGAGGTGAGAAGTCCAAGATCCAGGCAGATTGAGCATCTGGTGAGGTCCCTCTTCTGGGTTCATAGATGATACCTTCTTGCGATGTACTCACATAGCAGCAGGGAGACAGCAGCTCTCTGGGGCTTCTTTGATGAGGTCACTGTAGGAGTCTATTCTTACGTTGCTATAAAGACATATCTGACACTGGGTAATTTATGAAGAAAAGAGGTTTAATTGGTTTACGGTCCTGCAAGCTCTACAGGAAGCATGGCGCTAGCATCAGCAAGGCCTCTGGGGAGGCCTCAGGAAGCTTCCAATCGTGGCAGAAGGCAAAGTGGGGAGCAGGCTTCTCACATGGTGGGAGCAGGAGCAAGAGTTGGGGAGAGATGCCACACAATTTTAAATAACAGATCTCATGAGAACTCACTCACTGTGGTCAGAATAGCACCAAGCCATGAGGGATTGATCTGCCCCCATGATCGAAATACCTTCCACCAGGCCGTACCTTCAACATTGGGGATCACATTTTAACATGAGACTTGGGCGGGGACAGATACCCAAACTGTATCAGTTACTAATCCCATTCATGAGGGCTCTGCCCTCATGATCTAATCACCTTCCAAAGGAACCACTTCCTAATACCATCATGTTGGGAATTAGGTTTTCAATGTAGGAATTTTGGGGTAACACAGACATTCAGTCCATAGTAACCTACATTTGGTAACATAGATGAATTTTTTAAACAATGCAAATCTCTGTCTTTCCATCTATCCATCCATTCATTCATTTATGTACCATTTTTTTCTTGGCAG
Seq C2 exon
GATTTGGCTCATTTGTGGAAAAGACTGTGATGCCTTACATTAGCACAACACCAGCTAAGCTCAGGAACCCTTGCACAAGTGAACAGAACTGCACCAGCCCATTTAGCTACAAAAATGTGCTCAGTCTTACTAATAAAGGAGAAGTATTTAATGAACTTGTTGGAAAACAGCGCATATCTGGAAATTTGGATTCTCCAGAAGGTGGTTTCGATGCCATCATGCAAGTTGCAGTTTGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000150093-ITGB1:NM_002211:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.001 A=NA C2=0.037
Domain overlap (PFAM):
C1:
PF0036213=Integrin_beta=FE(13.2=100)
A:
NA
C2:
PF0036213=Integrin_beta=FE(18.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCTGAAGACTATCCCATTGACCT
R:
TGGCATCGAAACCACCTTCTG
Band lengths:
353-2337
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)