HsaINT0082890 @ hg19
Intron Retention
Gene
ENSG00000132470 | ITGB4
Description
integrin, beta 4 [Source:HGNC Symbol;Acc:6158]
Coordinates
chr17:73747055-73748437:+
Coord C1 exon
chr17:73747055-73747192
Coord A exon
chr17:73747193-73748254
Coord C2 exon
chr17:73748255-73748437
Length
1062 bp
Sequences
Splice sites
5' ss Seq
ACCGTAAGA
5' ss Score
6.66
3' ss Seq
AAGCACTCTCTCTGCCCCAGGAC
3' ss Score
6.92
Exon sequences
Seq C1 exon
TGCCCAGCGAGCCAGGGCGTCTGGCCTTCAATGTCGTCTCCTCCACGGTGACCCAGCTGAGCTGGGCTGAGCCGGCTGAGACCAACGGTGAGATCACAGCCTACGAGGTCTGCTATGGCCTGGTCAACGATGACAACC
Seq A exon
GTAAGAACCAGATCCTTCTTTCCTGCCCACAGGGAGAACAGCCATGGAAGGGGAGGGGACAAAGCTGGAGGGAGCTCTTGGTCACTCCCTGGACCTGCTGTGCAGGGCACTCGAGGCCTTCATCCTGGTCAGCGGATAAGCCTGAGGCATCTTTAGGGTTTTGGCCAGATTTGGGCTGGGTTGCATTCTAAGACCAAACCCAGAAGGTTGCAGGGTGGGTGGTTACCTATGTGGAGTGAGGTCACAGGCCCAGGGGTACCCCTCCCCATGCAGGTAACCAGGGAGCTCACACGTGCATGGTTTTCTTAGGGTGAGAGGAAAGTTACCGGATTTAGCAAACAGAAATACAGGAGGTTCTGAATTTCAGATAGCACTTTAAAAGATTATTTTGTACATTGAGAGGCCGAGGCAGGTGGACTGCTTGAGGTCAGGAGTTCAAGACCAGCCTGGCTAACATGGTGAAACCGTTTCTACTAAAAATTAGACAGGCATGGTGGCTCATGCCTGTAGTCCCAGCTAGTCAGGAGGCTGAGGCAGGAGAATCACTTGAACCCAGAAGGCGCAGGTTGCAGTGAACCGAGATCGTGTTACCGCACTCCAGACAGGGTGACAGAGCCAGACTCCGTCTAAAAATAAATAAATAAAAAGGATTATTTTATACATTATTTTATCTAGCAGCCCGAGATCAGAGGTGCCTAGCAGAACAGTTATTTCTCCAGTCCTGGAAGGGAGGCAGGGTGGGCAACCCCTATGCGTGCCCTTGCCTTGTGTGGAGGCACCGTGGATATATGGGTAGAGGTGACATCGAGGCCAACTTGAGTCCAGCCCTGGCTCTGCCACTTACTCAGCAGAGTCCCTTGGAGGACTGGTGACATATGTCCACGCCAGTCATGCTGACGCTCAGGGCTCCGCAGGCGGCAATTCAGCAGTGGCTGGCTTTGCCTTGCTTCCCCAGCCCCTGGGTGCCATCCAGGGGATGCACGGCCGTCCTGCTGTGTCAGGGGTGGTGTTGGGACCAGGCTGGGACCTGGGTGACCCTCTGAAGCACTCTCTCTGCCCCAG
Seq C2 exon
GACCTATTGGGCCCATGAAGAAAGTGCTGGTTGACAACCCTAAGAACCGGATGCTGCTTATTGAGAACCTTCGGGAGTCCCAGCCCTACCGCTACACGGTGAAGGCGCGCAACGGGGCCGGCTGGGGGCCTGAGCGGGAGGCCATCATCAACCTGGCCACCCAGCCCAAGAGGCCCATGTCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000132470-ITGB4:NM_001005619:29
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.064 A=NA C2=0.261
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(48.9=93.6)
A:
NA
C2:
PF0004116=fn3=PD(50.0=72.6)
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:
CGTCTGGCCTTCAATGTCGTC
R:
TGGACATGGGCCTCTTGGG
Band lengths:
304-1366
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)