HsaINT0082888 @ hg19
Intron Retention
Gene
ENSG00000132470 | ITGB4
Description
integrin, beta 4 [Source:HGNC Symbol;Acc:6158]
Coordinates
chr17:73746192-73746941:+
Coord C1 exon
chr17:73746192-73746349
Coord A exon
chr17:73746350-73746760
Coord C2 exon
chr17:73746761-73746941
Length
411 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
ACCCCTGTCCCTGGGGGTAGGTA
3' ss Score
8.3
Exon sequences
Seq C1 exon
ATGAACTGGACCGGAGCTTCACGAGTCAGATGTTGTCATCACAGCCACCCCCTCACGGCGACCTGGGCGCCCCGCAGAACCCCAATGCTAAGGCCGCTGGGTCCAGGAAGATCCATTTCAACTGGCTGCCCCCTTCTGGCAAGCCAATGGGGTACAGG
Seq A exon
GTAAGGCGGGGGGCTGAGGGTCACGACAGGTGGATGGGCGGTCTGGCACCAGCACTCACAGAAGAGGTGGGCCGTCCAAGGCCAGGGCCCCCTGAGAGAGAGCAGACAGTGGAACCTAGCACAGGTGGTCAGAGGGAAACCCGGTCTGTGCTGGGAAAGAGGGAAGACCCATTCCTGAGTTTATCAGACATTTGCCCTCCTTCCTAGAATGGGGCCCCCTCCCACCCCCGCATGGGAGATACCCCCACCTGCTCTGCCCTAGTCCTGACGTGTGCACATGGCAGATCTCTCAGCCCCTCCCTCGGGCCTCATCTGTGCAAAGAGGACAGTAAGGGCAGAGGTCAGAGGAGGGACAGGCAGCTTGGGTGCCTGCTGCTCCCTGCTGACCAGGACCCCTGTCCCTGGGGGTAG
Seq C2 exon
GTAAAGTACTGGATTCAGGGTGACTCCGAATCCGAAGCCCACCTGCTCGACAGCAAGGTGCCCTCAGTGGAGCTCACCAACCTGTACCCGTATTGCGACTATGAGATGAAGGTGTGCGCCTACGGGGCTCAGGGCGAGGGACCCTACAGCTCCCTGGTGTCCTGCCGCACCCACCAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000132470-ITGB4:NM_001005619:27
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.491 A=NA C2=0.131
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(37.0=56.6)
A:
NA
C2:
PF0004116=fn3=PD(60.5=80.3)
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:
ATGAACTGGACCGGAGCTTCA
R:
CAGGACACCAGGGAGCTGTAG
Band lengths:
322-733
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)