HsaINT0082510 @ hg19
Intron Retention
Gene
ENSG00000091409 | ITGA6
Description
integrin, alpha 6 [Source:HGNC Symbol;Acc:6142]
Coordinates
chr2:173354213-173355850:+
Coord C1 exon
chr2:173354213-173354386
Coord A exon
chr2:173354387-173355751
Coord C2 exon
chr2:173355752-173355850
Length
1365 bp
Sequences
Splice sites
5' ss Seq
ACGGTATGT
5' ss Score
9.94
3' ss Seq
TTGGATATAATTTTTTTCAGGAG
3' ss Score
6.02
Exon sequences
Seq C1 exon
GTAATAAACTTAGGTAAACCTCTTACAAACCTCGGCACAGCAACCTTGAACATTCAGTGGCCAAAAGAAATTAGCAATGGGAAATGGTTGCTTTATTTGGTGAAAGTAGAATCCAAAGGATTGGAAAAGGTAACTTGTGAGCCACAAAAGGAGATAAACTCCCTGAACCTAACG
Seq A exon
GTATGTCGGTAGATTTATCTAATGTCTCCATAAATGCAAATTAGAGAAACTAACTTGTTAGGGGAAAATCATTACTGTTCTTAGGAAAGTGGCATATTCTGGCAGGTTGACTTTCTCTTTGGTTGTCACAATTTCTCTTTTCTAGTTGGGTAACTGAGGGAGGCTGAGGCATTTTTGCTGGTTAATGACCATTATAGTACATAAGGCAGAGTCATTCAGTGCTTGCTGAGGCAAATGGTATTTTCTGATGTTTCATCATGACCCAGTATGTTACATAATAAGGAGAACTGGGGGATGCTCCTGGGGTAATAGTAGCTGCTGTTATCCAGGGGCCAGCCAGTGTTCACTCCAAGTAGAACCAAACTCATTGGAAAAGATAATGGCATCTCAGCAAGTAACCTTGAAAGCTTTTTATGCTTATTTTTAAAATAGTAATTATTTATTGTGTACTCATTGTGTCTCAGGAACTATGCTAAGCATTTTGTTTTCATTTTCTCATTTCATTCTCTGGATGGTCCTATGAGGGCGTTTCATTATCCTCACCATTTCACAGATGAGGACATTAAGATTCAGAGAGCAAGTAACTCTCTCAGTCACTCAGGCGTTAAGAGACAGATTCCACATACAAGCCCTGCTCTGCCTGATGTCAAAGCCTGTACTGTTAACCCCTCTCTCTATACTGCTCCATGCTTAGATAACTGGCCTATCATTTGTGTTCCAGTTTGATGAAGGTTTGCATGTTTATTTCTTTTATTTTAAATTCTAAGGTGACTGGGTATGATCAGTGATCAGAGTTGGTGGCTTATAGCATGATCTTCTACTCATCAATGTTAAAAATCAAGATAATCGGTTATTACTAATCTTTGCTATAAGGAAAATGCAATTTTAAAAGTTCTTGTATGGCTTAGTTTTCATTGCTCTGCTCTGAATGAGCTATATAATGGGTCTTTTTGCTTCTTTCTCTGTTCTTCAGTGTCACTTATTCCTTCAAGATGTGCTGACTACCATGTTTTAGGAACAGAGCTGGAGGCTAGGGATACAGGAATAAGATTTGATCTCTGATCTCAGTATGCCCACAGTTTGGTGGGGATACAGAGGAACAAAGAAAGCATATTTCTCTTTCTCTGAGTTTTAAGGTCAGAGTGGGAATGAATTACTTAGTCCTATGAGTAAATCAATAAACTTGAATTTAGAGTGATAATACTTGCTGGTTTTACACTTACTTCTGTGCCTTTGGCAGGAGAGAGGCAAATATTGTTGATTATGTGAATCTGGCACTGTTTGGGAGGATATGCTCAAGAGGCTTGTATGGTAATGACAAAGAATTACATAAATTGGAACTATTTTGGATATAATTTTTTTCAG
Seq C2 exon
GAGTCTCACAACTCAAGAAAGAAACGGGAAATTACTGAAAAACAGATAGATGATAACAGAAAATTTTCTTTATTTGCTGAAAGAAAATACCAGACTCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000091409-ITGA6:NM_000210:20
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.034 A=NA C2=0.209
Domain overlap (PFAM):
C1:
PF084417=Integrin_alpha2=FE(12.0=100)
A:
NA
C2:
PF084417=Integrin_alpha2=PD(6.2=12.1)
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:
AGGTAAACCTCTTACAAACCTCGG
R:
AAGAGTCTGGTATTTTCTTTCAGCA
Band lengths:
262-1627
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)