HsaINT0082508 @ hg19
Intron Retention
Gene
ENSG00000091409 | ITGA6
Description
integrin, alpha 6 [Source:HGNC Symbol;Acc:6142]
Coordinates
chr2:173352854-173354386:+
Coord C1 exon
chr2:173352854-173352956
Coord A exon
chr2:173352957-173354212
Coord C2 exon
chr2:173354213-173354386
Length
1256 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
TATGTATTATTTTCTAACAGGTA
3' ss Score
10.11
Exon sequences
Seq C1 exon
AGTTGCTAAACCTTCCCAGGTGTATTTTGGAGGTACAGTTGTTGGCGAGCAAGCTATGAAATCTGAAGATGAAGTGGGAAGTTTAATAGAGTATGAATTCAGG
Seq A exon
GTAAGTTGGAGCAGTTGGTCTTTTCATTATACCAAAAGCTGACATATACTAGGTATGGTCTTGAGTATGTCATTTTAATAAATCAGCAATATTAATAAGCATTGTAAGTAAATCATGAGTTAAAAATTAGTTTGCCAGCTTTTAAAGAACATACTGGCTTATAGTAAAAATTTTATCCTCCAGGATGGAGAACAATTGTCACTGTTCAGAATCCAGTTCAGTTTAGAATGCGTTATGATTTATTCCTTCCTCCTTTATAAGGTCATCTTTCTCACTGCTTGTGGTTGAAAGAATATTAATGTATGCCTACCTTTCACAAGCCCAGTTTTTGTGGTGAATGTAGATTTGGTATATGCCTGTAGGAAAGGCAGTGACTGGCTCTGAACCATTTCAAAGTAGGCAATCACAGTGACTCTCTGTCCTGTTGAATAAACATAAACATAGGGTACAGAGTCTGTTCGTAACTCACACATGGGTTTAGGTCTGTGTGGCTGAAATCACATTCCTGAAGGCATAGTGACCACTGTGGTGAAAGCCTCAAATGGCAAGCATGGGCCCACCTGACTCCGGCAGAATGAAGAGGCTGAATTCTCCTCTGTGTGTCTCTTAGCATTATAGACACAGCTGGGGCAGGTGGTGGTGGTGGTTATGATCTCTATGCAGGTGCAGCTGGAAAAGAAGTCTTTGGGTTCTGGAACAGTCTCGACACCAAGAGGGCTCTTACCTCCTGTGTTTGGCTTCTGCCGCAGGACGTCACTCTGTTCCCAGCTTGGACTCTCAGATTCATGGCTGTCCTAATAATGGTTTTGCAGAATCTCCTCTGGGACAGAGGCAGCTTCATTTTTGCAGTGGATGGGGTTTTCCAGAAGCAGGTTGTTGGTACACTGCCTTGGCCCAGGACTTGTCATTGGCCAAGCAGGGTGGTTACAGGGCAGTTCACAAATTCACACATGATTTTCCCTGGGCGTATGTTGAGAACATGGTATATCTACACTGCTGATTCTGTTGCATACAGCAGTTGTTCCTAGAACGAGTTAGCTATCAGTTGTCCTTTGACCTTTTTGTTTTTATTTACAAAAATCTTTAGGCACAAGTCTTTATTTTGAATGCCCTATCTATAGTCCATTTTTGGAGCCTGTGCTTTTATTATAGGATTACGTTAGATATTTTAGCTTCTTTCTCTTGGTAAAAGGAGCTGCTACTTAAATTTACATTGAGAAGATTAGACTGAGATAATATGTATTATTTTCTAACAG
Seq C2 exon
GTAATAAACTTAGGTAAACCTCTTACAAACCTCGGCACAGCAACCTTGAACATTCAGTGGCCAAAAGAAATTAGCAATGGGAAATGGTTGCTTTATTTGGTGAAAGTAGAATCCAAAGGATTGGAAAAGGTAACTTGTGAGCCACAAAAGGAGATAAACTCCCTGAACCTAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000091409-ITGA6:NM_000210:19
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.034
Domain overlap (PFAM):
C1:
PF084417=Integrin_alpha2=FE(52.3=100)
A:
NA
C2:
PF084417=Integrin_alpha2=FE(12.0=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:
CCTTCCCAGGTGTATTTTGGAGG
R:
CGTTAGGTTCAGGGAGTTTATCT
Band lengths:
267-1523
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)