HsaINT0082516 @ hg19
Intron Retention
Gene
ENSG00000091409 | ITGA6
Description
integrin, alpha 6 [Source:HGNC Symbol;Acc:6142]
Coordinates
chr2:173332209-173334108:+
Coord C1 exon
chr2:173332209-173332288
Coord A exon
chr2:173332289-173333852
Coord C2 exon
chr2:173333853-173334108
Length
1564 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
TTTCTTCCATCTGCTTGCAGACA
3' ss Score
11.06
Exon sequences
Seq C1 exon
CTGACCCCACGTCAGAAAGCAAGGAAGATCAGTGGATGGGGGTCACCGTCCAGAGCCAAGGTCCAGGGGGCAAGGTCGTG
Seq A exon
GTAAGTGTAGAGACACATGTTCATCCTATACTGTTGGACTGCTGGTTATGTGCCAGCACCAGGCTTACAGCAGGGGACAGCAGGGAGCATACATTCTAGCGAACTTACTGCTTTAAAGCAGGAATGGATGTCAAAAAGAAATCAGACTGGGCGTGGTGGCTCATGCCTGTAATCTCAATACTTTGTGAGGCCAAGGCGGGCGGATCACCTGAGGTCAGGGGTTTGAGACCAGCCTGACCAATATGATGAAACCCCATCTCTACTAAAAATACAAAAATTAGCTGGGCGTAGTGGCATGCGCCTGTAATCCCAGCTACTTGGGAGACTGAGACAGGAGAATCGCTTGAACCTGGGAGGTGGAGGTTGCAAGAGCAAAACTCCATCTCAAAAAAAAGAAAAAAAAAGAAGAAGTAATCACGTAATCAAAGCCTTATTTCTCCTGTGATTCCTGATATACTTAGAAGCAATCACACAACCTACTTTTCTTTAGAACTTTCAGATTTAAATAACTTATTAAAGAACCTTTACTAAATATTCCTACAACTCTAGATGGTATTAAAAACAAAACAAAACTAGACATCATTTCTGTCCTTGGAATTTTATAGCTTTATAGATAAGTTAGTAAAAATATGGGCATGGTCTTAGAAAGTAATAACCAGGTAGTTTTAACCTCTTGTTATTTATTCTGAGTTTTTTCAAATAGAAGGGATAGCAAAGAAAAGAGGGTTTGTTAGGTGGATTGGGCTAGATGGTCATGGTAAGGCCTTCCTGGTTGGAATATGATCTTTTTGTCTCCTTCAAAATCTGGTTGCTGTAACGAAATTTATACAGAATTTTGAGAAAAAAAATTTAGTGAACATTGAGTTTTGATATTTAAGGAATGACATTTATGGAAAATTGATTTGATACTGTATTTTTAGGCTGTGTTTACATGGAGGTTAGCCATTCATACCCTGTAGAAATTATAGAGATTATTTCTGTCTCTTCTGGCCTTGTAATTCTCTCTGCCTTTTAAAAGTAGGCATATTTTGGGAAATAATCTCAGAGCTCAGGGTGTAAGTTAGGACTGATTACAAGGAAATAGTGTGGGGAAAAGGAAATGTCTTTGTTTTAGCTGTGTTTGTTTGATCCCTATGAAAACAGGTCCATGATTTCTCTCCTCTAGAACATAATTACCCACTTTCACACTGATGTTCTGAAGGTTTATACAGCCACTAAAAGCCAATTTGAATTAAGAAAATGAAATAAGGTGTTTCTCTTTGTTTATGTGACAGGTAAATTTACAAATAAATTGCCTATGGATACAGATTGTCATTCAATTTTGGATTGGAGGATTATTCTGAGTGAGAATAAGGCACATTCTAGTTTCTATATGTCTTCATAATGGTCTCCTTAGTGCCACTTTGGGGAATATTTGCTGGTCTGGGATCCGGTCCCAAGATGAGGACATGCTTAATCATCCTCTTTAGAATTAACCTCTGTATTGACCATTTTATTCATATGTAATTTTTTAAAAACAAGGTTTATAGACAAGAATGGGCTACTTTCTTCCATCTGCTTGCAG
Seq C2 exon
ACATGTGCTCACCGATATGAAAAAAGGCAGCATGTTAATACGAAGCAGGAATCCCGAGACATCTTTGGGCGGTGTTATGTCCTGAGTCAGAATCTCAGGATTGAAGACGATATGGATGGGGGAGATTGGAGCTTTTGTGATGGGCGATTGAGAGGCCATGAGAAATTTGGCTCTTGCCAGCAAGGTGTAGCAGCTACTTTTACTAAAGACTTTCATTACATTGTATTTGGAGCCCCGGGTACTTATAACTGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000091409-ITGA6:NM_000210:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.537 A=NA C2=0.002
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
GACCCCACGTCAGAAAGCAAG
R:
CTTTCCAGTTATAAGTACCCGGGG
Band lengths:
334-1898
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)