HsaINT0082517 @ hg19
Intron Retention
Gene
ENSG00000091409 | ITGA6
Description
integrin, alpha 6 [Source:HGNC Symbol;Acc:6142]
Coordinates
chr2:173333853-173335833:+
Coord C1 exon
chr2:173333853-173334108
Coord A exon
chr2:173334109-173335701
Coord C2 exon
chr2:173335702-173335833
Length
1593 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGA
5' ss Score
9.11
3' ss Seq
TTACCATTTCATTCCTTTAGGGA
3' ss Score
11.14
Exon sequences
Seq C1 exon
ACATGTGCTCACCGATATGAAAAAAGGCAGCATGTTAATACGAAGCAGGAATCCCGAGACATCTTTGGGCGGTGTTATGTCCTGAGTCAGAATCTCAGGATTGAAGACGATATGGATGGGGGAGATTGGAGCTTTTGTGATGGGCGATTGAGAGGCCATGAGAAATTTGGCTCTTGCCAGCAAGGTGTAGCAGCTACTTTTACTAAAGACTTTCATTACATTGTATTTGGAGCCCCGGGTACTTATAACTGGAAAG
Seq A exon
GTATGACCTTTGTATTTATAGAAATAGAGATTAGTTCCCCTAATTTCTGTAATATGATTTAGTACATTTTGAGCTAAAATGTGTTAGAAGACATTCGTATATTATAAAAGTTGGGTAGGATATTAAAAATCTCTAAATGATATGATTTTTAAAAGCTAATAATAGTGGAATATATGTTTTGGTGTTGACATTCTTTTCCCCTCTACCAGTACTTTACTTTAATTCAGGTAGTTAACTTTTTTTTAGCAGGAATATAATAATTAACATTAGTATTTTTTGCTGTTTTAGATTTGTGCGACTCATGAAGCTGGAAGTGTTAATTTTAAGTTAGTGATCTGAAAACTTAGGAGGATTAAATAATGGTATATACAAATAACAGTGTATTAACATGGACATTAATAACAGAGTATTAATATGGACATTTCTCTCTGTATATGTTATTTTCAAAGGCCATGCTTTGCTAATAATTCAGTAGAGTTAGAAGGGCAGATTACAGACGAATTGGGGAATTTTGAGGTATAATTTCAGATATGTGAGGAAAAGTCGTTTGATTATTGTGATGTGAGTAAATGGAGATGTAGAGAGGTAAAGAAGAAAATGGCCCACATTTTTTGACTGTGTATGTATAGAAAATGCTATATCATAAAAGACAACCTAACTCTCATCCATGATGAAGAGAACTGCATCTGATTTGGAAATAAGCCATTTTTGAGAAATGTATTAATAATAAGTCACATAACACTTTCACTCATCAGGGAAAACTTAGGAAAATGGTCCCTTTTCCATTCAACAATTTGTTTTAATTGTGGTTCTAAATGACTCTTGAACACCTTTCTCTGTGTGCAATCTTCAAGGGTAATTTCCCTTTGCCCCCACCTCCACCCCAACAGAATCTTCATGTACAGTATTTCCCAGGTTATTTTGACCTAACTGAAATAACATGTTGAATTTAGTTTTATTTTAGCATGAATAAATGCTTTATATAGTAAAACAAAACAAAAATATCCACCAATTATGTATATTTTAATTCATGGAAAATATGGTTTACCTGCTTTATAAACCTGACCTAAAATGTCGCCATTTAAAGCCATATAGTGATTTGGGCTTACTATATGAAAACTTATGTTTTAAATTACTAATTGTAAGAATTTTTAAAAGATGAAATCTTGGTTAAAGTGATCTAAAGAAAAGATCAATATGTCTCACTTTTACACTGCAAAAAAAAGACAAATTGAGGCAGGATTACAGAGAATGTAAAATATATATATCAAGTTCATGTCATTTAAAAATTGGTTCTCTGTAGATTTTGTTAACTAAGCAAACCTTCCATTTTTCATCTAGTTTCATGGCATTATAAAGATAGTTCATGAAAATGCATGGGACAGTTTTTAATGACTCAAACAAATTTCTTTCCCATAAAAATTTACACAAATGTATTTTACAACCATAAAAGTCATCTCTGTCCTTCCTTTTTTTCCTCCAAATTTTTTTTCCTGTAACTAGTGATAGCATGGGGGATGTTTATTAGGAACCATTTATTTTCTTTTGTTTCATCTTCATTTTTTTGTTGTTTTTACCATTTCATTCCTTTAG
Seq C2 exon
GGATTGTTCGTGTAGAGCAAAAGAATAACACTTTTTTTGACATGAACATCTTTGAAGATGGGCCTTATGAAGTTGGTGGAGAGACTGAGCATGATGAAAGTCTCGTTCCTGTTCCTGCTAACAGTTACTTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000091409-ITGA6:NM_000210:4
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.002 A=NA C2=0.111
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:
AGGCAGCATGTTAATACGAAGCA
R:
AGCAGGAACAGGAACGAGACT
Band lengths:
351-1944
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)