HsaINT0148406 @ hg19
Intron Retention
Gene
ENSG00000107290 | SETX
Description
senataxin [Source:HGNC Symbol;Acc:445]
Coordinates
chr9:135161810-135163738:-
Coord C1 exon
chr9:135163623-135163738
Coord A exon
chr9:135161882-135163622
Coord C2 exon
chr9:135161810-135161881
Length
1741 bp
Sequences
Splice sites
5' ss Seq
CAGGTATCT
5' ss Score
7.33
3' ss Seq
ACATTTGAATTTTTTTCCAGAGG
3' ss Score
7.68
Exon sequences
Seq C1 exon
AAAAAGAGTTACCTTCTCATGTTCAGGCGATGCATAAAAGAAAGGAATTTCTAGATTATCAGCTGGATGAGCTTTCCCGGCAGCGAGCTCTATGCCGAGGTGGACGGGAAATACAG
Seq A exon
GTATCTTTGCATTTCTTGAATAATAACTCAGGTATACGAACTAGTTAACAAGTTTTTTTTGAGACAGAGTCTTGCTCTGTCTTCCAGGCTGGAGTGCAGTAGCACAATCCTGACTCACTGCAGCCTCACCTTCCTGGGTTCAGGTGATCCTCCTGCCTCAGCCTCCCGAGTAGGTGGGATTACAAGGTTGTGCCGGCACACCTGGCTAATTTTCTGTATTTTTAATGGAGATGGGGTTTCACCATGTTGGCCAGGCTAGTCTCGAACTCCCGGCCTCAAGTTGATCTGCCCACCTCAGCATCCCAAAGTGCTGGGATTACAGGCATGAGCCATTGCGACCAGCCTAATTAATGAGTATTTAATGCCCTTTATTTATTGGGGAATGGCATGATTCATGTATAAAAATGTGTACTAAGACACTAAAAATGTGTCTCAGATTAACACATTTCTTTCTGCTTTTTTTTTTTTTGTCCTTTTGGTTTTAATTTTTTTTTTCATTTTTTCTTTTATTAAAATTACTTTTGTTAAAAATCTTTTTAAAAACTTTTTTGTAAAGGGCAAGATATTCTAGTAAAGATTTTAGGCTTTGCAAGCCATATGGTTGGTTTCTGTTGCAGCTATTCAACTCTGCTTTTGGTAGCACAAAGGCAGCCATAGATAATACATAAACAAATGGATGTGGCTGTGTTCCAGTAGAACTTTATTTACGAAAATAGATGGGGTGTTGCGTTTTTGTTTGTTTTTGAGATAGGGTCTCACTTTGTGGCCCAGGCTGGAGTGCAGTGGTGCAGTTGTGGTTCAATTTAGCCTCAAGCTCTTGGACTCAAGTGAGCTGTCTTTCTGCCTCAGCCTCTTGAGTAGCTGGGACTACAGCCGTGTGCCATCATGCCTGGCTAATTTTTTTGTTTGTTTTCTGTAGAAACTGGGTCTTGCCATGTTGCCCAGGGTGGTCTGAACTTCTTGCCTCAAGCAGTCCTCTCACCTTAGCCTCCCAAAGTGCCAGGATTACAGGCATGAGTCCCTGCACATGGCCTTGCATTTGGCTTATAGGCTGTACTGCCTTATATTAAAGCTATACTGAGTTTATTAGTTGCCTTTCAGTTGCATGTTGAGCCCAGTTCAAATTAGGTTAGACAGAAAGGGAATTAGCTTCAGTATGGGTGGATCCAGAGGGTCACATGATATCATTTCTCCACTCCATAATTTGTTTTTCTGTGTGTCAGCCATTTCTTCTGAGAAAGGTGAGTGTCAGCATCTCAGGGCTTCCACCATCTCAGCTTTGAAACCCCAGAGGGAGAGAAAGTCTTTCTCTTAGCATCCATATATCCAAAGAAGCAGTTAGTTTAGTCCCTGGGTGAGCAAGCAGGTCTAATCCCTATTTTTAAGAAGATGGGTGCATGATTGGCCAGGCCTGTGTTAGATGCCCATCACTGTGGCCAGAGGAATGGTTGGGGTGTGATTTACAGCCTCATTTGAATCACCTGGAAGTTAAGGGTGGCGTGATGCTCCCAGTGCTGGAATGCTAAGCAGACAGCTCACGTGCAGCGCACAGAACACAGCTGAGTCTTACGCAGCAGCATACAGAGTGTGTCAGGACTCCAGTGGTAAAGAGGAAATAAGCTGGGTAAATACATTTTTCATTGGTGAAATACAGGCTCTTTTAAAATTAGAGGTAGTCCATTGGAAGGCATTTAAAAATGCTTAGTTTAGTTTTAATTGTGACATTTGAATTTTTTTCCAG
Seq C2 exon
AGGCAAGAATTAGATGAAAACATTTCCAAAGTTTCTAAGGAAAGGCAGGAACTTGCTTCTAAAATTAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107290-SETX:NM_015046:17
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.231 A=NA C2=0.464
Domain overlap (PFAM):
C1:
PF130861=AAA_11=FE(13.3=100)
A:
NA
C2:
PF130861=AAA_11=FE(8.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGAGTTACCTTCTCATGTTCAGGC
R:
TTTAATTTTAGAAGCAAGTTCCTGCC
Band lengths:
182-1923
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
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)