HsaINT0148411 @ hg19
Intron Retention
Gene
ENSG00000107290 | SETX
Description
senataxin [Source:HGNC Symbol;Acc:445]
Coordinates
chr9:135152447-135153644:-
Coord C1 exon
chr9:135153457-135153644
Coord A exon
chr9:135152540-135153456
Coord C2 exon
chr9:135152447-135152539
Length
917 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGT
5' ss Score
8.83
3' ss Seq
CTGCTTTTTTTTTTTTACAGACA
3' ss Score
10.54
Exon sequences
Seq C1 exon
AAAGCACAGGAGTATGGCTACGACCAGTCAATGATGGCTCGCTTCTGCAGACTGCTGGAAGAGAATGTAGAACACAACATGATCAGCAGGCTGCCCATTCTACAGCTCACTGTTCAGTACAGGATGCATCCAGACATATGCCTCTTCCCTTCTAATTATGTTTATAACAGAAACTTAAAAACAAATAG
Seq A exon
GTGAGTTCCCCTTATTGTTTGTGACCTTATTTTGTTGTAGTTTAGCTACTTATGAAGAATAGACATTTTACTGTCGTCTTAGGTCTTGTCATAAAAAGCATAAATCATGAAGGGTTAATAATTTTGTCCTGTTATAATAGCCATCATGTTGAATACAGCAAAGCACATAAAAAAGAAAAGGGGAAAAAGTCACCTATATTTATACTACCCAGAAATAATCACTGGTAACATTTTGGTATATCCACTTTCAGCAGTCCTTTTTTTTTTTTTTTTTTTTTTTGAAGACAGGGTCTCATTCTGTCACTCACACAGGATGAGTGCAGTGGCACACAGTCCTGGCTCACTGCAGCTTCGACCTCCCAGGCTCAATCAATCCACCTGCCTCAGCCTCCTGAGTAGCTGGGACTACACTCAGTCACCACCATGCCTGGCTAATTTTTGTATTTTTCTTTTTGTAGAAACGGGGTTTCGCTATGTTGCCCAGGCTGCTTTCGAACTCCTGAGCTCAAGCAATCCACCCGCCTTGGTCTCCCAAAGTGCTGGGATTACAGGCGAGAGTCACCGCACCTGGCCAAGTTTCAGTCCTTTTACTATGCATATCTTTTTTTACTTTTTAAATTTTTGAAGGAAAAATGTGGGACCATACTTAACATAGTATTCTGTGGCTTACTCTATTATGAGTGTCTTTCCAATCATACTTGTTATATTTTAATGATATAGACACCTCTCCCAGCACCAGGAAAGAAATAGAATTTGTTTTGTACCTTTCACTAATACACGTCTAGAAAAGAATATTCCTGCTATCCCCTTACTTGCCCCAGCCCACATCACCACACAGAAAAAATTGTAGTAATACCAAGATATTTTCTTAAATCTTGACTTTATTCTGAATGTTGACTGCTTTTTTTTTTTTACAG
Seq C2 exon
ACAGACAGAAGCCATTCGATGTTCATCAGATTGGCCATTTCAGCCATACCTTGTGTTTGATGTTGGAGATGGTTCAGAAAGACGGGATAATGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107290-SETX:NM_015046:21
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=0.000
Domain overlap (PFAM):
C1:
PF130871=AAA_12=PU(27.7=88.9)
A:
NA
C2:
PF130871=AAA_12=FE(15.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCACAGGAGTATGGCTACGA
R:
TCATTATCCCGTCTTTCTGAACCA
Band lengths:
279-1196
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)