HsaINT0148405 @ hg19
Intron Retention
Gene
ENSG00000107290 | SETX
Description
senataxin [Source:HGNC Symbol;Acc:445]
Coordinates
chr9:135163623-135164038:-
Coord C1 exon
chr9:135163937-135164038
Coord A exon
chr9:135163739-135163936
Coord C2 exon
chr9:135163623-135163738
Length
198 bp
Sequences
Splice sites
5' ss Seq
TGAGTAAGT
5' ss Score
8.82
3' ss Seq
TTATTTGTTATTTTTATTAGAAA
3' ss Score
6.57
Exon sequences
Seq C1 exon
GAAACTGTGGAGATATAAATTTAGTACGACTGGGTCCAGAAAAGTCTATTAATAGTGAGGTTCTAAAGTTCAGTTTGGACAGCCAAGTAAACCACAGAATGA
Seq A exon
GTAAGTACTGAATGTGGTATATACTAGTGTTTTCTCTGTTTTGTTTGGTGGAAAATGACTTGGGCACTAAAGGTAATTTGAAGCCTCCAGAATTAGTCTGGCTTTGGGAACTAATTTTCCTTCTCATTGTGTTGTATATGTGTGTGAGTTTGTTAGAATTAGAATAGCATATAATTTTTTATTTGTTATTTTTATTAG
Seq C2 exon
AAAAAGAGTTACCTTCTCATGTTCAGGCGATGCATAAAAGAAAGGAATTTCTAGATTATCAGCTGGATGAGCTTTCCCGGCAGCGAGCTCTATGCCGAGGTGGACGGGAAATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107290-SETX:NM_015046:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.029 A=NA C2=0.231
Domain overlap (PFAM):
C1:
PF130861=AAA_11=FE(11.9=100)
A:
NA
C2:
PF130861=AAA_11=FE(13.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGATATAAATTTAGTACGACTGGG
R:
CTGTATTTCCCGTCCACCTCG
Band lengths:
210-408
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)