GgaINT0124333 @ galGal4
Intron Retention
Gene
ENSGALG00000003661 | SETX
Description
senataxin [Source:HGNC Symbol;Acc:HGNC:445]
Coordinates
chr17:6499838-6500508:-
Coord C1 exon
chr17:6500407-6500508
Coord A exon
chr17:6499937-6500406
Coord C2 exon
chr17:6499838-6499936
Length
470 bp
Sequences
Splice sites
5' ss Seq
TGAGTAAGT
5' ss Score
8.82
3' ss Seq
TTTCCTTCAATTTATTATAGAAC
3' ss Score
8.09
Exon sequences
Seq C1 exon
GAAACTGCGGTGATATCAAATTAGTGCGACTGGGTGCTGAAAGATCAATCAACAGTGAAGTCCGGGCTTTTAGCCTGGATAAGCAAGTTGAACATAGAATGA
Seq A exon
GTAAGTAGTGTGCAAATTGGGCTTTTCTTTAGGTTTTATTTAAGTGCTGGATTATGTTATACATGTGGGACTGTATGTCCTTTAAAAAGGAGATCACGTGAAAGATTTTCTTTCTGCAATGGCATGCATTGTGCCTGAGTGCTTTGTAAGCATTCAGCACATGTACAGCCTGAAGTCGGAGTAAAACCCCCAGAAATTAAGCAACACCATTTCTAGTACATTTTAAAGTAGTAATAATAATAATAAATGCATGTTAAAGCCATTCTTTTTAAGCCATATTACTATGCATCATTCGAGAGCTACAGTTGGAACCAAGAAGTGTATCATTTTACTGTCTAAGATAAAAGACCTCAATAGGAAGAAGGAAACTGCAACAAAAAGTGACTTTCTGTTCAGTGTTAATGACGTAATGCTGTTACTGTAACCAGTTGAACTATTCCCCCTCCTTATTTTCCTTCAATTTATTATAG
Seq C2 exon
AACGAAAGCCAACTGACCGTGACCAGGATATTCAGAAGAAAAAAGCAGCTCTGGATGAGAAGCTGGACATGCTCTCTCGTCAGCGTGCCATGCACAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003661:ENSGALT00000005801:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.229 A=NA C2=0.426
Domain overlap (PFAM):
C1:
PF130861=AAA_11=FE(11.9=100)
A:
NA
C2:
PF130861=AAA_11=FE(11.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCGGTGATATCAAATTAGTGCG
R:
CATGGCACGCTGACGAGAG
Band lengths:
190-660
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]