GgaINT0124339 @ galGal3
Intron Retention
Gene
ENSGALG00000003661 | SETX
Description
NA
Coordinates
chr17:7127814-7128446:-
Coord C1 exon
chr17:7128259-7128446
Coord A exon
chr17:7127907-7128258
Coord C2 exon
chr17:7127814-7127906
Length
352 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGT
5' ss Score
9.1
3' ss Seq
GTGATAAAACTTATTTACAGAGC
3' ss Score
4.56
Exon sequences
Seq C1 exon
AAAGCTCAGGAATATGGCTATGGTCAGTCCTTAATGGCACGCCTGCAGAGACACCTAGAAGAACAAGTACAGAATAATCTTTTACGACGTCTGCCAGTTGTGCAGCTGACTGTGCAGTACCGAATGCACCCTGACATCTGCCTTTTCCCATCCAGTTATATTTATGACAAGACTCTAAAGACTGACAA
Seq A exon
GTGAGTAGCTGTCTGTTCTGATTTCTGAGCAGTGGGGATTTCAAATGAGCCTTTTCATATCAGGATTTTTTTTTTTATTCTAAAAGTTCTTGAGGGTTTGGGGGAAGATGCTTAGTGGGAGACTTGCATTTAATCTCTTAGTGCTTGCTGTTATACATAACATAACTAGTTCACTTGAAAAGGATCATACTCCTTACTGCATGGAGTTCATTTTTAGGTTTCAGTTTGTGCAGGTAACAGTGAAAATTAAGAGCTCTGGAAAAAAGCTGAAGGTTGCCTTTATGAAAATGATGGTGGAAATAAATTGTGCATCACTTTCTTATGGTTACCTAGTGATAAAACTTATTTACAG
Seq C2 exon
AGCAACAGAAGAGAACAGATGTTCTTCAGAGTGGCCATTCCAGCCCTATCTTGTTTTTGATGTAGGAGATGGCCATGAGGAGCGTGACAAAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003661:ENSGALT00000005801:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.125
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:
GCTCAGGAATATGGCTATGGTCA
R:
TCTTTGTCACGCTCCTCATGG
Band lengths:
278-630
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]