GgaINT0046556 @ galGal3
Intron Retention
Gene
ENSGALG00000012513 | STAM2
Description
NA
Coordinates
chr7:37042671-37043057:-
Coord C1 exon
chr7:37042982-37043057
Coord A exon
chr7:37042767-37042981
Coord C2 exon
chr7:37042671-37042766
Length
215 bp
Sequences
Splice sites
5' ss Seq
ACAGTGAGT
5' ss Score
8.34
3' ss Seq
AGTTGTGTTTCTGTTGTCAGCTT
3' ss Score
5.99
Exon sequences
Seq C1 exon
GGCAAAGGATTGCCTTAAAGCCATCATGAGGAGAGTAAATCATAAAGTTCCCCATGTGGCTCTGCAAGCGCTCACA
Seq A exon
GTGAGTAGCCTGTCACTATCTTCCAAAACTTCTGTATTTCTTCATGTAATGGAGCTATTAAGTGTGTGCTAATCAATTAATAAGTTTCTGTATATCTTCAGTAGAAGTCACTGGGAGCGTTCATGCTGAACAAAGGGTTAAATTTAAGTTTTCTATGTGCTTTTGTTTTGGATTATTGTTGTCAGACATTTTCATAGTTGTGTTTCTGTTGTCAG
Seq C2 exon
CTTCTAGGAGCCTGCGTATCAAACTGTGGAAGAATATTTCACTTAGAAGTTTGTTCTCGTGATTTTGCTACTGAAGCTCGAGGTATAATAAATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012513:ENSGALT00000020440:3
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=0.000
Domain overlap (PFAM):
C1:
PF0079014=VHS=FE(18.5=100)
A:
NA
C2:
PF0079014=VHS=FE(23.0=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:
TGCCTTAAAGCCATCATGAGGA
R:
TCAGTAGCAAAATCACGAGAACA
Band lengths:
140-355
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]