GgaINT0098825 @ galGal3
Intron Retention
Gene
ENSGALG00000008654 | STAM
Description
NA
Coordinates
chr2:19581789-19582518:-
Coord C1 exon
chr2:19582372-19582518
Coord A exon
chr2:19581880-19582371
Coord C2 exon
chr2:19581789-19581879
Length
492 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAG
5' ss Score
8.73
3' ss Seq
CATCTTTTATTTTTGGCTAGGCT
3' ss Score
6.43
Exon sequences
Seq C1 exon
GGTCATCCAAAAGTTTGTGAAAAGCTGAAAGCCCTTATGGTGGAATGGACTGATGAATTCAAAAATGACCCACAGCTTAGTTTAATATCTGCTATGATAAAAAATCTGAAGGAGCAAGGAGTTACTTTCCCAGCTATTGGTTCACAG
Seq A exon
GTATAGTACTACAAAAATAGCAATACAAAAAGTCACAAATTCTTTTTATCCTCAGTTCTGTATTTTAGTATTTGTAGCCTTGAATACTATAGTGTGTTTGGCAAACAAAATGAAATCTTCCTTGTCTAAATAAAGCATTCATTTGAGGGCTGAAATGCTCTGGCTTCCTTTAATTTTTATATCACAGATCACAGAATCATAGAATCAAAGAACATCCTGAGTTTGAAAGTTCCCTCCAGTTCCAACCCCATGCCATGGGCAGGGCTGCTCTCCATCAGCTCAGGCTGCCCAGGGCCCCATCCAACCTGAACTTGAACACCTCCAGGGATGGGGCATCCGCAGCTCTCTGGGCAGCAGTGCCAGTTTCTTACTGTCCTCTGAGTAAAGAATTTCCTCCTGAAATATAGATGAATACAAATCAAAATAGTGAATGTTAATGCATTGTGACAGTTTTTCAATGATTTTACTTCTGCATCTTTTATTTTTGGCTAG
Seq C2 exon
GCTGCTGAGCAGGCAAAAGCAAGTCCAGCCCTCGTTGCCAAAGATCCTGGTGCAGTAGCTAACAAGAAAGAAGAAGAAGATTTAGCTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008654:ENSGALT00000014097:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.355
Domain overlap (PFAM):
C1:
PF0079014=VHS=PD(28.9=79.6)
A:
NA
C2:
PF0280915=UIM=PU(50.0=29.0)
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:
GGTCATCCAAAAGTTTGTGAAAAGC
R:
AGCTAAATCTTCTTCTTCTTTCTTGT
Band lengths:
234-726
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]