GgaINT0102972 @ galGal4
Intron Retention
Gene
ENSGALG00000016111 | CSMD3
Description
CUB and Sushi multiple domains 3 [Source:HGNC Symbol;Acc:HGNC:19291]
Coordinates
chr2:132920885-132921748:-
Coord C1 exon
chr2:132921635-132921748
Coord A exon
chr2:132920981-132921634
Coord C2 exon
chr2:132920885-132920980
Length
654 bp
Sequences
Splice sites
5' ss Seq
CAGGTATCT
5' ss Score
7.33
3' ss Seq
TATTTGCTTTGTTTGAGTAGGTG
3' ss Score
4.85
Exon sequences
Seq C1 exon
TGGTTTTTGGCCAGTTTGTATTTTTCCAGACATCACTCCATGATGTGGTTGAAGTATACGATGGCCCAACTCTGCAGTCATCTTTGTTATCTTCTCTCTCAGGATCTCATTCAG
Seq A exon
GTATCTTTTAATAGGACTGTCATTAAATTGTTGTTTATTTTATATAGCCTATAAAAATAGTGCAGCTGAAAGAAACAGAAAAGGAAGCTCGTATTGTCTGAGATATAATTTGGTGACATATATAAAATCTGGATTTGGAAAGAACAACTTAAGCACTCAGAACAGTTTTAAGTAATGAAGGAACAGAAATCAAATAAGATCTTTTCTTTAGAACTTTTTCTTACGATGTTTGGTTATTATAGTGAGTATTTTGGGCTTCTTTCTTTGTGCCTTTATTGCTCTTATCTAGTGAGTAATTTAAAATGAATATTAGACATTTAAAAGGGAAAAAGGCATATGTTTATAATAAAGTGAAACTGTATAGTTTATATCATGACTTGATTTGAAGAGGTATGTTGTCTAAAGATATGTATTACTTTATTTATGAGGGAAATACATAAATTCATGATAACTGAGACAAGTTTCAATCTCTCTTTTTTAGAACAACATAATACTGCCATCTTAAGGTGTTGAAGTCATATATATTTATCAAAGTTACTGAAGCAGAACAGTATTTTGGATGTTATTTTTAACTGCAAAGTTATTGATAGATATTTTGACCACTTCTTTAGTAAAACTGGTTATGATAGCATTGTATTTGCTTTGTTTGAGTAG
Seq C2 exon
GTGAATCCCTTCCGTTGAGCTCAGGTAACCAGATCACAGTTAGATTTACTTCAGTTGGACCAATAACAGCTAAAGGATTTCATTTTGTTTATCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016111:ENSGALT00000025958:33
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:
PF0043115=CUB=FE(35.8=100)
A:
NA
C2:
PF0043115=CUB=PD(28.3=90.9)
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:
TGGTTTTTGGCCAGTTTGTATT
R:
AATGAAATCCTTTAGCTGTTATTGGT
Band lengths:
198-852
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]