GgaINT0102972 @ galGal3
Intron Retention
Gene
ENSGALG00000016111 | CSMD3
Description
NA
Coordinates
chr2:139091443-139092306:-
Coord C1 exon
chr2:139092193-139092306
Coord A exon
chr2:139091542-139092192
Coord C2 exon
chr2:139091443-139091541
Length
651 bp
Sequences
Splice sites
5' ss Seq
CAGGTATCT
5' ss Score
7.33
3' ss Seq
TTGTATTTGCTTTGTTTGAGTAG
3' ss Score
-2.64
Exon sequences
Seq C1 exon
TGGTTTTTGGCCAGTTTGTATTTTTCCAGACATCACTCCATGATGTGGTTGAAGTATACGATGGCCCAACTCTGCAGTCATCTTTGTTATCTTCTCTCTCAGGATCTCATTCAG
Seq A exon
GTATCTTTTAATAGGACTGTCATTAAATTGTTGTTTATTTTATATAGCCTATAAAAATAGTGCAGCTGAAAGAAACAGAAAAGGAAGCTCGTATTGTCTGAGATATAATTTGGTGACATATATAAAATCTGGATTTGGAAAGAACAACTTAAGCACTCAGAACAGTTTTAAGTAATGAAGGAACAGAAATCAAATAAGATCTTTTCTTTAGAACTTTTTCTTACGATGTTTGGTTATTATAGTGAGTATTTTGGGCTTCTTTCTTTGTGCCTTTATTGCTCTTATCTAGTGAGTAATTTAAAATGAATATTAGACATTTAAAAGGGAAAAAGGCATATGTTTATAATAAAGTGAAACTGTATAGTTTATATCATGACTTGATTTGAAGAGGTATGTTGTCTAAAGATATGTATTACTTTATTTATGAGGGAAATACATAAATTCATGATAACTGAGACAAGTTTCAATCTCTCTTTTTTAGAACAACATAATACTGCCATCTTAAGGTGTTGAAGTCATATATATTTATCAAAGTTACTGAAGCAGAACAGTATTTTGGATGTTATTTTTAACTGCAAAGTTATTGATAGATATTTTGACCACTTCTTTAGTAAAACTGGTTATGATAGCTTTGTATTTGCTTTGTTTGAG
Seq C2 exon
TAGGTGAATCCCTTCCGTTGAGCTCAGGTAACCAGATCACAGTTAGATTTACTTCAGTTGGACCAATAACAGCTAAAGGATTTCATTTTGTTTATCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016111:ENSGALT00000036594:30
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(35.5=100)
A:
NA
C2:
PF0043115=CUB=PD(29.0=91.2)
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:
TGGTTTTTGGCCAGTTTGTATT
R:
AAACAAAATGAAATCCTTTAGCTGTT
Band lengths:
207-858
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]