GgaINT0136543 @ galGal3
Intron Retention
Gene
ENSGALG00000002602 | CSMD2
Description
NA
Coordinates
chr23:5159051-5160228:+
Coord C1 exon
chr23:5159051-5159224
Coord A exon
chr23:5159225-5160054
Coord C2 exon
chr23:5160055-5160228
Length
830 bp
Sequences
Splice sites
5' ss Seq
TCCGTGAGT
5' ss Score
8.93
3' ss Seq
CCTGCTCTCTGCTGTTGCAGCCG
3' ss Score
9.77
Exon sequences
Seq C1 exon
CTATCATCTGTAAACCCCCACAAGCCATCCCCAATGGCAAAGTGGTGGGCTCGGATTTCAGCTGGGGCTCCAGCGTCAGCTATGCCTGCCTGGAGGGGTACCAACTGTCCCTGCCCGCCGTGCTGACCTGCGAGGGGAACGGGACCTGGAGTGGGGAGATCCCCCAATGCTTCC
Seq A exon
GTGAGTAGACAGCCTCTGCACATCCACGGCTGGGCTGGGAGAGGGATGGGGCTGAAACACCTGGATGCACTCACTCCATTTCTGTATGTAGGTGTGAGGTCGGGTTTGTAACAGGCGTGAACTCCTTGCATGTTCGTGTTTGTGTAACACCCTTAAAGCTCGTGGCTGTTTGTCCATGTGCCTCCTTGAGTTTGGAAATCAGGGCTCCTGAAACTGGCAGAGGTGGTGAGAAAAGCCCTTTGGCAAAGGGCGCTGTGGAGTCACAGCAGAAGTTAGGAACGTTTTGTGAAGACAGAGCTTTGGCTCTTGGAAACCTGTGTACTCCATTAAATAGCTAATGCAAAAAATTAGTTAAATGTCTCATTGTGATAAAGGCAGATTTGAGTTTCTTTTCTTGGCTGAATGGCTGGCAGCTGCACAATAGCCATTTTCGTATTAAATCACACAAAGCCCTCGCTGTGTTCCTTGCACCCTTCCCTGGATCTTGTATAATTAGCGGGCTTTCTGTGTGACATGGAACCATATAGCAATTTGACATCATGCAATTAGGGACACGTTTTAAAGCTAAGCGTGCTGCTAGGGGGGAAAGAAAAGGGAGAACGAAAAAGATGGGGAGAAGTGGAAGTTAATTAACAGCAATTGGCAAAAAAGAGAGAATTAGAAGGAAAGCAGCCAGCAACGCCTCCTGCCACCAATCATCCCCTGGTCAATCACTGAGCTCCGTGGTAGTGAGCAGTGAGCTCTGGCCCATTAATAGACCCATTGCTGGTGTTTTAGCATTGCTTGCTCTCGGGGAGGTTTTCACCACCCCCTGCTCTCTGCTGTTGCAG
Seq C2 exon
CCGTGTTCTGCGGAGATCCAGGGATCCCTGCCCAGGGCCGGCGGGAGGACCGAGGCTTCACGTACCGCTCCTCTGTGTCCTTCTCCTGCCTGGCCCCACTGGTGCTGGTGGGCTCAGCACGCCGCTTCTGCCAGTCTGATGGTACGTGGAGTGGAACCCAGCCCAGCTGCATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002602:ENSGALT00000033174:65
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=0.017
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=91.5)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.5)
Main Inclusion Isoform:
NA

Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTATCATCTGTAAACCCCCACAAGC
R:
AGCTGGGCTGGGTTCCAC
Band lengths:
342-1172
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]