GgaINT0136511 @ galGal3
Intron Retention
Gene
ENSGALG00000002602 | CSMD2
Description
NA
Coordinates
chr23:5097966-5098700:+
Coord C1 exon
chr23:5097966-5098104
Coord A exon
chr23:5098105-5098512
Coord C2 exon
chr23:5098513-5098700
Length
408 bp
Sequences
Splice sites
5' ss Seq
CATGTGCGT
5' ss Score
5.1
3' ss Seq
TGTTTTATTTTTCTTTGCAGCTT
3' ss Score
11.27
Exon sequences
Seq C1 exon
CTCCCTGCGGAGGGATCCTGACCGGACCAGCAGGGGTGATCCTGTCCCCGCAGTACCCGGAGCCCTACCCGCCGGGGAAGGAGTGCGACTGGAAGCTGACCGTCTCTCCTGATTATGTCATCGCCCTGGTATTTAACAT
Seq A exon
GTGCGTACCCCAGAGCTGCTCCCTTCTGTGGGGTGGGGAGGGGATGCTGTCAGAGGGGCGCTGCCTGGCTCTGGGCTGCCTGCGGGCTCAAATCTCCCTGGAGGAAGCAACCCAGAGCTGGTAGGACTGGCCCCGAACATGACCATGTAACTGGTGCAGCATAGGAAACCCCTGTAGCATCACTGGACATAAACTTGACTGTATCACCACTCCTTGATGCTTACATGTGTGCAGGATGGAGGTAGCGGTGTCCCATCCTTAGCTGGGGAGCTGGCTGGGGGCAGCAGCTGCCTCTCAGCATTGTGGCAGTGCAGCCCACCCAAACCCCAGCCTGGTGTTCTCCAAGGGGCTTCTGCAGCATGCCAATGCTTCACACGCCCTTCTTTTATGTTTTATTTTTCTTTGCAG
Seq C2 exon
CTTCAGTTTGGAGCCTGGCTATGATTTCCTTCACATTTACGATGGACCCGATTCGCTCAGCCCCCTGATTGGAAGCTTTTATGGCTCCCAGCTACCTGAGAGGATAGAGAGCAGCAGTAACAGCCTCTTCCTCGCCTTCCGGAGCGATGCATCTGTCAGCAATAGTGGATTTGTCATTGAATACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002602:ENSGALT00000033174:33
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043115=CUB=PU(41.5=93.6)
A:
NA
C2:
PF0043115=CUB=PD(57.5=95.3)
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:
GAGGGATCCTGACCGGACC
R:
CTGTGTATTCAATGACAAATCCACT
Band lengths:
318-726
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]