GgaINT0136547 @ galGal3
Intron Retention
Gene
ENSGALG00000002602 | CSMD2
Description
NA
Coordinates
chr23:5166292-5167001:+
Coord C1 exon
chr23:5166292-5166471
Coord A exon
chr23:5166472-5166935
Coord C2 exon
chr23:5166936-5167001
Length
464 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGA
5' ss Score
10.53
3' ss Seq
GGTTTGTTCCTCTCTTCCAGCTG
3' ss Score
10.19
Exon sequences
Seq C1 exon
CTCACCACTGTAAGCAGCCTGAGACCCCCTCCCACGCCAACGTCGGCGCTCTGGATTTGCCATCTCTGGGCTACACCTTGATCTATTCCTGTCAGAGTGGGTACTACCTCACCGGGGGGTCTGAGCATCGGACCTGCAAAGCAGATGGCAGCTGGACGGGGAAGCCTCCCATCTGCCTCG
Seq A exon
GTAAGAGCTCTGAGCAGCACGGCTTTGGCTTTGGCCTCCATCTCTGCAGAGGGGGGATTCGCAGCCTGTGAGAAAAGAGCAATTCTCTTTGAGCTACGTGGGTGCTTTAGAGAAGCCATGGGTTTGCGTGGCTGAGCTGGTTGCAGCAACCACAGCACGGATCCCAGAAAACAGGGGGAAGAGAAGGGATTTTCTGCCTGATGTTTTGGACTTAGAAACATCTGCACCAGCTGAACCTGGTCTGTACCTTACCTATGTGTCATGAGCCTCGAAGCTCAACTCTTAGTTCAAGATCATGCGGTCTTGAACCCATCTGAAGCTCTTGTGTGGTGATTAGCCCTGTTACGTGCTCAACCAGTGTCAGTTGAAGGCTGTCCTGTATGAGCACCACTGCAGCAGAGGTGTCTCAGCACAGTCAGGTGCAGCACAGTTCATTTAGCTGTGGGTTTGTTCCTCTCTTCCAG
Seq C2 exon
CTGACATCCGCCCCAGCGGCCGGCCGGTGGGCACTGCGCGGGACCCTCCGCTCTCCAAGCTGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002602:ENSGALT00000033174:69
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.049 A=NA C2=0.348
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=91.8)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCACCACTGTAAGCAGCCTG
R:
CTTGGAGAGCGGAGGGTCC
Band lengths:
239-703
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]