GgaINT0136533 @ galGal3
Intron Retention
Gene
ENSGALG00000002602 | CSMD2
Description
NA
Coordinates
chr23:5140538-5141153:+
Coord C1 exon
chr23:5140538-5140723
Coord A exon
chr23:5140724-5140958
Coord C2 exon
chr23:5140959-5141153
Length
235 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
CTTCTTTCCCTGGCTTCTAGCTG
3' ss Score
8.31
Exon sequences
Seq C1 exon
CTCTCTCCTGTGGAGTTCCCAGGGCCCCAAAGAACGGCGTCGTCTTTGGCAAGGAGTACACAGTGGGGACGAAAGCTGTGTATCACTGTGACCAGGGCTTCCAGCTGGCTCCTGGTGAGCCGCCCAGCACCGAGTGCCTGCAGGAAGGGCAGTGGAGCAACGGCAACCAACCCCCACCCTGCGTGG
Seq A exon
GTGAGTACCATGAGCACCATCGGCCTCATCCAGCAGGGACAGTTCTGCCTTTCGGGTACAACATTTAGTACACAAGGATCTTCAGCCTGTAGCTAACTTGTGCCTCTGGCGCTTCATTTTCCCACTTGCAAAATAGAGATGTTGATGCTACCCCCGTTTAAAAAGCCAGCATGCTTCCTGAGATACCCCAAAGCACCCTATTAATAGCTTTGTCTCTTCTTTCCCTGGCTTCTAG
Seq C2 exon
CTGTCACCTGCCCCGATATCAGCAGCATTGCTGTGGAGCACGGCCGGTGGCGGCTGACCTACGAGATCCAGTACCACTACAACGCCCAGCTGATGCTCATCTGTGACCCTGGCTACTACTACACAGGACAGCGGGTCATCAGGTGCCAGGCCAATGGGAAGTGGAGCATCGGCGAGCCAATGCCAACCTGCAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002602:ENSGALT00000033174:55
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.063 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=92.1)
A:
NA
C2:
PF0008415=Sushi=WD(100=92.4)
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:
GTACACAGTGGGGACGAAAGC
R:
CGATGCTCCACTTCCCATTGG
Band lengths:
302-537
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]