GgaINT0136528 @ galGal3
Intron Retention
Gene
ENSGALG00000002602 | CSMD2
Description
NA
Coordinates
chr23:5132146-5132703:+
Coord C1 exon
chr23:5132146-5132226
Coord A exon
chr23:5132227-5132586
Coord C2 exon
chr23:5132587-5132703
Length
360 bp
Sequences
Splice sites
5' ss Seq
TAGGTAGGC
5' ss Score
7.72
3' ss Seq
ATATTTTCTCTTTCTTTCTGCAG
3' ss Score
1.68
Exon sequences
Seq C1 exon
CCTACCAGCTCTTCAGGTGTCAGCCTCCGACCATGGTTCCCAACGCAGAAATCATCACTGAGAATGAGGAGTTTAACATAG
Seq A exon
GTAGGCTCATGGTCCCTGAGCCCTCCTTCCCTTGCTGTCCTCAGCTGCTGGCAGTTTCCACAAGAGGACACGACGTGTTGTCCATCCCGAATCCCAGGCTCCAGGAGACCCCTTTGCACGTGTAGCTGTGTGACACTGCCTGATGTGTGACCCTGCTCAACAGCCACTATACAGAATTCCCGACACTTCATAGAATCATAGAATTGCTCAGGTTGGAGAAGACCTTCAAGATCAAGTCCAACCTCAACCTAACCATACTACCCTAACTCTAACAACTCACCATTAAATCATGTTCCTGGCCCTCTTCTCAGGGCACAATTCATCCTTCTCCTCGATCAGGATATTTTCTCTTTCTTTCTG
Seq C2 exon
CAGGAGACATTGTGAGGTACAGATGCCTTCCTGGCTTTACACTGATTGGAAATGAAATCCTGACCTGCAAACTAGGCACTCACCTGCAGTTTGAAGGCCCTCCGCCCACCTGTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002602:ENSGALT00000033174:50
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:
PF0008415=Sushi=PU(35.6=75.0)
A:
NA
C2:
PF0008415=Sushi=PD(62.7=92.5)
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:
CCTACCAGCTCTTCAGGTGTC
R:
CTTCACAGGTGGGCGGAGG
Band lengths:
198-558
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]