GgaINT0136497 @ galGal3
Intron Retention
Gene
ENSGALG00000002602 | CSMD2
Description
NA
Coordinates
chr23:5070116-5072453:+
Coord C1 exon
chr23:5070116-5070442
Coord A exon
chr23:5070443-5072258
Coord C2 exon
chr23:5072259-5072453
Length
1816 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGA
5' ss Score
5.9
3' ss Seq
CTCTCCTCTTTGCCTCTCAGCAT
3' ss Score
8.42
Exon sequences
Seq C1 exon
TTTCCTGCTTTTTCAACTTCACCACCCCGTCTGGGATCGTGCTGTCGCCGAATTACCCCGAAGAGTACGGGAGCAGCTTGCACTGCGTTTGGTTGATCATAGCTAAACCCGAGAGCCGAATTCATTTGGCTTTCAATGATTTTGACGTGGAGCCTCAGTTTGATTTCCTAGCCGTGAAGGACGGCGGCACCGCGGAGTCTCCGGTGCTGGGCACCTTCTCAGGAAGCCAAATCCCCTCCTCGCTGACCAGCAGCGGCCACGTTGCCAGGCTGGAGTTCCAGACCGACCACTCCATGGAGAAGAGAGGCTTCAACATCACCTTCACCA
Seq A exon
GTAAGAGCTCGGTCCTTTGCTTTTCATTTCAAGCTCCAAACTCTCATTTCAAGCAAAAGCCTGACCGTACCAAAATCGTTGCAAATCCAGAGTGAGGCTGAAAACTGGGGATCGTGTCTGGCGTGCAGTTGGGTAACAGAGGGTTGGTTCCGTGCTCAGAGCTGGTTGCACAAGTGTTGTCTGGCTGTGTTGTCCAGCAGTAAATTGAGGTTATCTGTCCATGGAGCATCCTAGCAGCCTCCAGCTCGCCCTGTGCCAGGGGCTGTCTGCCTCCCCTCTGCCTGCATGCTGCTCGCTGGGTGGACAGCAGATGCATCGGTTGGGGCCCAGATGGCTGAGTCCATCCATCAGCACCATCGCTGTTTGCTGAGTCCCTATGCAGGGCTTTAAGCACTGGAGGAAACGTGTTGCTCTGTGTTCTATTCTAAAGCACTGAAACTTCCTCAGGGACGTTTGGCTTCACTTAAGTCCAGTCTTCAAATCTCAGATGAATGCTGTGGTAATTTTATCCTCGTATTGTCCTATAATTTTCTAGAGAGCATTGTTAAACCTATTCAGCAGAACTGATAAATGATTTTGTTATAATAGCCTTTAGTGGCACCGCTAAATTAATAGCCTTTCCAGTTATGATTGCAAATCCTCTATTTAAAAAAAAATAATAATAATAATTCAGAGGTCTTAAGAAATCCTTGGCCACACAGAGCAGGCTGAGGGCTCATCAGGTGGAACAGCATCGTGGGGCAGAGCTGTGTGCCCAGGATTGAGCCCTGGGTGCTGTGAAGTCAGGAGCTCTCCTATGGATGCTGGCAGTGCAGGAGGCAGTTCAGATCCCTCCATACCCACACTGGGGGCTGTGGTTGCCCGTTGTATGAAGACGTTTTTAAGGTGGTTTGTTGTGTTTTTGCTATTGTAAATGACGCAGCTCCCTTTGAGTTTGTGTGTTCTGACTGCTTGAGCTGCCAAAAGGGAACTGCTGAGCCTTTTCTCAGGCACCTTGCTGTTCTGAGATAGGAGACAGGAGACAATATATTGCTACAAGTTCCAGGAGCACAAGGCAGAGATTCAGCCCGTGTTTTCCCCTTCAGCAGTGTATGGTAACACGTTATTGTAAGGGAGAGGATGCTTTGTAGGGAATTCAGGACTGTGCTTGGGCAAATGCATTAAAGAAACGGATAGCGTGTGGGTGTAATGAATCTGAAGGCTTTAATCTTTTATATATTGTTCATCTCAGAAGACCACCTCTGAGCCTGCAAGATACAGTACATAATTACGCACTTAATGGGAAGTTAAGGCTATGGGCTCGTTCTCTGGTTGGTTGGCTGGCCGAGCTGTAGCTGCAGGAAAAGGGCAGTCCTTTAACCAGAGCAACGCGTGTGTGCAATCCCATCCTTAACTCTGCAACGTGTAGAAAGGTAATGGCTTTGTGTCCTTGCTTTTATCCCAGTAATGGTGACAAGGCCGGGGACCGTATGGCAGCGGATCGCACAGTGTGCTTAATGGGTAACTTATGTCCCATCTATGTAGGTGCACACATGCACTACGGTATTTTTAGAGCTCTTTTTTTTTTTAATCTGTCTCTATTTTGAGTATTTATGCGTTTCACACGGGAATGGTTGCTAAGATGGGGTGGTTTGCACACTCATTTCTGGTCCCGGCTGCAGCACTGTGAGAAGGGTCAGCATCCCAAGGGCAGGATCGTGTGCTAATTGCACACGTAGAAACGGTGTGGGAATAGCAATTCTTCACGTGTGGTCTGACCTGATCACTGTTACATCAGGGCTGGGAAGCTCACTGTCCTCTCCTCTTTGCCTCTCAG
Seq C2 exon
CATTTAGGCACAATGAGTGCCCGGACCCCGGCGTGCCCGTGAATGGGAAGCGCTTTGGGGACAGCCTGCAGCTCGGCAGCTCCGTGTCCTTCCTTTGTGATGAGGGCTTCATCAGAACCCACGGCTCAGAGACCATCACCTGCATCCTGAAGGAAGGCAACGTGGTCTGGAACAACGCCGTGCTCCGATGTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002602:ENSGALT00000033174:19
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:
PF0043115=CUB=WD(100=96.4)
A:
NA
C2:
PF0008415=Sushi=WD(100=87.9)
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:
TAGCTAAACCCGAGAGCCGAA
R:
GAGCCGTGGGTTCTGATGAAG
Band lengths:
355-2171
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]