GgaINT0136503 @ galGal3
Intron Retention
Gene
ENSGALG00000002602 | CSMD2
Description
NA
Coordinates
chr23:5080286-5082379:+
Coord C1 exon
chr23:5080286-5080501
Coord A exon
chr23:5080502-5082190
Coord C2 exon
chr23:5082191-5082379
Length
1689 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TGCCCATCTGTCCCCCATAGAAT
3' ss Score
9.96
Exon sequences
Seq C1 exon
GCGTGTTCTTCACCTTCCATACCTTCCACCTGGAGAACGGCCACGATTACCTCCTCATCACCGAGAACTCCAGCTTTGCACAGCCCCTGAAGCAGCTCACCGGCTCCCGCCTGCCTGCCCCGCTCAGCGCGGGGCTCTTTGGGAACTTCTCTGCACAAATCCGCTTCATCTCAGACTTCTCCATGTCCTATGAGGGCTTCAACATCACCTTCTCAG
Seq A exon
GTAAGAACAGAGGGGCAGGCTTCATTCCTTCCCTTTCCTTTACACTTCAGCGTGCAGCTTGGGAATAGGTTCCCATTGATGTATGTGGTTGCAGCTCTTGGAGCTGGATGCCCAAAGGAGCTGTGGGTGCCCCATCCCTGGAGGTGCTCATGGCCATGGATGTGCCCTGGGCAACCTGGGCTGGAGGAGCAGCCATCCCACAGCAGGGCCGGGGTCTGGCTGGGCTGTAAGGTCCCTTCCAACCCAACCCTCCCGTGATTCTATTCAGTTGTTCCACTGATAGATTGTGCCAGCATCGAACCGCTGTGCGTCCCAGGAAATGTTCTGTTTACAGCCCTGTATGTCCATACGCAGCAGTTCTGTGTGCCATCAGCCCCAGTAGGTGACTGATTGGACCCCCTGGAATTATATCCCCCTGCTGGGCCGTTTGTTGCCTCCTCCCTCCTCACCCAGTTGACCTTTCCTTCTCTGTTTATGGGTGGAATTTCAGCTCATTTTCTCGGGGTACCCCCGGGAGGCCATTCCTTATGCAGAACATCACACCTGTCAAAGATGGCTTTGCTCGGGCAGCCTCAGGTTGAGGTGTGTCCTTAACCCCGATGTCCTACAAATGACTGCTGCAATGTTGGCCTGTGCACACGTTTCAGAAAATGCCATCTTTGCTGCCTGCCTGCCCTGACATCAGACCCACAGAACAGCCAGGTCCCGAACCAAAGCTCGTTGTATGGCTGCCATTCCCTTCTGTATCTCAGCACACCTTTCAGTCCCCCTATTCTGCCTGCTGAGGAAGCACTGTGAGCACAGTTATTTGGGGCGATGTGTTTGCTGTCTTTGAGGGACAGAGCTGCTGCCGTAGATGCAGTTAAAACCTGCCACGCTCCAAACTGGTTTCCAGTGCCTTTGTTCTGCCCTCTGCAGTCGGGGATTTCCATGTGATGCTCTGAAAACCAGACATAAAAATTCCAATTAACTTTCATTTTGATGGGGAAAAAATGGCTTTTTGTCGAAACAAATTGCCTCACGTTGTCCAATTATAACTTTCGGCTTATTTTGGGACTTATTTCCTTTCTCAGAAAATGAAAACGGGAGTCAGTTCTGTATTTCAGTTCTCTATATAAGTGCATACTTTGTGTTTTGCAGCTCCGTTGTTTGTTCAAAGAATAACCCCCAAAAGAGGTTTCCTTTAAAATGCTTTGTGGCCAAAGGCAGACATTTGGCTCCTCTCCATAATGCTCCATGACCTTTCATTCAGTAGCAGCTTAAATGTTCTCCTGCATTCCCCAGGCAGGACGCTGCGTTCATTCATTTGCAGGATTAGTAACGTAGAGGCAACAGAAATCCCATCCGGATCAGTTCATCTTCATTTTACTAAACCTGGGGGAGAATGACAAACCTCCATCGTGCTGTGCCACCACCGGTGTCACTTTCTGCTTTGGCTGGCAGCAGTGACAGGAGATGAGGGATGGTTTGGATCGGTTATCTGGTGGGACCCCGAGGGCTGTTCTGAGGGTGAGACCCGAGCTCTGCTGTCCTTGGTCAGACGGGTCATATGTGTTGCACGAGTGCTTCTTTTTCAGACCCAACCCACATCTGAATCATGACCCACAGGGCTTGGAGCACCCTTGTTGGGGAGGATGGGGTACGAGGTGTCACGGAGCCGTGCAATAAATGCCCATCTGTCCCCCATAG
Seq C2 exon
AATACGACCTGGAGCCCTGCGATGAGCCAGAGGTCCCAGCCTACAGCATCAGGAAGGGGCTGCAGTTCGGCGTGGGCGACGTCCTCACCTTCTCCTGCTTCCCCGGGTACCGCCTGGAGGGCACGGCGCGCATCACCTGCCTCGGGGGGAGACGGCGTGTGTGGAGTTCGCCTCTGCCAAGGTGTGTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002602:ENSGALT00000033174:25
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=PD(64.8=95.9)
A:
NA
C2:
PF0008415=Sushi=WD(100=87.5)
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:
TCATCACCGAGAACTCCAGCT
R:
CAACACACCTTGGCAGAGGC
Band lengths:
351-2040
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]