BtaINT0044530 @ bosTau6
Intron Retention
Gene
ENSBTAG00000005784 | CSMD2
Description
CUB and Sushi multiple domains 2 [Source:HGNC Symbol;Acc:HGNC:19290]
Coordinates
chr3:112783463-112784525:+
Coord C1 exon
chr3:112783463-112783587
Coord A exon
chr3:112783588-112784428
Coord C2 exon
chr3:112784429-112784525
Length
841 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
CACTCCCCCTGCCTTCCCAGATT
3' ss Score
8.72
Exon sequences
Seq C1 exon
TGCCCTGTGGCGGAAACCTCACGGAGCGCAGGGGCACCATCCTGTCCCCCGGCTTCCCTGAGCCCTACCTCAACAGCCTCAACTGTGTGTGGAAGATCATGGTCCCGGAAGGCGCTGGCATCCAG
Seq A exon
GTAGGAGCCAGGGGGAGACTTCGCAGCCTGTCTCCAGCCCCTCAGGGCAGGGACGCAGTGGAGGCCCACAGTCAGAAAAACACAACAGCTCCCAGCTCAGGAAAAATGAGGTGTGGGAGCTGGCTGGGCCGTCGGGGAAGTCGCCGAGAGGAGGAGGTGGGCCTGGAGGTGGAGTGTGAAGCCTGGGAGGAGTCACAGGAGGTGTTTTTCAAGTGAAGGGTACTGTTCTTAAGATTTTTCTGGGAGTTGGGAGAGGAGGCATTGCAGGTGAGGGGAAGGCGCAAACCGACAGGCACCCCCTCACACACATCGGGGGTGTTGCGCCCGCAGCCCGAGGCAGCAGCAGAATCGGGGCCAGACTGGTGCGTGCGGATGCGAGCAGGTGGAGGACCCCCAGGACGGCTGCTGCTCCTGGGAGGAGGGGGACAGCCCGCAAGGCCGACAGAGAGAAACCACAGGGACTCCCGGTGGACAGGTCCACCCAGGGGTGGGTTACTGGCTGGCAGCTGCAGGATGTCTGGAGACAGGACAGTGAGGAAACTCAAGGAGTATTGGAGAGATGAGGAGGAGGCTAGTCACCCCAAAGTAGCCCTACACCCTGGACTGTCCTTTCCTGCTTCTCTGCCTGACAAAGCACCCCACTGTCATGCAACCATCCCACCTCTCTCTCCCTCAATGAACTCCTTGGGAACAGGGATAGCGTCTTCCTTTTATCAGAGTTCCCAGCACAGTGTGATCCGGATGAGGTGCTCAGTAATTGAATTAACTACATGAAAGGAGGAGGGGGAAGGGAGTGGGGAAGAGAGGGTTGCCTAACAGTTCACTCCCCCTGCCTTCCCAG
Seq C2 exon
ATTCAAGTCGTCAGTTTTGTCACAGAGCAGAACTGGGACTCCCTGGAAGTGTTTGATGGTGCAGACAACACTGTTACCATGCTGGGGAGCTTCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005784:ENSBTAT00000007609:39
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=PU(36.8=92.9)
A:
NA
C2:
PF0043115=CUB=FE(30.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGTGGCGGAAACCTCAC
R:
GCTCCCCAGCATGGTAACAG
Band lengths:
212-1053
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]