BtaINT0044528 @ bosTau6
Intron Retention
Gene
ENSBTAG00000005784 | CSMD2
Description
CUB and Sushi multiple domains 2 [Source:HGNC Symbol;Acc:HGNC:19290]
Coordinates
chr3:112781688-112783092:+
Coord C1 exon
chr3:112781688-112781783
Coord A exon
chr3:112781784-112782888
Coord C2 exon
chr3:112782889-112783092
Length
1105 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGC
5' ss Score
9.55
3' ss Seq
AGCACCCCTGTTCCCTGCAGCGG
3' ss Score
8.16
Exon sequences
Seq C1 exon
GAGAATCGCTGCCCTTGGCCACCTCCAATCAAGTCCTCGTTAAGTTCAGTGCCAAAGGCCAAGTACCAGCCAGAGGCTTCCACTTTGTTTACCAAG
Seq A exon
GTATGCAGGATGTGATGTGGGAGGTGTGAAGGCAATCTCCATCTTCGGGGATCAAGGAGAACAGGGACCTTTGACCTCCCCCCAGTCTGAGCCTCATTCTTATGGTGTTTGTGGAGCAATTCCCTGAAATTCAGTTGAATTTTATACATTCAATATAGACAATTCTTGGACCCAACTCCATATTGGATAAAGGGAGAAATCAGAGAAGGGAAGCTAATTTGTGCCCTCCCCCACTCCCCATTGTGTGGCACAGTCCTCATGGCATTGAGAGGACCAGTCCAGGCCTCTTACCTAGACCTTCTCCCATGGAGTATGGCTTTGTCTGCAAGGCCTGTAAAGGTCCAGGAAAAACATGGGCTTTAAAGTGAGCTGGACATGGATTTGAACCCCAGCCCTGGCACTGTCTAACTGGGCACCAGCTACTCCCCCTCTCAGAGGCCCAGTTTGCTCACCTATAAAATCAGGGTGACCATGTCACCTCACAGAGTAGCTGGTGCGAAGCGGGTAATCAGTGTCTGTTCCCCTCCTTACGGCCCTGAAAGGCCAAGTCTCGGAGCAGCCTAGCCTTCCCCTGCAGGCCCCAGCCTCTCTTTGCTGAGGAGAGTGTCCACTCTCCTGGGGCTCGGGTTCCAAGTGAGGTCCTGTATATTCCACTGCCCAGAAGGAGCTGCACTGCCCTGTGTAGGGGTAATCCTGCCCCGGAGACACCCTTCCTGGGCCTGGGGGTTAAAGGTCCTATCGCCCCCTGTAGGTGGGGAAGGGAAATTCAGGTCTGTGAGAGCAGGGCCCTGGGCAGGGTCCTAGGGGACATCGGACCCTACTGTGCAAGGGGCTTCATTGGGAAGGCGAAGAGCACAACTGAGCCTAAAGGCTCGGCCTGTGGCTCTTACTGTTTTCCGTAGTTTACAGAAGCTGTGCTACCTGGCATGTCCGACTGTATTTCAGGAAGATGGGCTTCATCCTAGAAAGCCCCCTACCCCCGTCCTAAGGGAAAGCACCCAGAGCCTCTCAGAGTCCCACCCCATTCCAGCCCCGCGATGTGTCCATTCCCGGACCCGTTTCTAGAGGGGTGAGGCCTGCCCCTCAGCACCCCTGTTCCCTGCAG
Seq C2 exon
CGGTGCCCCGAACCAGCGCCACGCAGTGCAGCTCAGTGCCAGAACCCCGCTACGGCCGGAGGCTGGGCAGTGACTTCTCCGTGGGGGCCATCGTCCGCTTCGAATGCAACTCTGGCTATGCCCTGCAGGGCTCCCCAGAAATTGAGTGCCTCCCCGTTCCTGGGGCCTTGGCCCAGTGGAATGTCTCAGCACCAACGTGTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005784:ENSBTAT00000007609:37
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(28.3=90.9)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGAATCGCTGCCCTTGG
R:
ACGTTGGTGCTGAGACATTCC
Band lengths:
294-1399
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]