BtaINT0044557 @ bosTau6
Intron Retention
Gene
ENSBTAG00000005784 | CSMD2
Description
CUB and Sushi multiple domains 2 [Source:HGNC Symbol;Acc:HGNC:19290]
Coordinates
chr3:112880494-112882235:+
Coord C1 exon
chr3:112880494-112880670
Coord A exon
chr3:112880671-112882055
Coord C2 exon
chr3:112882056-112882235
Length
1385 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
GCTCTGTCTCCACCCCCTAGTCA
3' ss Score
7.29
Exon sequences
Seq C1 exon
TGATCTCTTGCGGGAATCCTGGGACTCCAAGCAATGCCAGAGTCCTGTTCAGTGACGGCCTGGTTTTCTCCAGCTCCATCGTCTACGAGTGTCGGGAAGGCTACTATGCCACAGGCCTACTTAGCCGGCACTGCTCGGTCAATGGCACCTGGACGGGCAGTGATCCGGAGTGCACAG
Seq A exon
GTGAGAGCCTCTGGGCTCCATGGCAGTGGGGCTCCTCCACGCCAGAGGAGAAGGCTGTCTGCTAGAGATTGGGAAGACTGGCTGGCGTTGAGGGACTTGACCCTGAATGAGGATCATACAAGTCGCCTCCATTTACTGAGCACGTTCTGTGGGACTGCCACTGAGCAAAGTGCTTTGTTTTCGGATCTTTTGATGCTCACCACAATCCCCTCCCTGTGAAAGTAGGAAAGTGAAAGTCACTCCGTCGTGTCCAACTCTTTGCGACCCCATGGACTACGTAGTCCATGGGATTCTCCAGGCCAGAATACTGGAGTGAGTAGCCTTTCCTTTCTCCAGGGGATCTTCCCAACCTAGGAATCGAACCCAGGTCTCCCGCACTGCAAGCAGATTCTTTACCAGCTGAGCCACTATTAGCTCTACTTTCCCATATGAGACAGATGAGGCTCAAGAAAGCTTCAAAATATGTCATTGCTATTTTCCAGGCTCTAGCCAGTTCCTGGGGCTTTCTTTTTCTCTTTTAGGGCAAACCCCCAGTGCTGAGCCTGATTCTCTATCTACCTTAAAGCTGCTGCCATCTGTCATCTTTGTTAGCTGCGTTTCTCCCTTCAATCCATCCCCACCCCAGCCTGGCTCCTCTTTCTTGCTTCTCTTAAAAGCAGCTCTAGACCCTTTTCCTTGAAAAGCAAATCGCTGTGGGGCCCAGATGGAAGGAAGTGATTATAAAAGGGAATCCTATACAACATTCTCCCTTTCAGAGTCCTAGCTGTGCATCCAGGCTCCATCTGAAATCCCCTGTCAGCTTCACTGTTGTTCCGAGGTCAGAGCTCACCAGTCCCCACCCTCACTTGAAACCGTAACACAGAAATAACCACTGCATCAGTCACAAGGCCCTGCTCCTAGTCCACTGAGCCCACGGAGGCCTCCTGGGCAGAAGGGCAGTCAGTAAGAGGCCCTTCCCAGCAGACAAATTGTCTTATCAACACACCTTAGGTCCACCATGTGGTCCATCAACACATCTTAGGCTCTTCAACCTGGAAACCTCCCTCCCTCTGGTCCCCAGCCTCATTTACGAAGGGAGCCCCCTGAATATTTCTCTTAGAGGAGTGGGCCTTACATGAACAAGACGGGTTTCCCAGCCCAAGTTGCTGGGGTGTGTAAGGATGGTGCGGCAAGGACGGGGGTGTAGGACAGCCTTTGCAGGGAGACTTGGCTACGGGGAGTTAGAATGAACGGCACCCCAACTGGGAACCTGGGGGGAGATGCGACATCCCTTCTCTGACAGTTTTCCTTCCCAAACGTGTGGGGAGCGATCGGGATGGTGTTGGGATGCTAAGGAGGAAGGAGTCTATGCTGGGAGTGAACGGGGCTCTGTCTCCACCCCCTAG
Seq C2 exon
TCATAAACTGTGGCGACCCTGGGGTTCCAGCCAACGGCCTCCGGTTGGGCAGTGACTTCAGGTACAACAGAACTGTCACCTACCAGTGCGTCCCTGGCTACACGATGGAGTCGCACAGGGTGTCCGTGCTGAGCTGCACCAAGGACCGGACGTGGAATGGCACCAAGCCCGTCTGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005784:ENSBTAT00000007609:64
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=WD(100=91.7)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.8)
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:
GATCTCTTGCGGGAATCCTGG
R:
CTTGGTGCCATTCCACGTCC
Band lengths:
343-1728
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]