BtaINT0044540 @ bosTau6
Intron Retention
Gene
ENSBTAG00000005784 | CSMD2
Description
CUB and Sushi multiple domains 2 [Source:HGNC Symbol;Acc:HGNC:19290]
Coordinates
chr3:112807486-112808835:+
Coord C1 exon
chr3:112807486-112807663
Coord A exon
chr3:112807664-112808689
Coord C2 exon
chr3:112808690-112808835
Length
1026 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGG
5' ss Score
6.35
3' ss Seq
GATCTTCTTTCCTCTTGCAGGGA
3' ss Score
12.28
Exon sequences
Seq C1 exon
TCCCCTGCGGCAGCAACATCACCTCCTTCAATGGCACTGTGTACTCCCCGGGCTTCCCCAGTCCCTACTCCAGCTCCCAGGACTGCATCTGGCTGATCACCGTCCCCATTGGTCATGGCGTCCGCCTCAACCTCAGCCTGCTGCAGACAGAGCCCTCTGGAGACTTCATCACCGTCTG
Seq A exon
GTAGGGCCAGCTGCCGTGTCGGCAGGGAAAGGGGCTTGAGCTGGGCTCTCAGCTGGGTCACCCATTTGTTAGTCCAGAAAACCAAGGGCTGGATAGTTTTAATGGCTGTCAGCCTCCTGGGTCTCAAGCATAGTGGCCTAAGAACTCAGCTTCCACCAGCCCTTTTGACTCCTCGATGGGAAAGGACTAGCAGGGCAGTGTGTTCCCCACCTGGCATTCTGCTGGCGGTCAGTCAAAATACCAATGGGTGTGGGAATCTGGATCCATGAGCAGACTTTTCTCAGTGTTTCCAGAGTCCAAACCAAAATTCTGCATTTACTGGATAAGCTACCCAGACTAAGGGAAGAGCTGTGCAGTGGAATTTTATGAAGTCCCACTGGCATCTCATGCTGAGCTAATGCTGACCACAGAACTGTCTGCAGTGATGGAAACGTTCCGTATCTGTGCGGTCCAATATCATAGCCCCTCTCTACATGTGGCCCTCGAGCACTCGAATGTGACTAGAGTGACTGAGGAGCTGATTTTTTAAATTGATTAAATTCTAAATAATTTAAATGTAAATAGTCACGTGTAGCCTAGTGGTTACCAAGTTGGACGGCTCAGCTCTGAGTTATACAGTTAGAGTTTCTTGTGTTAATTTTAAAATGAGAATGTGAATTACTAGTTGATTAGTACAGTTTCCTCGACAGTTTTTTCCAAACCTCTGAATCTCTGAACAAAGATATCTTTTTAAAATTCCTTTGTTTAGAGCTTCTGGGAATCAGCAGGAGATAGTAGCATTCTGTTCTCAAAATTCCCAGAGCTGGATAACTGTCACCTGACTGCCCTGAATGGATTTCTCACTGAGTTTCCAGACAATGGCTGAGATCAGATGGAAGGGACTAGATAAAATTCCAGGGAAGAAATCCTTGGGCCCAGGAAGGCAACATGGGTGTGTCTCTTTGCTCACTGAAGGCCACTGATGCACCAGTTAGAACAGGCAGGCATGGTGACGCATGACATGCAGGATCTTCTTTCCTCTTGCAG
Seq C2 exon
GGATGGGCCACAGAAGACAGCCCCACAGCTTGGAGCCTTCAGCCGGAGCTTTGCCAAGAAGACAATGTACAGCTCATCCAACCAGGTGCTGCTCCAGTTCCACCACGAGTCAGCCATGGGCGGGATCTTCGCCATAGCTTTCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005784:ENSBTAT00000007609:49
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.017 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043115=CUB=PU(54.3=95.0)
A:
NA
C2:
PF0043115=CUB=PD(44.8=94.0)
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:
GCGGCAGCAACATCACCTC
R:
CAGAGAAAGCTATGGCGAAGA
Band lengths:
318-1344
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]