BtaINT0044564 @ bosTau6
Intron Retention
Gene
ENSBTAG00000005784 | CSMD2
Description
CUB and Sushi multiple domains 2 [Source:HGNC Symbol;Acc:HGNC:19290]
Coordinates
chr3:112892045-112894127:+
Coord C1 exon
chr3:112892045-112892206
Coord A exon
chr3:112892207-112894014
Coord C2 exon
chr3:112894015-112894127
Length
1808 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGG
5' ss Score
9.68
3' ss Seq
TCTGCACTTTCTTTTCCCAGGAA
3' ss Score
9.8
Exon sequences
Seq C1 exon
TTCCTGGGGATGTTTTTGCCAAGAATTCCCTATGGAAAGGGGCCTATGAGTACCAGGGGAAGAAGCAGCCAGCCATGCTCAGGGTGACTGGCTTCCAGGTCATCAACAGCAAGGTCAACGCCACCATGGTTGACCACAGCGGCGTGGAGCTGCACTTGTCTG
Seq A exon
GTAAGGTGCAAGCCACCCGCGGGAAAACCTGCCAGATGGTAAGGGTGATGGGCACACGCTCAAATGCCACTTCCTTGTGCTGTCCTGCAAGGTTCAGATTGGTCTGGTAGGCAGGGGAAGAGGAAATGTCTATTCATCTTTGTTTACATGGTAAAAGCACCACCGACTACAGGGAAATGGTTAGATGACAAACATTAGTAAATGGAAAGTAGGGAAAAAAAAAAAAAAACTCTTACGAATAAAGAAAAAAGAGACAGATATCCCTAAAAACCGAACCAAAAATAGAGGCAGATAACTCCCAGAAGCCAAAGTACAGTTAATAAATAAACGGAAAAATAGTTTTAGCAATAATCAAAAGAAGTGGAAAATGTCACTTTCCGCTTATTCCACTTTTTTTAAGCCATAAATATTGGTGCTAGTCCAGTAAAGGTAGTACTCTGGTCAAAGTATGAAATAGTGTAGTTGAACAAAATAATTTGGCAATTTGTATCAAGACCCAGGAAAATGAGTAGACCCGTCAATTACACTGCTAAGAATTTTTATCATAAGAAATAGTTATAGAGGGAATCAAACATTTCTGAAAAAAGAATGAGCTAATTGCATCACATAACACCTGGGAATAGAAAATTGTCTCAAAAGAAATGGATACATTAATTATAGTATGTCTGCTGGATAAAATATTATGCCAATTTGGGAGAAAGTACATCCACTATAATGCATTTAAAATGTGACTCCAGTTTTTAAAGGAAAAAAAATATATTCATAAGAAAGAAAATTGAAAGTAATTACACCAAAGTGTTAACAGTGGTTATTTCTCAGAAATGAGACCAGGAATGAATTTTCTTTCTTCATGCATCTCTGCATTTGCCAAAATTTCCCCAATATTCAAATTTTATACAATCAGAAAAACTAAATATCTTGGAAAGCAAACGTTTGTTGAATAGAGGGGTAGATGGATGGAAGCATGAGTACATGTGGATACACAGTCCTGCGTGCGGTTACAACTACTCACTCATGCGTGCACACACGAACACAACTAATGTTCATATTCACTCAGCTGCTCTAAAACACAGTCCTAAACGCACCCACACGCTCTGGTACACGTGCCCTCGTGTGTTCCCTGCACCCGCTGAATCATAAGCACGCCATGTGTTAACTGACCCTTAACATATACAAAACCCTATTCCCTGTATTCTCAAGCATGCATGTCTAAACAGGAACACAACCACAGACCAGTAATCCAGTTCTTTATTAGCACGCATACGCACATTCTTGCACAGCCTCACATTTCAGCCTACACAGACTCACAGGCCACACTACACTTACCTAACTACAGTTATACATGGGATGTTTACAGCAAAATCTACACATGAAGTCCTGCTCAGGGGCTTCCCTGGTGGCTCAGTGGTAAAGAATCCACCCGCCAACACAGGAACACACCTTTGATCCCTGCTCCAGGAAGATCTCAAATGCCTCAGAGCAATTAAGCCCATGTGCCACAACTATTAAGCCTGTGCTCTAGAGCCTGGGAACCAAACCACAGGCTTGGTGAAGCCTGGGCACCAAGAGTCCATGCTCTGCTGCAAGAGAAGCCACTGCAGTGAGAAGCCCATGCTCAGCAACCAGAGAGTGGCCCCCACTCACAGCAACTAGAGGAAAGCCCAAGAAGCAGCGAAAACCCAGCACAGCCAAAAATAAATAAATTTTTAAAAATCCTACTCGGACACTCACACCCACATACCCACAAACTTGGGTTTTGAAAATTTACCAGATCTTTCAAGTGTACCCTCTGCACTTTCTTTTCCCAG
Seq C2 exon
GAATTTATAAGAAAGAAGATTTCCATCTCCTCCTTCAAGTTTACCAGATTACAGGGCCTGTGGAGATCTTTGTGAATAAGTTCAAAGATGATCACTGGGCTTTAGATGGGCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005784:ENSBTAT00000007609:72
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:
NO
A:
NA
C2:
NO
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:
TCCTGGGGATGTTTTTGCCAA
R:
TGCCCATCTAAAGCCCAGTGA
Band lengths:
273-2081
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]