BtaINT0044467 @ bosTau6
Intron Retention
Gene
ENSBTAG00000009739 | CSMD1
Description
CUB and Sushi multiple domains 1 [Source:HGNC Symbol;Acc:HGNC:14026]
Coordinates
chr27:1168813-1171044:-
Coord C1 exon
chr27:1170867-1171044
Coord A exon
chr27:1168959-1170866
Coord C2 exon
chr27:1168813-1168958
Length
1908 bp
Sequences
Splice sites
5' ss Seq
TTGGTATGA
5' ss Score
5.24
3' ss Seq
GCTCCTCCTCTCTTTCCCAGGGA
3' ss Score
10.25
Exon sequences
Seq C1 exon
CTCCTTGTGGATATAACGTGACATCTCAGAACGGGACCATCTATTCTCCTGGATTTCCAGATGAGTACCCCATCCTCAAGGACTGCATCTGGCTCATCTCAGTGCCTCCCGGCCATGGCGTCTACATCAACTTCACCTTGCTGCAGACGGAAGCTGTCAACGACTACATCGCAGTTTG
Seq A exon
GTATGAGAACCTTTCCTGAAAACACCCATCTGTCCTTGTGATAAACTGTTCTTGTAACCACTTACATGTCACTTTCGTCGATTTAGAGATGAAGTAGTTAGGTAGATGTCAAAACAGAAATTTACCAACTAAATCTAGAGATAGAATAAACCTCATGTACCATGCTACATGGTAGATATATTCAAGATTACTCTAGATAGAGGAGAATATCCCAAACGTATTTTATTTTCATGTTTATTTCTTGTTTTAATTTTTATTTACTTACCTTTTTGGCCATATCACATAGCTTTTGGGATCTTAGTTCCCTGACCAGAGATTAAACCTGGGCCCTTGTCAGTGAAAGAGTTAAGTCCTAGCCACTGGGCCACTTGGGAGTTCCTTCTTTTCTTTTTCATTTTCAAGTATAAATCTTTTTTTTCTTAAAAAAAAGCTTGTTGGTTCCTTTGCCATATAATAATTTGATGCTTCTGGAAATATTGAAGAAATGATCACACACAGCTTTCTCTCTGTACTTTATAAACCTTGCGGAACTGCCCCCACCCACCTCCACCTTCCCTACCATGGGCTGTGTAGGGGATGCCGAGGGGGATGTAGCCCTAGCTCCCCATCTAATGAGCCATGTAGCCTGGGTAAGTTAATCTAAACTCTCCTTCACTGAATGTTCATGTCTATGAGAATTACTATTTCTACCGTTGCCTTTGGAGGTGAGAATTTATAGGGGAAATGGGAATGACAAAATATGATGGGAAGAGTAGAGCTTACCATTGGGGCACAGCCCAGATTTGGAATAAGTTGGATGTGCTTTAGGAATAAAATGCCCTGAAAACTCAAGCATAATCACAGTTAACAAAGCTGTGTGTGTGTGTGTGTGTGTGTGTGTTGGTGAAGTTGTAAATGTAGGGGTTGTCTTAGCCATTGAAAATTCTCTGAGGCAAGAGAACAGGTGAGTTGCAGGCACTGGGAGATCCCAAGTGTGATGTGGCTTTGGGAAAGCACAGAAGAGAGAAGGGGTGACCTGGCCAGGTAAGCTGGCCTCATACATCATGTTAAGGATTTTGGGCTTTATACTAGAGCAACACAGATTCACTTTAGAGTCATAAGAAGGAGAATTATAGGACTAGGTCCTGGATGCAGAATACCCATTATTATTGTGTAGGGGGGCAGGTCAGCTGGATAAGATGGGAGACTGGCCTTTGAGGCTATTTCTATAGGGGGGAGATTCTATAGGGCTATTTCTCACAGGAGGGGAGATTGGGGGATAGGACCTGTGTTGTGGCAATGAGCAGAAATGGAGAACCTGAAATATTAAGTTGACCTATGAAGCAAAGCAAGACAGGCAAACAACACTGAAATGAAAAGCCACACTATAATATCAGCAGGTTTACCCAGATTAATCAGTAGATTTAGCAGTAGGAGCAAGGTCTCCCTCCAGCAGTGGAGGGAGTCCCTGTCCTCTGAACACTCATGAGACAGACTGGAGTGCAGTCATCTATGAATATTAAACATCTTAGTATTTCTAAACACGGAATCTAGAAGATGGTAATATTTTATTCAGTTTTTTAAAATATTTCAATTCAGCCATAAGAGCTCCATAAATCTCACCCATAATTAAAGAGACACCCTGAATTTAGACTTTAAAATGGGAACATTTGAAAGGAAGTTGATAAGTGGTACTGACGTCACTAGAATAAATGTGACCTTGTCTCAAAAACACCTCTGAGAAGGTCAGGTGCAGGAGGAACAAGGGAGCCCAAAGCTGCTGTTTGAAGACCAGGCTTTTCAGCTGGATCCTGGGGTCAGAGCATCATCTTTCACCAAGACCAAGCCCTGCAGTCAGAAGAAAACGGTTGTGAATTTAAGCTGTAACTGGCAACTTTCTATTTAGAGGGCTCCTCCTCTCTTTCCCAG
Seq C2 exon
GGATGGTCCTGATCAGAATTCTCCACAGTTGGGGGTTTTCAGTGGGAACACCGCCCTGGAGACAGCATACAGCTCCACCAACCAAGTCCTGCTCAAATTTCACAGTGACTTTTCAAATGGAGGTTTCTTCGTCCTCAATTTTCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009739:ENSBTAT00000012850:40
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=0.020
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:
CTCCTTGTGGATATAACGTGACA
R:
AATTGAGGACGAAGAAACCTCCA
Band lengths:
318-2226
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]