BtaINT0044613 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038281 | CSMD3
Description
CUB and Sushi multiple domains 3 [Source:HGNC Symbol;Acc:HGNC:19291]
Coordinates
chr14:54351570-54353783:+
Coord C1 exon
chr14:54351570-54351755
Coord A exon
chr14:54351756-54353609
Coord C2 exon
chr14:54353610-54353783
Length
1854 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGT
5' ss Score
9.14
3' ss Seq
TCAATAATTATGTATTGTAGTGA
3' ss Score
4.23
Exon sequences
Seq C1 exon
TGGTCAACTGTTCTGATCCTGGAATTCCAGCCAATTCCAAAAGAGAAAGTAAAATAGAACATGGGAATTTCACCTATGGCACTGTGGTATTCTACGACTGCAATCCTGGATATTTCTTATTTGGATCTTCAGTTTTGATATGTCAACCAAATGGACAATGGGACAAACCTTTACCAGAATGTATCA
Seq A exon
GTAAGTAGATAATGTGAACTCTTTTTTGAGAAAATGCCCTGAAACCATACATGTATATTTATTGTTTTTATGAAATATTTAGAGCTGTGTATCAGACGGAAGTGTACTGATTGTACTTTTTTATTGTTTTGAAAGTGCCCTTCCTGTATTCTGCCAATTCAGTGCCCATGTGCCATCCATATTAATATTAATATGATTAATATTTCTCTATTATTCCTTGATTTTGAACCTTCATGGAACAGACAGAATATTAAAGGCAGATATATTTCATACTCTGTGATGTTGCCACTCCATGAGAGGCAACTATAATTTTATTTTCTCTTGTACTACTATTTCAAATTTCATTTAAAGCAAAATGAGTCAATATAAATAGCCACTAGGGCTGCAAAATGCTTGAGAAAATTAGAGTGTTACTTAAAACTCATTGACTTTAAATATTTATCTTATACAGGCACATACATATATGAAATGTTAATATACATTGTCTTTAAGGTAGTAGGAATAAGAGTGCATTTTGTTATATGTTATTTTGGAGCTATAGAATATAAATAAAATAAATTATAGCAGTTTTGCATATAATTAGCATGTATAGTGATAAAATAATTTAATAGAAATAAATCAAAAGTATCTGAAGACAGAGAAATGAACTTGAATTCTAAGCATTCAGCTTATAGATAGGACTTAGTTACATTTGCTTCTCAGAGTTGAATATTGGACATAATAGGAAAGAAACAATCATTGTGCAAGTAATTTTTGGTTATACTAAATTGCTAAATTACAAAATCATTTTATGATTGTTTTGTTTAGAGGTACTTTATGTACATGCAGTTTTTTAAATAGTTGTGGCATCATTTATGAACTCATTCATGAACAAATAAAAATAGAGTGCCTATCTAATTTCATATACTATGCAGATAATTCAGTCAATTGTTGATCCCTTGTTTAAAATGTATTTGATTTCTCTTCGTAGACTAGTTAGTCTAATGGTTTAAGTAATTCACTTATCCTTGTATGGCTACAACATGAAAGTTAAAAATCTTTTGTAGGACCTGTAAACATGAACTTCTTCAGATTTTCATAGCTCTCATATACTTTTTACCTTTTCCTTATTTTCTATTGTACTTCCTGGTAGTGTGCTATTTACTCAGGGATTTTATTAAGTTTATATCTCCTGTGTGATATTTAATACTCATCATATGTAATACTCTAGTCATGAAAGGGAACACATAGTAAGTCCCCAAGCTACTTCCAGCTTATAGAGAATTCTCAGTGTTTTAACATCTGATTCTGCTCAGCTCAGCTGTATTTTGGTTAATAAGCCTTTGAGTATTTTCATTTTACAGGATGATTTATTTATTAATGGTCAGGAGTAGAATTTAGACTATATATGCATAGTCTGAATCATGTGCCACAGATCCATCTTCCATCCTTCTTTACCCTCAAAGTTTTTCCCTTTTAATTTCTGTAGGGCATTTTGAATTCTATATGGAATCCTATAACCTTATTTAGCCAATCCATACCACTCCTCTCCCTATCTTTCACATCCTTATCTAGATGAATGCTTCCAATCCATGTACATGTGTATATAAACAAACACCCACCACCCCAATACATACAAGCTTATTGACTCAGTCATTTAAGCTTACTTACAGTGTTCCTATTAAACTCATACTCAGGGTGAGTGGGCTAACAGAATAACTCCTGTAACTTCAACTTCATATAAATGTTTGATTTTCAGAGGATGTATACAGTGGAGCAGATAATTCTGATTCATTAACATTTCAAAAAAAGTTGGTGCAGGTTGTTCGATAGGAGATATAAAAAAATTTTATATTCAATAATTATGTATTGTAG
Seq C2 exon
TGATTGACTGTGGACACCCTGGCGTTCCTCCTAATGCAGTCCTGTCTGGTGAGAAGTATACCTTTGGTTCTACTGTTCACTATTCCTGCACAGGAAAGCGTACACTTCTAGGCCAATCATCAAGGACTTGCCAATTAAACGGCCATTGGAGTGGATCACAACCTCATTGTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038281:ENSBTAT00000027766:53
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.032 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=92.1)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGTCAACTGTTCTGATCCTGG
R:
GATCCACTCCAATGGCCGTTT
Band lengths:
343-2197
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development