BtaINT0044619 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038281 | CSMD3
Description
CUB and Sushi multiple domains 3 [Source:HGNC Symbol;Acc:HGNC:19291]
Coordinates
chr14:54387002-54389032:+
Coord C1 exon
chr14:54387002-54387175
Coord A exon
chr14:54387176-54388958
Coord C2 exon
chr14:54388959-54389032
Length
1783 bp
Sequences
Splice sites
5' ss Seq
TAGGTAATA
5' ss Score
6.84
3' ss Seq
AATATTTTCTTTTATTTTAGAAC
3' ss Score
9.18
Exon sequences
Seq C1 exon
CAAAATTTTGTGGTGACCCTGGTATACCTGCCCAAGGAAAAAGAGAAGGCAAAAGCTTTATATACCAGTCAGAGGTTTCATTCAGCTGCAATTCTCCTTTCATATTAGTGGGATCTAGCACCAGAATATGTCAAGCAGATGGCACTTGGAGTGGTTCATCACCTCACTGCATAG
Seq A exon
GTAATATTAATGAAAGATGGACAGTGCTCAGTAATTTTGGAATTAATAGCTAGTAATGACATTTAATGATTTACTTTATCCTATAAATTATAGTTGGCTAAATGTGAAAACGGAGAAGGCAATGGCACCCCACTCCAGTACTCTTGCCTGGAAAATTCCATGGATGCAGGAGCCTGGTGGACTGCCGTCTATGGGGTCGCACAGAGTCAGACATGACTGAAGTGACTTAGCAGCAGCAGCAGCAAATATGAAAAACAAAAATGTAAAATATAGCCATTGTAAGGCACTGAAAATTAATATTATTAAACATTTATTACTTTAGTACTTTTGAAATAGTTTTCCTGTTTACCAGTAAAATGAAAAAAGCTTCCATATCACTATCATGAAGTACTGACATTTGTATCAGTTCAGTTCAGTTGCTCAGTCGTGTCCGACTCTTTGCAGTTAATAAAACATACTCAAATGAAATTAAACTTGCTTCAAAAATATTACAAAGGTATATTGATTTCAAATGGTTCTAAGTACATTGCTCTAATCCTAATTTTTGTGTGTTTTTATTGTCTTATTTTTTCATTCAAATATAGTTGATGTACAAAATTATATGTTACAGGTGTTTAGTATAGTGATTCACAATTTTTAAAGGTTATACTCATGTGCAGTTATAAAATATTAGCTCTATTTCCCATGTTGTACAATGTATCTTCTTAGTTTATTTTATGCATAATGGTTTGCACCTCTTAATTCCCTACACCTCTTTTGTCCCTCCCTCCTTGCCTCTTTCCACTGGTAACCACTAGACTGTCTTCTACATCTGTGAGTTTGCTTCTTTTTTGTTATATTTACTGTTTTTTTTTTCTTTTTTTTTTTTTAGAATTCACATATAAGCGGTATCATACAGTATTTCTTTCTCTGATTTATTTCACTCAGCATAATACCCTCCAACTCCATCCATGTTGCTACAAATGGCAGATTTTCATTCATATATATGTATATCACATCTTATTTATCCATTCATCTGGTGGTCGCTTCTGTATCTTGGCAATTGTAAATAATGCTGCTGTGAATATCTTTCAAATTAGTGCTTTAGTTTGTGGGGTGTATACACCCAGGATTGAAATTGCTGAGTCACAGGGTAGTTTTATTTTTAGTTTTTAAATAGCAGCTGTACCAATTTATATTCACACCAATAGTGTATTTAGGGTTCCTTTTTCTCCTTAAATTAAATTTCACATTGAGTAAACTAATGAAAAATTCTGTCATACAAGCTAGCCAACTCAGGGGCTATCAGCCCTACCATTTTTGTGTTTGACTCTCTTACAGGTATCAGTGAAAATGCAAATAACTAAGTCTTGTTTCTGGAAAATAAATTATTTCTTAAAGGCACTATTACCCTACTTGAGATTAATTCTTAGAAAAGTCCCTAAGCAGATGTTTTATGCATGTGGTCCTCTTTCATATCCTTCATTTTCCTTTAACTTTTTATTACCAGAGTTAGTTGGATGTCAAATGCTTTTATATTAGAAGTGTTCAAAGTTCATGGATTGCATAATTTGTTTAAACTGCAGTATTATACCTGAGTTTTTGGTTTTAAGATTAGCAAGTTTCTGTTCATGGAGATATTTATTAGATTTTTTTGTTTATTATTACCAGGACCCTTTCATGAAACCCTAGATCTCTTAAAATTATTTTACATAGGATAAATATACATTTAAATAAACCTATATGTTTTAAAGGAATATTACACTTTTTATTTTAAGAGAAAGAATATTTTCTTTTATTTTAG
Seq C2 exon
AACCCACCCGTACATCATGTGACAATCCAGGCGTGCCACGTCATGGATCTCAGAACAATACATTTGGATTTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038281:ENSBTAT00000027766:59
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=0.200
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=91.5)
A:
NA
C2:
PF0008415=Sushi=PU(32.7=72.0)
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:
CAAAATTTTGTGGTGACCCTGGT
R:
TGAAATCCAAATGTATTGTTCTGAGA
Band lengths:
247-2030
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development