BtaINT0044587 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038281 | CSMD3
Description
CUB and Sushi multiple domains 3 [Source:HGNC Symbol;Acc:HGNC:19291]
Coordinates
chr14:54226888-54228757:+
Coord C1 exon
chr14:54226888-54226986
Coord A exon
chr14:54226987-54228553
Coord C2 exon
chr14:54228554-54228757
Length
1567 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
CCACAATTATTTGTACGCAGCTG
3' ss Score
4.77
Exon sequences
Seq C1 exon
TAGGAGAATCACTTCCACTGAGTTCAGGTAATCAGATCACAATTCGATTTACTTCAGTTGGACCAATAACAGCTAAGGGATTTCACTTTGTTTATCAAG
Seq A exon
GTAAGTGACCCTGTAGCATAGAAACACACTAAGGAATGTAATCAGTTTCCATGCTATGTTCAGAATTGTTGAATGATGAGAGCCTCATAACCATAAAGGACAGATAAAAGTTGTGTGCTTTAAAAAAAAAATTGTTTTGCATTTTCCCCTTCCCCATTATTAAAGCATTATTACTTTTACCAAAGTAAAAAAAAAAATCTGTTGCTTCCATCATCATTCTCAAGCAAATTTCATGCTTTTCCTTGTTTTTAACATACTGTTTTTAAAACATCTTTTTTTTTGACAATGCTTCACTCTACATATTCTATTTCCTTATAGTCTAGCACTCTAAGAATGTAAAAACTTTTTGTGTTGATGTACTTAGACATGCCAAGGAAATCATTACTCCATTCTAAAATTGTAGTTTCTCATTCTCTTAGGAGAATTCAAACTTTCTTCATGATTATTAAATATTTTTGCACAATTCAAAATTAGTTTACACAGTTTTTCTGTCACTTATAATAGACAAACTTCCACATTATATAAAACTAAATTAAGAGCTATCTTCTGAATATTTTATTTGAATTATATATGATCAATGTAGTTATTCTCAAATGTATCTTGAACTTTATTCCAAATAAATTTATAAACACTTGTGATTTGATATTCTTATTAAACCCTCTTATTCTAATTATAATATTGGCTATAATATTACACTGTTTCATTCTTAATAATAGTCCCTCTGTAACAATGCGTGGTATTATGATTTTTAAAAGGCACTCTAACAAATGAAATTATTTTCACTCAAGTGACATAAGAGGAATCTATTTGGAATTCATCTTATCATTTTTTGGACTATTGTCAAACTCCTTAATCCCATCTGTATGTGTTTTAAAAAGAAAAAACATCCTGTTATCATTCTGTCTTTAAAAAAGTCACAATTGAAGAACATACCTAAAAGGAATTTCAAATTTGATATTGTATGGTTATTAAAGTTTCTATTGTTGTTAATCTGTCTGACTTCTATTCTGCTTAGCCTGAACATATTGTCTTCATCAATAGCAAACATGTTTTGAACAACTAAGTTTATGAATATGTTGTGAAATTAATCAAGTGTTTTTGCTTTTTTAAAATCTGTGTTTTTAGGGAGCAAATAGTGTTAAAAAATTGGCATTGCTTTACATAACCTGACATCTGCTTTTTGTATGCTTGGCATTCCAATTTAAAAAGAAAAAAAAAAATGTATCTGTTACCATTCCTTAAATTGAAATATCTTTGCTCATGCTACATTGTTATATTTATAAAAGTATGGTAAAACAAAAAACAGAAAGTAACTGATATTGTTTAAAGAATCCAAAATAAAAATGTTTTTAAAGAAAAAATCTTAATGACAATAGCAATATTTATTCATTTTGAATTTATTCATTTCATCATGTATGAAATTTTAAACTTTTATAAATATGTTCAAATTGTTACCTAAAGTTCGAGTTAGTGAAGATTTCTCTGAAATCTGTTTGTATAGTCACATTTTGAAACCTATATTTCTCTACCAAACATGAAATTAAAATCCACAATTATTTGTACGCAG
Seq C2 exon
CTGTTCCTAGAACAAGTTCCACACAATGCAGTTCTGTACCTGAACCAAGGTTTGGAAGAAGGATTGGCAATGAATTTGCAGTTGGTTCATTGGTTCTTTTTGAATGTAACCCAGGATATATTCTCCATGGATCCATTGCAATTAGGTGTGATACAGTGCCGAATTCTTTGGCCCAATGGAATGATTCCTTACCTACCTGTATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038281:ENSBTAT00000027766:28
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:
PF0043115=CUB=PD(29.0=91.2)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.3)
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:
AGGAGAATCACTTCCACTGAGT
R:
CAATACAGGTAGGTAAGGAATCATTC
Band lengths:
302-1869
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development