BtaALTD0006108-3/3 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000038281 | CSMD3
Description
CUB and Sushi multiple domains 3 [Source:HGNC Symbol;Acc:HGNC:19291]
Coordinates
chr14:53956123-54016589:+
Coord C1 exon
chr14:53956123-53956173
Coord A exon
chr14:53956174-53956317
Coord C2 exon
chr14:54016420-54016589
Length
144 bp
Sequences
Splice sites
5' ss Seq
TGGGTACGT
5' ss Score
7.7
3' ss Seq
ATATTCTGTTTTACCTGCAGCTG
3' ss Score
11.36
Exon sequences
Seq C1 exon
TTACAGAGTATAATCTGGAACCTTGTGAAGATCCTGGAATTCCTCAATATG
Seq A exon
GTAACCGAATTGGGTTCACCTTTGGGGTTGGTGACACTCTGACCTTCTCATGCTCATCAGGTTATCGTCTGGAAGGGACATCAGAGATCATCTGTCTTGGTGGTGGCCGACGAGTGTGGAGTGCACCTCTGCCAAGGTGTGTGG
Seq C2 exon
CTGAATGTGGTGCATCTGCAACAAATAATGAAGGCATTTTGCTCTCTCCAAATTATCCACTGAACTATGAAAACAACCATGAATGCATTTATAGTATTCAGGTTCAAGCAGGAAAGGGAATCAATATTTCAGCCAGAACATTTCATTTAGCACAAGGAGATGTTCTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038281-15-17,16-17,17-17-3/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=84.8)
A:
NA
C2:
PF0043115=CUB=PU(50.9=94.7)
Main Skipping 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:
CAGAGTATAATCTGGAACCTTGTGA
R:
CTTAAGAACATCTCCTTGTGCTAAA
Band lengths:
218-362
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development