BtaALTD0006103-2/2 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000009739 | CSMD1
Description
CUB and Sushi multiple domains 1 [Source:HGNC Symbol;Acc:HGNC:14026]
Coordinates
chr27:1365663-1376492:-
Coord C1 exon
chr27:1376312-1376492
Coord A exon
chr27:1376304-1376311
Coord C2 exon
chr27:1365663-1365832
Length
8 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGT
5' ss Score
6.86
3' ss Seq
TAATGTCCTGTTTATTTTAGCTG
3' ss Score
7.73
Exon sequences
Seq C1 exon
AGTACGACCTCGAGCCATGTGATGACCCTGGCGTCCCTGCCTTCAGCAGAAGAATCGGCTTTCACTTCGGAGTCGGGGACGCACTGACCTTCTCCTGCTTCCCGGGTTACCGCTTAGAAGGTGCTACCAAGCTCACGTGCCTGGGTGGGGGCCGCCGTGTGTGGAGTGCACCTCTGCCAAG
Seq A exon
GTGTGTGG
Seq C2 exon
CTGAATGTGGAGCAAGTGTCAAAGGAAATGAAGGAACGTTGCTGTCTCCAAATTTCCCGTCAAACTATGATAATAACCATGAGTGTATCTATAAAATTGAAACAGAAGCTGGCAAGGGGATCCATCTCAGAGCACGAAGCTTCCAGCTGTTTGAAGGAGATATTCTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009739-9-9,10-9-2/2
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=0.018
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=87.5)
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
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGTTACCGCTTAGAAGGTGC
R:
TCCTTTGACACTTGCTCCACA
Band lengths:
104-112
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development