BtaALTD0003205-2/2 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000015789 | BCAN
Description
brevican [Source:HGNC Symbol;Acc:HGNC:23059]
Coordinates
chr3:14225699-14226473:-
Coord C1 exon
chr3:14226385-14226473
Coord A exon
chr3:14226265-14226384
Coord C2 exon
chr3:14225699-14225781
Length
120 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTC
5' ss Score
7.04
3' ss Seq
TCTCTGCGGTTGTCCCCCAGATC
3' ss Score
10.84
Exon sequences
Seq C1 exon
GAGCTGGGAGGAGGCGGAGAACAAGTGCCGGATGTACGGCGCGCACCTGGCCAGCATCAGCACGCCGGAGGAACAGGACTTCATCAACA
Seq A exon
GTGGGCTGGGGACAGGGAGGGAGGCGACCCTCGCCACCTGTTCTCTCATCCACACATTCCCTCACTCATCAGTCAGTCAGTTAAAGAGTGTGCTATTAACTCCCTTATACGTTCATTCAG
Seq C2 exon
ATCGATACCGGGAGTACCAGTGGATCGGGCTCAATGACAGGACCATCGAAGGGGATTTCCTGTGGTCAGATGGCGTCCCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015789-14-20,15-20-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005916=Lectin_C=PU(30.2=59.3)
A:
NA
C2:
PF0005916=Lectin_C=FE(25.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGGAGGAGGCGGAGAAC
R:
ACGCCATCTGACCACAGGAAA
Band lengths:
162-282
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development