BtaALTA0004503-2/4 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000002069 | BOLA
Description
Bos taurus MHC class I heavy chain (BOLA), transcript variant 1, mRNA. [Source:RefSeq mRNA;Acc:NM_001038518]
Coordinates
chr23:28505636-28506312:-
Coord C1 exon
chr23:28506219-28506312
Coord A exon
chr23:28505794-28505905
Coord C2 exon
chr23:28505636-28505793
Length
112 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
TCATCCCTCCCCTCCCCCAGGCT
3' ss Score
9.69
Exon sequences
Seq C1 exon
GCTTCTTCCCAGACCCAGAGGATGCGAGTTATGAGGCCGCGAACCCTCCTCCTGCTGCTCTCGGGGGTCCTGGTCCTGACCGAGACCCTGGCGG
Seq A exon
GCTCCCACTCCCTGAGGTATTTCTACACCGGCGTGTCCCGGCCCGGCCTCGGGGAGCCCCGCTTCATCGCCGTCGGCTATGTGGACGACACGCAGTTCGTGCGGTTCGACAG
Seq C2 exon
CGACGCCGCGGATCCGAGGACTGAGCCGCGGGTGCCGTGGATGGAGCAGGAGGGGCCGGAGTATTGGGATCGGGAGACGCGAAACTTAAAGGACGCCGCACAGACTTTCCGAGTGAACCTGAACACCCTGCTCGGCTACTACAACCAGAGCGAGGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002069-0-3,0-2,0-1,0-0-2/4
Average complexity
Alt3
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=0.187
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(0.1=0.0)
A:
NA
C2:
PF0012913=MHC_I=PU(50.3=98.9)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
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:
CTTCTTCCCAGACCCAGAGGA
R:
TCTGGTTGTAGTAGCCGAGCA
Band lengths:
242-354
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development