BtaALTA0004504-1/2 @ 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
chr23:28505259-28505905:-
Coord C1 exon
chr23:28505636-28505905
Coord A exon
NA
Coord C2 exon
chr23:28505259-28505364
Length
0 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGC
5' ss Score
8.69
3' ss Seq
TCCTCCGCGGGTACAGGCAGGAC
3' ss Score
-2.36
Exon sequences
Seq C1 exon
GCTCCCACTCCCTGAGGTATTTCTACACCGGCGTGTCCCGGCCCGGCCTCGGGGAGCCCCGCTTCATCGCCGTCGGCTATGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGGATCCGAGGACTGAGCCGCGGGTGCCGTGGATGGAGCAGGAGGGGCCGGAGTATTGGGATCGGGAGACGCGAAACTTAAAGGACGCCGCACAGACTTTCCGAGTGAACCTGAACACCCTGCTCGGCTACTACAACCAGAGCGAGGCCG
Seq A exon
NA
Seq C2 exon
GACGCCTACGACGGCAGAGATTACATCGCCCTGAACCAGGACCTGCGCTCCTGGACCGCGGCGGACACGGCGGCTCAGATCACCAAGCGCAAGTGGGAGGCGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002069-1-6,1-5-1/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence exclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.187 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(50.3=98.9)
A:
NA
C2:
NA
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
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:
CGCACAGACTTTCCGAGTGAA
R:
CAGGGCGATGTAATCTCTGCC
Band lengths:
95-99
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development