BtaALTA0004506-2/2 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000005182 | BOLA
Description
Bos taurus major histocompatibility complex, class I, A (BOLA-A), mRNA. [Source:RefSeq mRNA;Acc:NM_001040554]
Coordinates
chr23:27647470-27648112:+
Coord C1 exon
chr23:27647470-27647739
Coord A exon
chr23:27647936-27647955
Coord C2 exon
chr23:27647956-27648112
Length
20 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
GGGTGGTCGGGGCGGGTCAGGGT
3' ss Score
-2.39
Exon sequences
Seq C1 exon
GGTCCCACTCCCTGAGGTATTTCTACACCGCCGTGTCCCGGCCCGGCCTCGGGGAGCCCCGCTTCATCTCCGTCGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCCCGGATCCGAGGATAGAGCCTACAGCGCGGTGGGTGGAGCAGGAGGGGCCCGAGTACTGGCATCAGGAGACGCAGAGAACTAAGGACACCGCACAATTTTTCCGAGTGTACCTGAACACCCTGCGCGGCTACTACAACCAGAGCGAGGCCG
Seq A exon
GGTCTCACACCGTCCAAGAG
Seq C2 exon
ATGTACGGCTGCGACGTGGGGCCGGACGGGCTTCTCCGCGGGTATGATCAGTTCGCCTACGACGGCAGAGATTACATCGCCCTGAACGAGGACCTGCGCTCCTGGACCGCGGCGGACACGGCGGCTCAAGTCACCAAGCACAATGCTGAGGCGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005182-1-4,1-3-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.165 A=NA C2=0.130
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(50.6=98.9)
A:
NA
C2:
PF0012913=MHC_I=PD(48.9=94.6)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACTACAACCAGAGCGAGGCC
R:
CAGGGCGATGTAATCTCTGCC
Band lengths:
106-126
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development