BtaALTD0003355-2/3 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000002069 | BOLA
Description
Bos taurus MHC class I heavy chain (BOLA), transcript variant 1, mRNA. [Source:RefSeq mRNA;Acc:NM_001038518]
Coordinates
chr23:28503864-28505364:-
Coord C1 exon
chr23:28505259-28505364
Coord A exon
chr23:28505163-28505258
Coord C2 exon
chr23:28503864-28504139
Length
96 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGA
5' ss Score
7.75
3' ss Seq
ATTTTCTGATTCCTCCTCAGACC
3' ss Score
9.23
Exon sequences
Seq C1 exon
GACGCCTACGACGGCAGAGATTACATCGCCCTGAACCAGGACCTGCGCTCCTGGACCGCGGCGGACACGGCGGCTCAGATCACCAAGCGCAAGTGGGAGGCGGCAG
Seq A exon
GTGAGGCGGAGAGACGCAGGAACTACCTGGAGGGCCGGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGACACGCTGCTGCGCGCAG
Seq C2 exon
ACCCTCCAAAGGCACATGTGACCCGACACCCCAGCTCTGACCGTGAGGTCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGAGGAGATCTCACTGACCTGGCAGCACAATGGAGAGGACCAGACCCAGGACATGGAGCTTGTGGAGACCAGGCCTTCAGGGGATGGAACCTTCCAGAAGTGGGCAGCCCTGGTGGTGCCTTCTGGAGAGGAGCAGAGATACACGTGCCGTGTGCAGCATGAGGGGCTTCGGGAGCCCCTCACCCTGAGATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002069-2-8,3-8,4-8-2/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.075 A=NA C2=0.290
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(49.2=94.6)
A:
NA
C2:
PF0765410=C1-set=WD(100=89.2)
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:
CTCAGATCACCAAGCGCAAGT
R:
TCTCCACAAGCTCCATGTCCT
Band lengths:
183-279
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development