BtaEX6096783 @ bosTau6
Exon Skipping
Gene
ENSBTAG00000012451 | HLA-DMB
Description
Bos taurus major histocompatibility complex, class II, DM beta (BOLA-DMB), mRNA. [Source:RefSeq mRNA;Acc:NM_001040481]
Coordinates
chr23:7189575-7193645:-
Coord C1 exon
chr23:7193378-7193645
Coord A exon
chr23:7191688-7191969
Coord C2 exon
chr23:7189575-7189859
Length
282 bp
Sequences
Splice sites
3' ss Seq
CCTTTCTCTGGCTCCTACAGGTG
3' ss Score
11.95
5' ss Seq
CACGTAAGG
5' ss Score
7.47
Exon sequences
Seq C1 exon
GATGATCTGGCAAGGAACAGGTTTATCTCAGGCCTTAGTAGCCCCAAATTGCTCATTTAGAGAGCATCAAGGGGCCCCGGGCAATACCACATTCCCACTTAGTGTGTGGAGATCCTCTACCCAGGCTGGGACTTCTGGGGTAGACGAAGACCCAGGGCCCCTGGAGGAGCTGGTCCAGGGGACCGAACTCCCCGTGTCTCCCCAGAGCAGAGCATGACTGTCCTCCTGTCGCTGCTGCTGGGCTTCAGCCTGGGCTGCACCGCAGCAG
Seq A exon
GTGGTTTTGTGGCACACGTGGAAAGCACCTGTGTGTTGGACGATGATGGGGATCCGAAAGACTTCTCGTATTGCATCTCCTTCAACAAGGATTTGCTGACCTGCTGGGATCCCCTGCAGGCCAGTATGATTCCTCGTGAATTTGGGGTGCTGAACGGCTTGGCCCGGTACCTCTCACAGTTCCTCAACAATAATAGTTACCTGATCCAGCGCTTGTCCAATGGTCTGCAGAACTGTGCCGCGCACACCCAGCCCTTCTGGAGCTCTCTGACCCACAGGACAC
Seq C2 exon
GCCCACCGACCGTGCAGGTAGCCAAAACCACTCCTTTTAACACGAGGGAGTCTGTGATGCTGGCCTGCTATGTGTGGGGCTTCTATCCAGCGGACGTGGCCATCACGTGGAGGAGGAACGGGCAGGAGGTCCTCCCACACGGCAGGGCCTGGAGGATCATCCAGCCCAACGGAGACTGGACATACCAGACCGTCTCCCATCTGGCCACAACCCCCTCTTTTGGGGATACCTACACCTGTGTGGTCGAGCACATTGGGGCTCCTGAACTCATCCTTCAGGACTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012451-'2-4,'2-3,4-4=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=0.000 C2=0.031
Domain overlap (PFAM):
C1:
NO
A:
PF0096914=MHC_II_beta=WD(100=84.2)
C2:
PF0765410=C1-set=WD(100=87.5)
Main Skipping Isoform:
ENSBTAT00000016520fB3250
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
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAGGCCTTAGTAGCCCCAAA
R:
AGCATCACAGACTCCCTCGTG
Band lengths:
302-584
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]