BtaALTA0000983-3/3 @ bosTau6
Alternative 3'ss
Description
Bos taurus major histocompatibility complex, class I (LOC512672), mRNA. [Source:RefSeq mRNA;Acc:NM_001076841]
Coordinates
chr23:28304695-28306069:+
Coord C1 exon
chr23:28304695-28304970
Coord A exon
chr23:28305339-28305793
Coord C2 exon
chr23:28305794-28306069
Length
455 bp
Sequences
Splice sites
5' ss Seq
CTGGTAATG
5' ss Score
5.67
3' ss Seq
AATCTTACTTCCCTGACCAGGAA
3' ss Score
7.67
Exon sequences
Seq C1 exon
GCCCCCACACCCTCCAGTTCACCTACGGCTGTGAGCTCCTGGAGGACGGCAGGACCACGTGGCACTGGCAGTATGGCTATGATGGTGAGGACTACCTGAGCTTGCATATGGACCCTCTGCAATACACAGCAGCCACATTCGTTGCTCAGTACACCAAACAAAAATGGGAGGCCGGTGGGAACTTCATAGAGAGAGACAAGAACTACTTGGAGAAGGAATGCATCCTGTGGTTGTGGAGATACTTGACGTTTGGAGGGGAGAGCTTGAACCGCACTG
Seq A exon
GAATTGAACCCAAACCCCCTGCAGTGGAAGCATGGAGTCTTAACCACTGGACCACCAGGGAGGTTCCCTGAGCCACTCATTCTTATTAGTGCCAAGGAAACTACTCTCAGGAGGACACAGAGCTGCTTCATAGAGTCTTGAAGATTTCTCATCCTTTTGGTGCTTTCCCACTAGATACACACCTGTATGTAGAAAACATTGACCAAAGACTTGATACAAGAGTCGAGAGCCTTTGAAGGGGCTCTTATCCTGGAGGATAACGTTAGACTGAGTTCCCGCACCCTTGACTTGAAGCTGGCTCAGCTTACTGTGGGTCCCTCTACCCTCAGATAGAGGAAGTTCCCTTTCTCCCACTGGTTGGCAGATGAGCCATCAGGAGTTGTGGTGGCTTGGTCTTTGGAGTCGATGCTACTCAACAAACCTGGCCTGCACCCTCCCTGCTTTGTGTACCACAG
Seq C2 exon
AGCCTCCCAAAACACACATGACTCATCACCGCATCTCTGACCGTGAGGTCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGAAGATCTCACTGACCTGGCAGCGCAATGGGGAGGACCAGACCCAGGACATGGAGCTTGTGGAGACCAGACCTTCAGGAGACGGAACCTTCCAGAAGTGGGCGGCCCTGGTGGTGCCTTCTGGAGAGGAGCAGAAATACACGTGCCGTGTGCAGCATGAGGGGCTTCAGGAGCCCCTCACCCTGAGATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038619-5-4,5-3,5-2-3/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.022 A=NA C2=0.194
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(46.8=94.6)
A:
NA
C2:
PF0765410=C1-set=WD(100=91.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
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:
GGACCCTCTGCAATACACAGC
R:
AAGGTTCCGTCTCCTGAAGGT
Band lengths:
342-797
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development