BtaALTD0013626-3/3 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000009924 | MR1
Description
Bos taurus major histocompatibility complex, class I-related (MR1), mRNA. [Source:RefSeq mRNA;Acc:NM_001190298]
Coordinates
chr16:63652906-63654100:+
Coord C1 exon
chr16:63652906-63652981
Coord A exon
chr16:63652982-63653166
Coord C2 exon
chr16:63653825-63654100
Length
185 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGTG
5' ss Score
1.16
3' ss Seq
GCCATTCATGTGTCTTCCAGGGT
3' ss Score
8.71
Exon sequences
Seq C1 exon
GGACTCACTCTCTGAGATATTTTCGCCTGGGCATTTCAGAGCCTGGCTATGGGATCCCTGAATTTATTTCAGCCGG
Seq A exon
GTATGTGGATTCTCATCCCATCACCATGTACAACAGTGTGTCCCAGCTGAAGGAGCCGCGGGCCCTGTGGATGGAGGAAAACCTGGCACCTGATCACTGGGAGAGGTACACACAGCTGCTGCGGGGCTGGCAGCAGGCGTTCAAGGTGGAACTGAAGCAGCTGCAGCATCACTACAATCACTCAG
Seq C2 exon
GGTTTCACACTTACCAGAGAATGATTGGCTGTGAGTTACTGGAGGATGGAAGCATCACGGGATTTCTCCAATATGCATATGATGGACAGGATTTCCTTATCTTCAATAAAGATACCCTGTCCTGGATGGCCATGGATAATGTGGCTGACATCATCAGGCGGGTATGGGAGGCCAATCGGCATGAGTTACAATATCAGAAGAATTGGCTGGAAGAAGAATGCATTGCTTGGTTAAAGAGATTCCTGGAGTATGGGAAAGATGCCTTACAAAGAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009924-2-1,3-1,4-1-3/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.005
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(49.4=98.9)
A:
NA
C2:
PF0012913=MHC_I=PD(50.0=94.6)
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:
CCTGGCTATGGGATCCCTGAA
R:
TGCATTCTTCTTCCAGCCAAT
Band lengths:
257-442
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development