MmuALTA0008346-3/3 @ mm9
Alternative 3'ss
Gene
ENSMUSG00000073411 | H2-D1
Description
histocompatibility 2, D region locus 1 [Source:MGI Symbol;Acc:MGI:95896]
Coordinates
chr17:35400324-35401059:+
Coord C1 exon
chr17:35400324-35400593
Coord A exon
chr17:35400784-35400857
Coord C2 exon
chr17:35400858-35401059
Length
74 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGT
5' ss Score
10.49
3' ss Seq
CTGACCGCAGGGTCCCGCAGGCT
3' ss Score
1.19
Exon sequences
Seq C1 exon
GCCCACACTCGATGCGGTATTTCGAGACCGCCGTGTCCCGGCCCGGCCTCGAGGAGCCCCGGTACATCTCTGTCGGCTATGTGGACAACAAGGAGTTCGTGCGCTTCGACAGCGACGCGGAGAATCCGAGATATGAGCCGCGGGCGCCGTGGATGGAGCAGGAGGGGCCGGAGTATTGGGAGCGGGAAACACAGAAAGCCAAGGGCCAAGAGCAGTGGTTCCGAGTGAGCCTGAGGAACCTGCTCGGCTACTACAACCAGAGCGCGGGCG
Seq A exon
GCTCTCACACACTCCAGCAGATGTCTGGCTGTGACTTGGGGTCGGACTGGCGCCTCCTCCGCGGGTACCTGCAG
Seq C2 exon
TTCGCCTATGAAGGCCGCGATTACATCGCCCTGAACGAAGACCTGAAAACGTGGACGGCGGCGGACATGGCGGCGCAGATCACCCGACGCAAGTGGGAGCAGAGTGGTGCTGCAGAGCATTACAAGGCCTACCTGGAGGGCGAGTGCGTGGAGTGGCTCCACAGATACCTGAAGAACGGGAACGCGACGCTGCTGCGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000073411-1-3,1-2,1-1-3/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.264 A=NA C2=0.022
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(50.3=98.9)
A:
NA
C2:
PF0012913=MHC_I=PD(49.2=94.6)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGAACCTGCTCGGCTACTA
R:
CCCTCCAGGTAGGCCTTGTAA
Band lengths:
178-252
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: