MmuALTA0008359-3/3 @ mm10
Alternative 3'ss
Gene
ENSMUSG00000041538 | H2-Ob
Description
histocompatibility 2, O region beta locus [Source:MGI Symbol;Acc:MGI:95925]
Coordinates
chr17:34241008-34242718:+
Coord C1 exon
chr17:34241008-34241277
Coord A exon
chr17:34242437-34242514
Coord C2 exon
chr17:34242515-34242718
Length
78 bp
Sequences
Splice sites
5' ss Seq
ATGGTGGGT
5' ss Score
6.18
3' ss Seq
TTTGTTTCTTCTCTTGCCAGTGC
3' ss Score
9.34
Exon sequences
Seq C1 exon
AGAATTTTGTGATTCAGGCAAAGGCGGACTGTTACTTCACCAATGGTACAGAAAAGGTTCACTTGCTGGTCAGGTTCATCTTCAACCTGGAGGAGTATTTACACTTCGACAGTGACCTGGGGATGTTTGTGGCTCTGACGGAGCTGGGGGAACCTGATGCTGACCAGTGGAACAAACGCCTGGATCTCCTGGAGACGAGCAGAGCTGCTGTGAACATGGTCTGCAGGCAGAAGTACAAGCTGGGGGCCCCCTTCACTGTGGAGAGAAATG
Seq A exon
TGCCTCCAGAGGTGACAGTGTATCCAGAGAGGACCCCGTTGCTGCAGCAGCACAACCTGCTGCTCTGCTCTGTGACAG
Seq C2 exon
GCTTCTACCCCGGGGACATAAGTGTCAAGTGGTTCCGGAATGGACAGGAGGAGAGGTCTGGGGTCATGTCCACTGGCCTTGTTAGGAATGGAGACTGGACCTTCCAGACAACAGTAATGCTGGAAATGATCCCAGAGCTTGGTGACATCTACAGCTGCCTCGTGGAGCACCCCGGCCTCCTGAGACCTGTTTCTGTGGCATGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041538-6-6,6-5,6-4-3/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0096914=MHC_II_beta=WD(100=82.4),PF0765410=C1-set=PU(2.7=2.2)
A:
NA
C2:
PF0765410=C1-set=FE(90.7=100)
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGGATGTTTGTGGCTCTGAC
R:
ACACTTATGTCCCCGGGGTAG
Band lengths:
177-255
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types