MmuINT0075503 @ mm10
Intron Retention
Gene
ENSMUSG00000073411 | H2-D1
Description
histocompatibility 2, D region locus 1 [Source:MGI Symbol;Acc:MGI:95896]
Coordinates
chr17:35263379-35264114:+
Coord C1 exon
chr17:35263379-35263648
Coord A exon
chr17:35263649-35263838
Coord C2 exon
chr17:35263839-35264114
Length
190 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
GTGAGTGACCCCGCGTCGGAGGTCAGGCCCCTCCACTTCCCGACACAGGGACGCTGACGTCCCGGGTCCCAAGTCCGAGGTTTGGGAACAGAACGGACCCGGAACCGGTTTCCCTTTCAGTTTGGAGGAGTCCGCGGCCGGGCGGGCGGGGCCGGGGCGGGTGAGCGGGGCTGACCGCAGGGTCCCGCAG
Seq C2 exon
GCTCTCACACACTCCAGCAGATGTCTGGCTGTGACTTGGGGTCGGACTGGCGCCTCCTCCGCGGGTACCTGCAGTTCGCCTATGAAGGCCGCGATTACATCGCCCTGAACGAAGACCTGAAAACGTGGACGGCGGCGGACATGGCGGCGCAGATCACCCGACGCAAGTGGGAGCAGAGTGGTGCTGCAGAGCATTACAAGGCCTACCTGGAGGGCGAGTGCGTGGAGTGGCTCCACAGATACCTGAAGAACGGGAACGCGACGCTGCTGCGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000073411:ENSMUST00000172785:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
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 Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGAACCTGCTCGGCTACTA
R:
CCCTCCAGGTAGGCCTTGTAA
Band lengths:
252-442
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- 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