MmuINT0075502 @ mm9
Intron Retention
Gene
ENSMUSG00000073411 | H2-D1
Description
histocompatibility 2, D region locus 1 [Source:MGI Symbol;Acc:MGI:95896]
Coordinates
chr17:35400039-35400593:+
Coord C1 exon
chr17:35400039-35400131
Coord A exon
chr17:35400132-35400323
Coord C2 exon
chr17:35400324-35400593
Length
192 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
TCACCGCGCGCCGTCCCCAGGCC
3' ss Score
10.01
Exon sequences
Seq C1 exon
TCAGACACCCGGGATCCCAGATGGGGGCGATGGCTCCGCGCACGCTGCTCCTGCTGCTGGCGGCCGCCCTGGCCCCGACTCAGACCCGCGCGG
Seq A exon
GTGAGTGCGGGGTCGGGAGGGAAACGGCCTCTGCGGGGAGAGGGGCGGCACGGGGGAAGCCGCGTCCCCGCGTCGCCCACCGGACCCTCCGCCCCTTCTCCACCTGAGCCCCGCGCCCAGATCCCCTCCCGGCCTGCGCAGCCGCCCGGGGTTTGGTGAGGAGGTCGGGGTCTCACCGCGCGCCGTCCCCAG
Seq C2 exon
GCCCACACTCGATGCGGTATTTCGAGACCGCCGTGTCCCGGCCCGGCCTCGAGGAGCCCCGGTACATCTCTGTCGGCTATGTGGACAACAAGGAGTTCGTGCGCTTCGACAGCGACGCGGAGAATCCGAGATATGAGCCGCGGGCGCCGTGGATGGAGCAGGAGGGGCCGGAGTATTGGGAGCGGGAAACACAGAAAGCCAAGGGCCAAGAGCAGTGGTTCCGAGTGAGCCTGAGGAACCTGCTCGGCTACTACAACCAGAGCGCGGGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000073411-H2-D1:NM_010380:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.264
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(0.1=0.0)
A:
NA
C2:
PF0012913=MHC_I=PU(50.3=98.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGCCCCGACTCAGACC
R:
CACTCGGAACCACTGCTCTTG
Band lengths:
252-444
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: