MmuINT0075689 @ mm10
Intron Retention
Gene
ENSMUSG00000035929 | H2-Q4
Description
histocompatibility 2, Q region locus 4 [Source:MGI Symbol;Acc:MGI:95933]
Coordinates
chr17:35379617-35380173:+
Coord C1 exon
chr17:35379617-35379707
Coord A exon
chr17:35379708-35379819
Coord C2 exon
chr17:35379820-35380173
Length
112 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
CCGCCCCTTCTCCACCCTAGCCC
3' ss Score
7.45
Exon sequences
Seq C1 exon
AGATGCCCAGAATCCCAGAGGGGAGCAATGGCGTCAACAATGCTGCTTCTGCTGGTGGCAGTCGCCCAGACCCTGATCGAGATCCGCGCGG
Seq A exon
GTGAGTACCGGGTCCGGAGGGAAATGGCCTCTGAGGAAAGGGGAGGGGGCGGCACGGGGGAAGCCGCGTCCCGGCGTCGCCCACCTGACCCTCCGCCCCTTCTCCACCCTAG
Seq C2 exon
CCCCGCGCCCTGCTCCCCTCCCGGCCCGCTCACCCGCCGGGGGTCCCGGAAGGAGTTCGGGGTCTCACCGCGCCCTGCCTCCAGGCCCACACTTGCTGAGTTATTTCTACACCTCCGTGTCCCGGCCGGGCCTTGGGGAGCCCCGGTTCATCTCTGTCGGTTACGTGGACAACACGGAGTTCGTGCGCTTCGACAGCGACGCGGAGAATCCGAGATATGAGCCGCGGGCACCGTGGATGGAGCAGGAGGGGCCGGAGTATTGGGAGCGGGAAACACAGAAAGCCAAGGGCAATGAGCAGATTTTCCGAGTGAACCTGAGGACCCTGCTCAGCTACTACAACCAGAGCGCGGGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035929:ENSMUST00000081435:1
Average complexity
IR
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=0.412
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0012913=MHC_I=PU(50.3=75.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCAGACCCTGATCGAGATCC
R:
CGCGGCTCATATCTCGGATTC
Band lengths:
253-365
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