MmuINT0075622 @ mm10
Intron Retention
Gene
ENSMUSG00000079507 | H2-Q1
Description
histocompatibility 2, Q region locus 1 [Source:MGI Symbol;Acc:MGI:95928]
Coordinates
chr17:35320821-35321550:+
Coord C1 exon
chr17:35320821-35321090
Coord A exon
chr17:35321091-35321274
Coord C2 exon
chr17:35321275-35321550
Length
184 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGT
5' ss Score
10.49
3' ss Seq
CTGACCCAGGGTTCCTGCAGGCA
3' ss Score
3.13
Exon sequences
Seq C1 exon
GCTCACACTCGCTGCGGTATTTCGAGACCTCGGTGTCCCGGCCCGGCTTCGGGAAGCCCCGGTTCATCTCTGTCGGCTACGTGGACGACACGCAGTTTGTGCGCTTCGACAGCGACGCGAAGAATCCGAGATATGAGCCGCGGGCGCCGTGGATGGAGCAGGAGGGGCCGGAGTATTGGGAACGGAACACACGGAGAGTCAAGGGCAGTGAGAAGAGATTCCAAGAGAGCCTGAGCACCCTGCTCAGCTACTACAACCAGAGCAAGGGCG
Seq A exon
GTGAGTGACCCCTGGTCGGAGGTCACGACCCCTCGACGTCCCTACACAGGGGCCAGAGACCTCCTGCTTCTCAAGTCCCAGGTTCAGGAGCAGAACTGACCCGGGACCGGATTCCCTTTCAGTTCTGTGGAGTCGCGCGTGGGCGGGGCCGGGGGAGCGAGGCGCTGACCCAGGGTTCCTGCAG
Seq C2 exon
GCATTCACACCTTCCAGAAGTTGTCTGGCTGTGATCTGGGGTCAGATGGGCGCCTTCAAAGCGGGTACCTGCAGTTCGCCTATGATGGCCTTGATTACATCGCCCTGAATGAAGACCTGGAAACCTGGACAGCAGCAGATGTGGCAGCTCAGGAAACCCGACGCAAGTGGGAGCAGGCTGGTGCTGCTGAGAAACACAGGACCTACCTGGAGGGCAAGTGCCTGATGTGGCTCCACAGATACCTGGAGCTCGGGAAGGAGATGCTGCTGCGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079507:ENSMUST00000073208:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.165 A=NA C2=0.065
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
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAATCCGAGATATGAGCCGCG
R:
GGGCGATGTAATCAAGGCCAT
Band lengths:
254-438
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