MmuINT0075675 @ mm10
Intron Retention
Gene
ENSMUSG00000054128 | H2-T3
Description
histocompatibility 2, T region locus 3 [Source:MGI Symbol;Acc:MGI:95959]
Coordinates
chr17:36189601-36190287:-
Coord C1 exon
chr17:36190050-36190287
Coord A exon
chr17:36189871-36190049
Coord C2 exon
chr17:36189601-36189870
Length
179 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TCACCACATGCTGCCCCCAGGCT
3' ss Score
7.28
Exon sequences
Seq C1 exon
AGAACTATAGTTTCACTTTTTGCTCTCTGTACCATTGTCAGATTGTTTTCAAAGGCCTTGCACTCCTGTTGAGAGCAGGTACTTAGAAGATGCAATAAAACTCTCTGAGATTGCAAGTTACAAAGTCCAGGACTTTATACAACTTCAGATTTCCCTAACATGAGGATGGGGACCATGGTGCCTGGCACCCTCCTGATCCTCCTGGCTGCCTCACAAGGCCAGACCCAGACCTGCCCAG
Seq A exon
GTGAGTGCTGGATGAGGAGGGAAACAGCCTTTTAGGGGAGGGGCGGAGGTCCACCCTCCACCAGACCCTCCACCACTTCTCCACTCAAGGCCCTAGACCTGAGTCCTTCTACTTCCCTGACCTGCGCACCTGGCCGGGTTCTGGGAGAAGGTCACAGTCTCACCACATGCTGCCCCCAG
Seq C2 exon
GCTCACACTCGCTGAGGTACTTCTACACCGCCTTGTCCCGACCTGCAATCAGCGAACCGTGGTACATAGCTGTGGGCTACCTGGATGACACTCAGTTCGTGCGCTTCAACAGCTCAGGGGAGACTGCGACATATAAGCTAAGTGCGCCATGGGTGGAGCAAGAGGGGCCCGAGTATTGGGCGAGAGAGACAGAGATCGTCACAAGCAATGCACAGTTTTTCCGCGAGAATCTGCAGACTATGCTGGACTACTACAACCTGAGTCAAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054128:ENSMUST00000102675:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.062 A=NA C2=0.004
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(0.1=0.0)
A:
NA
C2:
PF0012913=MHC_I=PU(95.7=98.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCAAAGGCCTTGCACTCCTG
R:
TGTACCACGGTTCGCTGATTG
Band lengths:
257-436
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