MmuINT1020345 @ mm10
Intron Retention
Gene
ENSMUSG00000054128 | H2-T3
Description
histocompatibility 2, T region locus 3 [Source:MGI Symbol;Acc:MGI:95959]
Coordinates
chr17:36189177-36189870:-
Coord C1 exon
chr17:36189601-36189870
Coord A exon
chr17:36189453-36189600
Coord C2 exon
chr17:36189177-36189452
Length
148 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGG
5' ss Score
7.61
3' ss Seq
GACTAGGAGAGGGGGGCCAGGCT
3' ss Score
-17.63
Exon sequences
Seq C1 exon
GCTCACACTCGCTGAGGTACTTCTACACCGCCTTGTCCCGACCTGCAATCAGCGAACCGTGGTACATAGCTGTGGGCTACCTGGATGACACTCAGTTCGTGCGCTTCAACAGCTCAGGGGAGACTGCGACATATAAGCTAAGTGCGCCATGGGTGGAGCAAGAGGGGCCCGAGTATTGGGCGAGAGAGACAGAGATCGTCACAAGCAATGCACAGTTTTTCCGCGAGAATCTGCAGACTATGCTGGACTACTACAACCTGAGTCAAAATG
Seq A exon
GTGAGGAACCCCCCAAATCTAAGAGTCTGTCCCCACTCCTCTCCCTCTTATGCAAGCCACCTAATCATGGGGTGCAAAAGGGACCGGTTTCCCTTTCAGTTTGGAGAATTCCTAGGGTGGGCGGGCCTGACTAGGAGAGGGGGGCCAG
Seq C2 exon
GCTCTCACACCATCCAGGTGATGTATGGCTGTGAGGTGGAGTTCTTCGGGAGCCTCTTCCGCGCTTATGAGCAGCATGGCTATGATGGCCGCGATTACATTGCCCTCAATGAAGATCTGAAAACGTGGACAGCAGCAGACACGGCAGCAGAGATCACCAGAAGCAAGTGGGAGCAGGCTGGTTATACAGAGCTCCGTAGGACCTACTTGGAGGGCCCATGCAAGGATTCCCTGCTCAGATACCTGGAGAACAGAAAAAAGACACAGGAGTGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054128:ENSMUST00000102675:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.004 A=NA C2=0.035
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(95.7=98.9)
A:
NA
C2:
PF0012913=MHC_I=PD(49.2=94.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCAGGGGAGACTGCGACATA
R:
TGTAATCGCGGCCATCATAGC
Band lengths:
257-405
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