MmuINT0075604 @ mm10
Intron Retention
Gene
ENSMUSG00000024459 | H2-M5
Description
histocompatibility 2, M region locus 5 [Source:MGI Symbol;Acc:MGI:95917]
Coordinates
chr17:36988505-36989204:-
Coord C1 exon
chr17:36988935-36989204
Coord A exon
chr17:36988781-36988934
Coord C2 exon
chr17:36988505-36988780
Length
154 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
TACGACCGGGGCGGGGCCAGGCT
3' ss Score
-1.05
Exon sequences
Seq C1 exon
GCATCCATTCCTTGCAGTTTTTTGCCACCACCATGACCCAGCCTGGTTTGAGGGAGCATTCCTTCATCTTTGTCGTCTTCGTGGACGACACACAGTTCCTGTGCTACAACAATAAGGGGAAAAATCAGAGAATGGAGCCACGCGCTCTGTGGGTGAAGCAGATGGGGCCAGAGTATTGGGAACAGCAGACCAGGACTGTCAAGGTCATTGAGAAGATTGCCCTAGTGAATTTGCAGGAGGCCATGGACATCTACAACCACAGCAAGGATG
Seq A exon
GTGAGTAACCCTTTCACATCCCTTACGGACGGACGACCCTGAGTTCCCGGGTCCTCAGCTCCCGAGGTTTGGCCCCCAAGGTTGCCAGACTTGAGGAGACCCTGAACCGGTTTCGTGCAAGGTTGTGGTCCAAATACGACCGGGGCGGGGCCAG
Seq C2 exon
GCTCTCACGTCTTTCAGTGTGTGTATGGCTGCGAAGTGGGGCCAGATGGACTCTTCCTCCGTGGGCATGAGAAGCACGCATACGACGGCCGCGATTACCTCACCCTAAGCCCGGACCTGCACTCCTGGGTCGCAGGCGACACAGCTGCGCAGATCACGCTGCGCAGGTGGGAGAAGTCTGGTGTCTCTGAGCAAAGGCAATCCTTCTTGAAGGGCGAGTGTGTGGAGTCGCTCCGCACATACCTGGAGATAGGGAAGGAGACTCTGCTAAGAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024459:ENSMUST00000169189:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.032 A=NA C2=0.003
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(80.0=97.3)
A:
NA
C2:
PF0012913=MHC_I=PD(49.2=94.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAATTTGCAGGAGGCCATGGA
R:
TTGCCTTTGCTCAGAGACACC
Band lengths:
244-398
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