MmuINT0075605 @ mm10
Intron Retention
Gene
ENSMUSG00000024459 | H2-M5
Description
histocompatibility 2, M region locus 5 [Source:MGI Symbol;Acc:MGI:95917]
Coordinates
chr17:36987655-36988780:-
Coord C1 exon
chr17:36988505-36988780
Coord A exon
chr17:36987931-36988504
Coord C2 exon
chr17:36987655-36987930
Length
574 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAT
5' ss Score
7.88
3' ss Seq
TGTTCAACTCTTTCCCTCAGATC
3' ss Score
10.26
Exon sequences
Seq C1 exon
GCTCTCACGTCTTTCAGTGTGTGTATGGCTGCGAAGTGGGGCCAGATGGACTCTTCCTCCGTGGGCATGAGAAGCACGCATACGACGGCCGCGATTACCTCACCCTAAGCCCGGACCTGCACTCCTGGGTCGCAGGCGACACAGCTGCGCAGATCACGCTGCGCAGGTGGGAGAAGTCTGGTGTCTCTGAGCAAAGGCAATCCTTCTTGAAGGGCGAGTGTGTGGAGTCGCTCCGCACATACCTGGAGATAGGGAAGGAGACTCTGCTAAGAACAG
Seq A exon
GTATATGAGGCTGCCGGGAATCTCCTCCATCTGTTCTGGGGCTGGGGCTCACAGTCTCTCTGGAAGGGAGCAAAATGAGCTGGGCTAGAATACTGCTTCTTTTCTTTGCATCTGAAGAAGGAAGAGAGTTCTGGTTTTCCCGATCAAACACTAGACAGAGACTCTTGCGACTTTTTCTCGGGAGAGTTGAGATTGTCTCAGGAAGGAAAGAGAGAAGATCCCTAAACAGCTGCCCCTTTCAGTCTGCAGCCCTTTGTAAGCCATGCCCTTTCTCAGGCCATGTTCTCAGCCCACACCCAACCTCTTTGGAGTCTTGACTCCAATGATGCTAAGTCTCTCAGCCTTCACCCAGTCAAGACCTTTCTCCTTTCTTCCTTGGGAGTCCCGAAGTCCATCTTGTCATCCTATGTCTAGGGTTTCCCAAGGGGTCGATTATTCCAGATGCCTGAATCTAGAATACTGTATGGTGCTTAAATCCCTCAACTACCCATTCAATTTCCAAGATGGTCCATAAACATTGCTTCAGTTCAGGGAAGAATTCAAGATTCCTGAATTGTTCAACTCTTTCCCTCAG
Seq C2 exon
ATCCTCCCAAGGCACATGTGACCCATCACCCCAGACCTGAAGGTGAAGTCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCTAACATCATCCTGACCTGGCAGTGGGATGAGGAAGACCTGACTCAGGACATGGACCTCATTGAGACCAGACCTGCAGGGGATGGGACCTTCCAGAAGTGGGCATCTGTGGTGGTACCTTCTGGAGAGGAACAGAGATACACATGTCATGTGCAACATGAGGGGCTAACCCAGCCCCTTGTTCTAAAATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024459:ENSMUST00000169189:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.003 A=NA C2=0.136
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(49.2=94.6)
A:
NA
C2:
PF0012913=MHC_I=PD(15.6=7.6),PF0765410=C1-set=WD(100=92.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGATGGACTCTTCCTCCGT
R:
ACTGCCAGGTCAGGATGATGT
Band lengths:
343-917
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