MmuINT0075603 @ mm10
Intron Retention
Gene
ENSMUSG00000024459 | H2-M5
Description
histocompatibility 2, M region locus 5 [Source:MGI Symbol;Acc:MGI:95917]
Coordinates
chr17:36988935-36989504:-
Coord C1 exon
chr17:36989429-36989504
Coord A exon
chr17:36989205-36989428
Coord C2 exon
chr17:36988935-36989204
Length
224 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TTTGTGTCTTCCGTCGCCAGGCA
3' ss Score
8.78
Exon sequences
Seq C1 exon
ATGAGAAGCCCTGCGCTCTCTACCCTCCTATCCTTGCTGCTCACCGGAGCTTTGGCCTTGACCCTGGTTCGCGCAG
Seq A exon
GTGAGTGCGGGTCAGGAGGGAAACTGCCTCGGCCAAGGAGAGTGAGGGCAGCACTGGAGAAGCCAAGAAGCCGCACAACCGAAATAGCCTCACCACTCTTCCCTCTCCTTTCTCCAATCTTCATCCTGAACCCCACGCCCTGCTCCCCTTCTGTCACCTACACCTCTACAAGTCCCGGAAAAAAAAAAAAAAAAAAAAAAAGGATTTGTGTCTTCCGTCGCCAG
Seq C2 exon
GCATCCATTCCTTGCAGTTTTTTGCCACCACCATGACCCAGCCTGGTTTGAGGGAGCATTCCTTCATCTTTGTCGTCTTCGTGGACGACACACAGTTCCTGTGCTACAACAATAAGGGGAAAAATCAGAGAATGGAGCCACGCGCTCTGTGGGTGAAGCAGATGGGGCCAGAGTATTGGGAACAGCAGACCAGGACTGTCAAGGTCATTGAGAAGATTGCCCTAGTGAATTTGCAGGAGGCCATGGACATCTACAACCACAGCAAGGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024459:ENSMUST00000169189:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.032
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(0.1=0.0)
A:
NA
C2:
PF0012913=MHC_I=PU(80.0=97.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTCCTATCCTTGCTGCTCA
R:
TCCATGGCCTCCTGCAAATTC
Band lengths:
301-525
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