MmuINT0075604 @ mm9
Intron Retention
Gene
ENSMUSG00000024459 | H2-M5
Description
histocompatibility 2, M region locus 5 [Source:MGI Symbol;Acc:MGI:95917]
Coordinates
chr17:37125450-37126149:-
Coord C1 exon
chr17:37125880-37126149
Coord A exon
chr17:37125726-37125879
Coord C2 exon
chr17:37125450-37125725
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-H2-M5:NM_001115075:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.045 A=NA C2=0.007
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
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: