MmuINT0075597 @ mm9
Intron Retention
Gene
ENSMUSG00000016206 | H2-M3
Description
histocompatibility 2, M region locus 3 [Source:MGI Symbol;Acc:MGI:95915]
Coordinates
chr17:37407467-37408218:+
Coord C1 exon
chr17:37407467-37407736
Coord A exon
chr17:37407737-37407942
Coord C2 exon
chr17:37407943-37408218
Length
206 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGT
5' ss Score
10.49
3' ss Seq
GACACCCTGTTTGTGGCTAGGCT
3' ss Score
5.89
Exon sequences
Seq C1 exon
GCTCACATTCACTGCGCTATTTCCACACTGCGGTGTCACGGCCGGGCCGTGGGGAGCCCCAGTATATCTCTGTGGGCTATGTTGACGACGTGCAGTTTCAGCGCTGTGATAGCATTGAGGAAATTCCGAGGATGGAACCTCGTGCACCTTGGATGGAGAAGGAAAGACCAGAGTACTGGAAGGAGCTGAAACTCAAGGTCAAGAATATTGCACAAAGTGCCAGAGCAAACCTTCGGACCCTGCTCCGCTACTACAACCAGAGTGAAGGCG
Seq A exon
GTGAGTGACCCTAAGCCTGGGTCAGACTCCTTCCTGTCTGTCTACTGCCAAACCAGAGTAGCCCTGGGTGCCAGGTTAGATGTTTGGAGTTGGGCTTCAGAGCTCTCAGAAACCTTTAACCGGTTTCACTTTCAGTTTAGGTCCAAATCCTGTTGGCGGGCGGAGCAGGGTGAGGTGGCTAAGGCTGACACCCTGTTTGTGGCTAG
Seq C2 exon
GCTCTCACATCCTGCAGTGGATGGTTTCCTGTGAGGTAGGGCCAGACATGCGCCTTCTTGGAGCCCACTATCAGGCTGCGTATGATGGCTCAGATTACATCACCCTGAATGAAGACCTGAGCTCCTGGACTGCAGTGGACATGGTGTCTCAGATCACGAAGAGCCGTTTAGAGTCAGCTGGCACAGCAGAGTACTTCAGGGCCTATGTGGAGGGAGAGTGCCTGGAGCTGCTCCACAGATTCCTGCGGAATGGCAAGGAGATTCTTCAGCGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016206-H2-M3:NM_013819:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.033 A=NA C2=0.011
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(50.3=98.9)
A:
NA
C2:
PF0012913=MHC_I=PD(49.2=94.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
GTGCACCTTGGATGGAGAAGG
R:
ACGGCTCTTCGTGATCTGAGA
Band lengths:
296-502
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: