MmuINT0075599 @ mm9
Intron Retention
Gene
ENSMUSG00000016206 | H2-M3
Description
histocompatibility 2, M region locus 3 [Source:MGI Symbol;Acc:MGI:95915]
Coordinates
chr17:37409214-37409697:+
Coord C1 exon
chr17:37409214-37409489
Coord A exon
chr17:37409490-37409592
Coord C2 exon
chr17:37409593-37409697
Length
103 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGG
5' ss Score
8.05
3' ss Seq
ACCCTCCACTCCTTTCCCAGGAA
3' ss Score
9.95
Exon sequences
Seq C1 exon
ATCCCCCAAAGGCACATGTGGCCCATCACCCGAGACCCAAAGGTGATGTTACCTTGAGGTGCTGGGCTCTGGGCTTCTACCCTGCTGACATCACCCTGACCTGGCAGAAGGATGAAGAGGACCTGACCCAGGACATGGAGCTTGTGGAAACGAGGCCTTCAGGGGATGGAACCTTCCAGAAGTGGGCAGCTGTGGTGGTGCCTTCTGGAGAGGAGCAGAGATACACATGTTATGTGCACCATGAGGGGCTAACCGAGCCCCTTGCCCTGAAATGGG
Seq A exon
GTAAGGAAGAGAAGGGTAACAGAGTCAAGGAAAGAAGGAGCCTAGATTAAGATCAGAACTGAGAACTGGGCATCATGACTCTCACCCTCCACTCCTTTCCCAG
Seq C2 exon
GAAGATCGTCTCAATCATCTGTCGTCATCATGGTCATCGTTGCTAGTCTGGTTCTCCTGGGAGGTGTGATCACTATTGTTGTGGTGTGCAAGAGGAGGGGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016206-H2-M3:NM_013819:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.194 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0765410=C1-set=WD(100=90.3)
A:
NA
C2:
NO
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:
AGGATGAAGAGGACCTGACCC
R:
AGTGATCACACCTCCCAGGAG
Band lengths:
242-345
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: