MmuINT0075618 @ mm9
Intron Retention
Gene
ENSMUSG00000041538 | H2-Ob
Description
histocompatibility 2, O region beta locus [Source:MGI Symbol;Acc:MGI:95925]
Coordinates
chr17:34379382-34380523:+
Coord C1 exon
chr17:34379382-34379663
Coord A exon
chr17:34379664-34380412
Coord C2 exon
chr17:34380413-34380523
Length
749 bp
Sequences
Splice sites
5' ss Seq
GGAGTGAGC
5' ss Score
2.46
3' ss Seq
TAAGTCTCACTTTCCCACAGTGG
3' ss Score
7.48
Exon sequences
Seq C1 exon
TGCCTCCAGAGGTGACAGTGTATCCAGAGAGGACCCCGTTGCTGCAGCAGCACAACCTGCTGCTCTGCTCTGTGACAGGCTTCTACCCCGGGGACATAAGTGTCAAGTGGTTCCGGAATGGACAGGAGGAGAGGTCTGGGGTCATGTCCACTGGCCTTGTTAGGAATGGAGACTGGACCTTCCAGACAACAGTAATGCTGGAAATGATCCCAGAGCTTGGTGACATCTACAGCTGCCTCGTGGAGCACCCCGGCCTCCTGAGACCTGTTTCTGTGGCATGGA
Seq A exon
GTGAGCTTTATTAGTTTTCTGTACTTCTGGACCTTGACCTGTAGGAGCTGTCATTTCTGTGTTCATCTTGATGACAAGACAAGTTCCCCTGATCTAAGAATCCTAGTGCCAGGGGCAGGAGAAAACAGGACAGGCATCCATCCTCTGAATGTCCAAGAGATAGATAAGGAGGCTGTTAACCCACAACTTGCCTCTAAGCCTGGGACCTAGTATCCTTTAGCACTTTAATCTTTACAGACACTGCCACTGGCTCTAAGTCAGGGATCGGCCTGGAGAAGTAGCTTAGCTGGTGAAGGGCTTGTCATATAACTGTGAGGACCTGAGTTTGACTCCTACAGTCTATGTAAATAATCCAGGTTCTCTGGTCCATGATTGTAGTCCCAGGGCCTGGGAGGTAGAGACAGGCAGATCCCTGCAGTTCACAGGCTAACCAGCCTAGTCTACTTAGTGAGTTCTAGGTCAGTGAGGGACATTGAACTACAGCAAAAACAGCAAAGGAAATGGCACCTGAGGAATAACACCAGACATTGACCTCTGGTCTGTGGGAGTGTGTGCGTGCACACATACACACACACACACACACACACACACACACACACACACACACACACACACACAGAATCAGTGACAGATGGGAGACACATATCTAGACTTAACTCTTCCCTGAGCAGTACTGGGCTTTAGGGTTTTAAGAAGTTGGGTCCAGTACTGAGAGCATTGCATTGACTTTAAGTCTCACTTTCCCACAG
Seq C2 exon
TGGCTCAGTCTGAATATTCCTGGAAAAAGATACTGAGTGGAGCTGCAGTGTTCCTGCTTGGGCTGATTGTCTTCCTGGTGGGGGTTGTTATCCATCTCAAGGCTCAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041538-H2-Ob:NM_010389:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0765410=C1-set=PU(94.5=90.5),PF075566=DUF1538=PU(20.8=10.5),PF112393=DUF3040=PU(24.2=16.8)
A:
NA
C2:
PF0765410=C1-set=PD(4.4=10.5),PF075566=DUF1538=FE(77.1=100),PF112393=DUF3040=FE(56.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCAGAGGTGACAGTGTATCCA
R:
CACCAGGAAGACAATCAGCCC
Band lengths:
358-1107
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: