MmuINT0075617 @ mm9
Intron Retention
Gene
ENSMUSG00000041538 | H2-Ob
Description
histocompatibility 2, O region beta locus [Source:MGI Symbol;Acc:MGI:95925]
Coordinates
chr17:34377953-34379663:+
Coord C1 exon
chr17:34377953-34378222
Coord A exon
chr17:34378223-34379381
Coord C2 exon
chr17:34379382-34379663
Length
1159 bp
Sequences
Splice sites
5' ss Seq
ATGGTGGGT
5' ss Score
6.18
3' ss Seq
TTTGTTTCTTCTCTTGCCAGTGC
3' ss Score
9.34
Exon sequences
Seq C1 exon
AGAATTTTGTGATTCAGGCAAAGGCGGACTGTTACTTCACCAATGGTACAGAAAAGGTTCACTTGCTGGTCAGGTTCATCTTCAACCTGGAGGAGTATTTACACTTCGACAGTGACCTGGGGATGTTTGTGGCTCTGACGGAGCTGGGGGAACCTGATGCTGACCAGTGGAACAAACGCCTGGATCTCCTGGAGACGAGCAGAGCTGCTGTGAACATGGTCTGCAGGCAGAAGTACAAGCTGGGGGCCCCCTTCACTGTGGAGAGAAATG
Seq A exon
GTGGGTGACAATAAGATCTAGGGGTTCTCTGTGAGAACCTTGTAATAGGCATTTAAAAGGTTTTAAATTACAGCAATCATCTATCTGTCTGTCTATTATTTATTTGTGTGTGTTCCATGCATGCCATAGTGGAGGTTAGAGGACAATTTGAGGCAGTTGGGTCTCTCCTTCCATCATGAGGGTCCTAGAGAATGAACTCAGGTCATCAAGCTTGGGGGCCTGTGATTATACCCTGTCCTCAGCTGTGAATTGTTGGCTTAGAATTTTCAAAAGCTACTTTAATAATGGTTCTTAAGTGCTTCAACCTCCCTTCTAGCCCACCATCCACCATAGAGAGTGGAAAGGAAAGGTTGATAGGAAATAGGGGTTGTGGACCTGCTTAGAAATAGTTCTTTAGGGGCGATTCCAATCTTCGTTGTCAGCAGTCCACCCCTCTAGCATAGCATCAACACGAATCAACAGCTGCAGTCCAGTCCACTTGGCAATCACTGCTCATGAATTAGCAATGGCAATTTGATCCAGAAGAAACCGCATGGCTCTGCCAATTGGCCTGAGTCTACAGAGACAGGAAGAAGCTGCAAGAATATCACAAGTTCTTTACCAAGTTACTCTCTATGCAGTCATGTCAAGCGAAGATAAGTCATGCTATGCAAGGCAAACCAATATTAGGGTGTTGTCAGCAAAGACTAGTGAGGCACAGCAAGGCGAACCAATACCAGAGCCTCCTCCCACTGTCATTGGGGTCATATTTATGCTTTCTTCCACAAATCATGCTTTCTCTCACTTGTCTGCTTCAGCAAAACATCCTCTAACCTGTGTCAGCTTCAGCCAAGCATCCTTCCATCTGTCTGCTCTGGCAAAACATCATCTGACATAATGGAGTTTCCAAAGAAACCAGAAATTTCCACTTCCTCCTAAAACCTCAGAGTTCTCAGGGTCTTTGAGAACTGGTGTAGCCTTGAATACAGTGGGTGGCTGTGGGGTGACCTGGCAGAGTCTATGTCCTTCCTGTGGACATCCACACATGCTTCTCAGTCTATGGTGTTAGGTACCCACACTTCCAGCTTCTACTTGGCTAGTATGGGAGATGGATCACGGTGGTCACAGCCCCTCTAGATGGTCCTGTCCTTGCTGTGCTTTTTGTTTCTTCTCTTGCCAG
Seq C2 exon
TGCCTCCAGAGGTGACAGTGTATCCAGAGAGGACCCCGTTGCTGCAGCAGCACAACCTGCTGCTCTGCTCTGTGACAGGCTTCTACCCCGGGGACATAAGTGTCAAGTGGTTCCGGAATGGACAGGAGGAGAGGTCTGGGGTCATGTCCACTGGCCTTGTTAGGAATGGAGACTGGACCTTCCAGACAACAGTAATGCTGGAAATGATCCCAGAGCTTGGTGACATCTACAGCTGCCTCGTGGAGCACCCCGGCCTCCTGAGACCTGTTTCTGTGGCATGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041538-H2-Ob:NM_010389:2
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:
PF0096914=MHC_II_beta=WD(100=82.4),PF0765410=C1-set=PU(2.7=2.2)
A:
NA
C2:
PF0765410=C1-set=PU(94.5=90.5),PF075566=DUF1538=PU(20.8=10.5),PF112393=DUF3040=PU(24.2=16.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCAAAGGCGGACTGTTACTT
R:
ACACTTATGTCCCCGGGGTAG
Band lengths:
357-1516
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: