MmuINT0075617 @ mm10
Intron Retention
Gene
ENSMUSG00000041538 | H2-Ob
Description
histocompatibility 2, O region beta locus [Source:MGI Symbol;Acc:MGI:95925]
Coordinates
chr17:34241008-34242718:+
Coord C1 exon
chr17:34241008-34241277
Coord A exon
chr17:34241278-34242436
Coord C2 exon
chr17:34242437-34242718
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:ENSMUST00000095342:2
Average complexity
IR
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(95.6=90.5)
Main Inclusion Isoform:
NA
Other Inclusion 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:
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
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types