MmuINT0075671 @ mm10
Intron Retention
Gene
ENSMUSG00000053835 | H2-T24
Description
histocompatibility 2, T region locus 24 [Source:MGI Symbol;Acc:MGI:95958]
Coordinates
chr17:36015384-36017537:-
Coord C1 exon
chr17:36017241-36017537
Coord A exon
chr17:36015657-36017240
Coord C2 exon
chr17:36015384-36015656
Length
1584 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
CCTGTCCCCGGGGCTTCTAGGCC
3' ss Score
6.91
Exon sequences
Seq C1 exon
GGTCGCACTCTCTGCATTACTGTTACTCAGCTGTGACTGAGCCGGGCCCGGGAGTTCCTTCATTTTTCGCCAGTGGCTTCTTAGATAACCAGCCCTTCATCCACTACGACAGCAGGAGCATGAAGGCAGAGCCTTGTGCTGACTGGCTGAGGGAAAATGCACAGTACTTCACTCATGAGACTGAGGTTTTCACCAATCGGATGAAGATTTTCCAGTTGAGCCTGAGAAACATTCGGCAATACTACAACAGCTCTGGTACCCAGAGTCAGAGAGCAGATGGCTTCCGCCAGCAAGCAG
Seq A exon
GTATGTGCCAGGGATTGGAGGCAGGAAACAACTTAGCTGCCTCACCTAGTCCCTCAGTGCCCTGACAGCAGACTGTCCCTTGAGAACAGGCTGGCCACATCTGCTCCCAGAGCTCAGAGTCTATTTGACATTTACCTGTCAAATGAGTCGCAGATGTACACACAGTGTGCATTTTTTCAGAGGCTGCATCATAAGTAACCCTTTGCCTTCAAAGTGCTTACAACTTCTATGGGAAGGCACTCTAATGTCTGAAGACCCTTGTGACCCTGAGGCCAGCGCCTCTTTGAAACCCAAATGAGACGCACAAACATTTACCTTCCCTGACTGAAGCACGCAGGAGACACCCAATGTCAGCAAGTTTCAAAACTGAGATGAAACTGATATGCATCTATGAGGAATACAGAAGACAGGCACAGTGATTCACACTGTAATTCCTCCCAGCACTGGGAAGGCTGAGGCAGGAGGGTTGCCTCAAAGTCAAGGCCAGTTAGGGCTACACATAGTGAATTCCAGACCAGCCTGAGCTAAAGCATAGTATCTTGATTAATATGTCTCAGAGAGAGGGTGAGGAAGAGAGAGATTTTTCACACGACCAGCAGTCACGGTACAGCCACGTGCATGGTAGGACTCAGCAGAATGAGCTTAGAAAACAGATTTTAGACAAAAGTTTTTTTAGCAAATATTTCCCACTACTCAGCACAACTGAAACAAGTCTGAGACAGGCCATTAGGCCAGTGTGGATGAGGCTGCTGATCCTAAAACAACCAGAGATTCCACAAGAGTGGCCATGTAAGTGGTCACACCTTCCGAAACCCACAGTGTGGAAGAAGAGACACATACAGCCCCGTTAGATGTAGCAAGTAATAGTTAAAGAGCTTGGACCTGAAGCCCGTGGGGCAGGGAAGGACCTAAGCCGGCCAGGCAGTCAGTTACACTGGACTTTGAAATTGTTACAGAATTCTTCAGCATAAAGCCTATTCTCTTGGTGGTTAGTGGTTGGTCTGGTTCAGTTTGGGTTTTTTTGTTTTGTTTTATTTTGTTTGTTTCAAGACAGGGACTCAAGGAGCCCAAGATGGCCCCTAATTCACTGTGTAATTGAGCATGACCTTCTGCCTGCATCTCCCCAGTTACGGGATTGCAAGCGTGCACCACTACACCTGACAAATCAGGGCTTGCGTTCTCTAGAACCTCGAGGAGAAATACTGAGCATGGTGTGTCCTTTGCCACCATGCTCCTGCGCTGTGCTCTGCTCCTGGGAGGTTACTCCTGGACTCCAGGGACTGCTTGCACAGGAGTCCTGTGGTCATGCTCTGGGCTTGTGACTTGTGTGCAAGAGGAACAGAGCCACAGAGGGTGAAGAGCCTGTGACACAGCAAAGCCCGAGTTCTAGCTCCCTGTCAGAGCTCACAGCACTTCCAAGGTATCAGTGGAAAGCCAGCCTAGGTTATCTAGAGTGTGAACAGCCGTCCTCTAAGGAGAACCCAAGGAATCGGGGAGCAGTGCTAGGGCAGCAGGGACCATGATGGAGAGGCCTGGGAAATACATCTGTGGGGTCACTGACATGCCTGTCCCCGGGGCTTCTAG
Seq C2 exon
GCCCTCACACCCTCCAGTTCACATACGGCTGTGAGATGCGGTACAACAGGACCACAGGGCATTGGCAGTATGGCTACGATGGCAGTGATTACCTGACCTTGGACTTGGGCTCTATGCAATATATAGCAGCCACCTTCATTGCTGGCTACACCAAGCGCAAGTGGGAAAACAATGAGTACTGGCTGGAGAAAGAGAAGACCTACTTGGAGAAGGAGTGCATCCTATGGCTGCAGAGATACTTAACCATGGGAGGAAAGAACTTTACCCGAACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000053835:ENSMUST00000113760:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.045 A=NA C2=0.022
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(52.9=99.0)
A:
NA
C2:
PF0012913=MHC_I=PD(46.5=94.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCCCTTCATCCACTACGACA
R:
CAGCAATGAAGGTGGCTGCTA
Band lengths:
351-1935
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