MmuINT0075670 @ mm10
Intron Retention
Gene
ENSMUSG00000053835 | H2-T24
Description
histocompatibility 2, T region locus 24 [Source:MGI Symbol;Acc:MGI:95958]
Coordinates
chr17:36017241-36020560:-
Coord C1 exon
chr17:36020460-36020560
Coord A exon
chr17:36017538-36020459
Coord C2 exon
chr17:36017241-36017537
Length
2922 bp
Sequences
Splice sites
5' ss Seq
CCCGTAAGT
5' ss Score
9.09
3' ss Seq
AAATCCTATTCTAACCTCAGGGT
3' ss Score
5.53
Exon sequences
Seq C1 exon
AAGTCTAGTTTCTCAGGACAGTGGAAGCTTAAAGCTTGATCCTGACACCATGTGGGCTCTTATCTTCTGGCTTCTGAGTCACCCCCAGGACGGCGGAGCCC
Seq A exon
GTAAGTAGGGTTGTGTGCTGGGTAAATTTAAGACCGGAAAACCTCCAACCTCGAACCTTGGGCCATTTTGCAGAAGACTAGGTTTCAGTTAGTAGCTCTGTCTTCAAACTTGCTATGTAGACCAGGCTGGCCTTGAACTCAAAGGAGTTGGGACTAAAGGCATGCACCGCCAAACCAGCCCTTTCCTTACATTCTAATGTGGTTTTGAGTATTTGCTTGTATGTGTGCATAACATGCCAGAGGTCAGAAGAGGGCATGAAGCTCCCTCCAGCTGGTGCTCAGAACTATACCACAGTCTTCTGGAAGAACAGTAAGTGCTCTTAACAGCTGGGCTGCCTTCCCTACTTCTGCGAACTACATGTTTACTTATAAAGTATACACTGTGCACACTGTTGTGTAAATTTATCCATATGCATGTTTGTGTGTGCTCATGTGTAGCCTGCAACCCATAGTATAGCCCAGATGTGGAGGTCAGAGGACAACCTAATTTGGATCAGGTCTCCTTCCACCATATGGGTGGCAGCAGGTGCCTTTACTAGCTGAGCAGTCTGTCTCCCTGGCATCATCATTTGTTAAAGTCCTGGTTCTTTCTGCCAGCCCCATGCTCCTGGACATAAGATTCAGGCTCAAATTATATTTACAAATACCTTGGCCATATAGCTAGGCTCTACTCTGACTAGATTATAACTAAAAAATACCCATTTATTTTAAGCTGCATTTTGCCACGTGGCTGATTACTTGTGCTCAGGTACCACGTGTCCATGTGTCTGTCTCCTCACCTTTTTCCAGGCTCCTCTCTCTCCCGGACTCCTCCTCTCCCAGAATTCTTTCTCCTCCCAATGTCCCACCTCTATTTCCTGCTTAAGCTGTAGGCTTTTAAATTGACAGGTAAGGCATCCACAATACACAAGATGATCTCTCTACAGTCATTATCATTATCATCATCATTAATAATAATTATTGTATTATAGGATTCTATTTATGTGACCCTCAAATTCATGATCCTCCTGCCTCACACATACATGTATAATTATGTATTTCTGCTAGCTGGTTATAATGGTTGATTTCGTGTGTCAATTTGACTAGAACACAATATTCAGTTGAAATGGAGCTGGATATGGCATCTCACACCCATGATCCTGTAATCATTTGGAAGACTGAGTAGGAAGATTACTGAGTTCTAGGCAACCCTCCACCCAACCCCAGAAAAATAACTACTGTAGATATTTCAGGATGTGAGTGGCTTCCTCGTCCTCCTAAACAGGGACCACCCAGGGCAACCTGGAAATCCTGCCTGGGTGTGTATCCACTGTGTATCCACTGATAAAGACAAAAGCCAGGAGGCAGAGGCTGAGGACTTGGAAGGCAGGCGGATCTCTCTGAGTAAAGGACAGCCTGATCTACAGAGTGAGTTCCAGGACAGCCAAGGCTCCCCACAAAACAAAACAACAACAACAAAATGCAGTTCAATACACACTAGAATTTGATACAATACAATGAAATCTTATTTGGCTATAAAATGAAATTCTATGCCCTTTTTAAGCAAAATTAAATTATGATATTGGGAGAGATGGATAAAACTGAAAGAAGCAAACCTCAGAAAGACAAATATACATCTTGTCTCTGGAACTCCAGTTTACAATTATTATTATTTTGTATGTGCTGAGTATAATGGTGCACACCTGTGATCCCAGCATTGGGAGGTGCAGGCAGAAAGATCAGAAGTTCAAGGCCAGCCTCAGCTACATGAGACCCTGTCTCAAAAATAAAGATTAAAAAACAAACATATTTTTTAAAAGCGGGGGTGCTGGAGAGATGGCTCAGCAGTTAAGAGCACTAACTGCTCTTCCGAAGGTCCTGAGTTCAAATCCCAGCAACCACATGGTGGCTTACAACCATCTGTAATGAGATCGGATGCCCTAGTCTGGAGTGTCTGAAGACAGCTACAGTGTACTTACATATAATAAATAAATAAATCTTTTTTAAAAACCATAAAATTATACACGCATGTGTATATGTGCTTTTAAATATATGGGAGGACTGCAAAACAAAATGGAAACATGGAAGAGATCTTAGAGGAGGCAGGTGATGATACAGAACATGTGATAAAACAGAAGCAGCAGAGCCGGGTTTAACTAGGAAAGAAATGGAAGCAGCTGGAGGAGGGTGAGGAGTATGGGACAGAGCAGTGAGAGGAAGAGCACATGGTAGAAAGTCTAATGGCAGAGGCCACTGAGATAGTTTTCTGGTATCAAAGTCTAATGACAGAGGCTGCAGAGGGGGTCCAAATGGTAGCAGAGTCTAATGGCAGAGGCTGCAGAGGGGGTCCAAATGGTAGCAGAGTCTAATGGCAGAGGCTGCAGAGGTGGTCCAAATGGTAGCAGAGTCTAATGGCAGAGACAGCAAAAGTGGTTCAGCTCCCTGCACCCCCAGCACTTAGAATACAAAATAACCCTGTAGCAAGCATAATGCACATATACAAATATGATAAGATGAAACCCATTACTTTGTATCCTAACTTCTTTAATTAACCAAAAACAAAATCAAAACTCTGATACGGGAGAGCAAGTTACTGCAGCTTCATCTATGCGCGACACACAGACAGTGCCCTTGAGGGGCCAAAAGGCATCAGATCCCCTGGAGCTGGAGGTACAGATGGTTGGGAGAGGACACGTGGATGCTGGGAATTGAACTCAGGTCCTCTATAAGAGTGACCAATGCTCTTAACCACTGAGCCATCCCTCCAGCCCCTTACACTCACACTTTGTTGGTTCTCTGAATTATCCCAGTGAGCAGTATGGAATCCGATTCTCTTGGCTGGTGGGTTGTTATGAAGTGTTCTCATTTATGTTTGTGTGCCCTGTCTCTTCTAGAGCTGGGCCCTCACTCGGTACCTCACACTAAATCCTATTCTAACCTCAG
Seq C2 exon
GGTCGCACTCTCTGCATTACTGTTACTCAGCTGTGACTGAGCCGGGCCCGGGAGTTCCTTCATTTTTCGCCAGTGGCTTCTTAGATAACCAGCCCTTCATCCACTACGACAGCAGGAGCATGAAGGCAGAGCCTTGTGCTGACTGGCTGAGGGAAAATGCACAGTACTTCACTCATGAGACTGAGGTTTTCACCAATCGGATGAAGATTTTCCAGTTGAGCCTGAGAAACATTCGGCAATACTACAACAGCTCTGGTACCCAGAGTCAGAGAGCAGATGGCTTCCGCCAGCAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000053835:ENSMUST00000113760:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.045
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(0.1=0.0)
A:
NA
C2:
PF0012913=MHC_I=PU(52.9=99.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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