MmuINT1020333 @ mm10
Intron Retention
Gene
ENSMUSG00000056116 | H2-T22
Description
histocompatibility 2, T region locus 22 [Source:MGI Symbol;Acc:MGI:95956]
Coordinates
chr17:36041868-36042705:-
Coord C1 exon
chr17:36042342-36042705
Coord A exon
chr17:36042129-36042341
Coord C2 exon
chr17:36041868-36042128
Length
213 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
CATCGCGCTCCTCCTCCCAGGTT
3' ss Score
9.96
Exon sequences
Seq C1 exon
CAGGCAGGGTTGAGAGCAAGAAGGTGCAGGATGTAGGCCTGCAGAATTGTCAGACCCAGTGGCGGCTTTTGCCACTGGAAGAATTTCCAACATAAAACAGAGGATCAGTTTGGGACAATCGATTCTGCGACCAGAGGTAGTGTCATTTGGTTACTTTTAAAATTCAGATTTTCTGGTGTTTTCCAATCACTCGCGACTGTAATTTGAAGTTGGGTTCTGAGATAATACAATCGCTGTCGCTCTAGTTTATAAAGCTGTCCAAGATCTGCCCAGTCCCAGATGTCCTGGGTCCTCAGGGCCGCTGTGGTCTGCGCCCTTCTCCTGCAGCTGGATGCCAGACCATCCTGGACTCGGATCCCTTTGG
Seq A exon
GTGAGTGAGACCGGGGAGGGAAACTGTCTCTACTGGGAAGGCTAGGGATAGCACCACCCAGTCTCTGCACCACCCAGCAAGATCCTCCAGCCCCCCTTTTTCAGCTGTCCCGAGCTTGGCGCCCTGCTCCCTTCCCGGCCCGCACTCCCGCTCGAGATCGAGATGGGGATCGAGGAGGAGGAGGTCGGGGTCTCATCGCGCTCCTCCTCCCAG
Seq C2 exon
GTTCACACTCGCTTAGGTATTTCTACACCGCTGTGTCCCGGCCTGGCCTTGGGGAGCCCTGGTTCATAATCGTCGGCTATGTGGACGACATGCAGGTCCTGCGCTTCAGCAGCAAGGAGGAGACTCCGAGGATGGCACCCTGGCTGGAGCAGGAGGAAGCAGATAACTGGGAGCAGCAGACTCGTATAGTCACAATTCAAGGACAGCTGTCTGAAAGGAATCTGATGACCCTGGTTCATTTTTACAACAAGAGCATGGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000056116:ENSMUST00000080015:1
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=0.089
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(0.1=0.0)
A:
NA
C2:
PF0012913=MHC_I=PU(53.4=98.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAAGCTGTCCAAGATCTGCCC
R:
CTGCTGCTCCCAGTTATCTGC
Band lengths:
293-506
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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