MmuINT0075679 @ mm10
Intron Retention
Gene
ENSMUSG00000054128 | H2-T3
Description
histocompatibility 2, T region locus 3 [Source:MGI Symbol;Acc:MGI:95959]
Coordinates
chr17:36185573-36187118:-
Coord C1 exon
chr17:36187005-36187118
Coord A exon
chr17:36186711-36187004
Coord C2 exon
chr17:36185573-36186710
Length
294 bp
Sequences
Splice sites
5' ss Seq
ATGGTATGG
5' ss Score
6.63
3' ss Seq
ATCTTTTTTTTTTTAAACAGGTG
3' ss Score
11.48
Exon sequences
Seq C1 exon
AGCCTCCTCAGACCAGTATGCCCAACAGGACCACTGTTCGTGCTCTCCTTGGAGCTATGATCATCTTAGGTTTTATGAGCGGAAGTGTTATGATGTGGATGAGAAAGAACAATG
Seq A exon
GTATGGAAGAGTCTGTGGCTGGGTGCCTTATGATTGTAAACCAATACACATGCACTCTATGCAAAAGATTGCCTATCTCTGGGTCTGTTTGCAGACACTCACCTTACAATAAAAGACAGATTCATAATGGTAATGGGGGTTCTGCACAGGATTCTAAATGACCTCTCAGAGGTCAGAGGGCAAGGCTCATGCTAAACACTACAGATCTCCAGGCTGGCCTTGTTTCATCCCCTGCATATAATGTCCATGGCACAGAACTTCCTTGGTCTCTCATATCTTTTTTTTTTTAAACAG
Seq C2 exon
GTGGAAACGGAGACGATAACACTGCTGCATATCAGAATGAGAGGGAACACTTGTCCCTGAGCCCTCGGGCTGAATCTGAGGCACTCGGGGTGGAAGCTGGGATGAAGGATCTTCCTTCTGCCCCACCATTGGTCTCCTGACAATGTCTTGTTACTTCTTCTACTGCAGGCAAGGACAGCTTCTCTCTTGTCTCTGGATACTTGAAAAGGTGACACCTGGGAGCCTGGGATTGGGGCTGAGGCAAACTGGAAAGGACTGGGTCACTGGGCCTTTCCTATTTAAACCTTTGAACGAGAGGAAGGCCTTTGAGATGTTTTCACATTGACTGCCCTGACTCTTGTTCTTCATCTTGGGACAGCTGCCACATGGGACTGAGTCACTAGTTCTGACTTCTGAACAGTGGAATCACTTTGGGCAGCCGTGCCTGCCGTTTTATGCTTTTGACTATGCATACAATGGGAAAATCTGGAGAGCACAGCCTGCCCCTGCACACCAAGACTCAGACCCTACATTAGCTGTCATCCCTTGCACAGCCAACCTTCCTGGTCCTCAGGCATTGGGGGACATCTTCATCCTGTCAGCTCCACGCTGTCCTGGGCGTGTGTCTCCTCACACGGCACAGTGTGTCTACTCATTTCCACACTGAACATGAGAATCAGAATGTGGATGTCAGGCAGTGGTGGGCAGGCCATTAATCCTAGCACTTGGGAGGCAGAGGCAGGCAGATTTCTGAGTTCGAGGGCAGCCTGGTTTACAGAGTGAGTTCCAGGACAGACAGGGCTACACGGAGAAACTCTATCTTGGGGGGAAAAAAAAGACAGAAAGAAAAAAAAAAGAATCTGAATGTGGAGGCTGGAGAGAAGTCTCAGTGGTTAAGAGCACTGAGTTCTTTTCCTGAGGCCCTGAATTCAATCCCCAGCAACCACATGGTGGCTCACAACCATATGTAATAGCATGCAATGCCTTCTTCTGGTGTGTTGGAAGTCACCTACAGTGTACTCACCTACATGAAATAAATGAATCTTAAGAAAAGTATGAGTGTGAACTCCTTGACCTGAGCAGTTCACTTGTGGGTAAATTAAAGGATTGAGAATATCTGAGTATTGTGGAGGAAATAAATGGCAGCATGGAGGACCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054128:ENSMUST00000102675:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.359 A=NA C2=0.909
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCTCAGACCAGTATGCCCA
R:
AGAGAGAAGCTGTCCTTGCCT
Band lengths:
298-592
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