MmuINT0075677 @ mm10
Intron Retention
Gene
ENSMUSG00000054128 | H2-T3
Description
histocompatibility 2, T region locus 3 [Source:MGI Symbol;Acc:MGI:95959]
Coordinates
chr17:36187251-36189452:-
Coord C1 exon
chr17:36189177-36189452
Coord A exon
chr17:36187527-36189176
Coord C2 exon
chr17:36187251-36187526
Length
1650 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGT
5' ss Score
9.73
3' ss Seq
TTTCCAACTCTTCTCCTCAGATC
3' ss Score
10.05
Exon sequences
Seq C1 exon
GCTCTCACACCATCCAGGTGATGTATGGCTGTGAGGTGGAGTTCTTCGGGAGCCTCTTCCGCGCTTATGAGCAGCATGGCTATGATGGCCGCGATTACATTGCCCTCAATGAAGATCTGAAAACGTGGACAGCAGCAGACACGGCAGCAGAGATCACCAGAAGCAAGTGGGAGCAGGCTGGTTATACAGAGCTCCGTAGGACCTACTTGGAGGGCCCATGCAAGGATTCCCTGCTCAGATACCTGGAGAACAGAAAAAAGACACAGGAGTGCACAG
Seq A exon
GTGCGTGGCTGCAGACAACTCCATCTCCCTTTGCCTCTGTACTGGGTTCAGTCCAGAGAGAGCAGAAACTCACTAGGTGGGAAAACTCCCATCTCTTTTTCTTTTTTCTTTTTGTATTTTTGTTTGCTTGTTTGGTTGGTTTTTTTGTTTTTTAATTTTAAAAGGTGACAACAGAAAAATAACGTATGAAAATTACACAAACCAATGGCTATACACAGCTCAGTGAGCTTGTAAACAGTTAGAATCGCCACTTTGGACCAGTAGAGAACATGAATTTTACATATTTTCCATTAAATATACTCATGGCTATCCAACATCGACCCCAGGGGTGCAGGGCAGGGAGAGAGAGACAGAGACAGAGACTCACAGACACAGAGAGACAGAGGCAGAGGCAGAAAGAGATGGAGAGACAGAAACAGAGAATCAGTGGCAGAATTAGAAGTAGCTATCAATTATTCCCTGCCATTATCCATCGTGTACTTTACCTACATTTAGTCCTTGCTCATCTCCAAATATTAGCCTTTCCTGATTTCATTATGTCATGTTGCAAGTAACAACAGGTACATTTCTTAACAAGTATACGTTTTTTTGTTTCTTTTGTTTGTTCTTTTGTTTGTTTGTTTTGCTAAATTACCTCTATGAGCAAAAAAGACTGCAGTTTTACTTCCTGTTGTTGTTCTGAGATTGGGTGACTTCGTTTAATATTGTATATTCAAAGTTCATCAATTTTCCTAGATAATTGTGTGATTACATTGTGTAGTGCTCAACAGGATTCCACTTTATATATATACCACATTTTGTTAGTCACTTAAGTGAATAATGGGTTGCTTTACTGCAATAGCTAAGATGTCACACTCCATATCAAGGAAGAGAGTAGAGAGTGGACAGTTCTTTCTTTCTTTTTTTTTAAAGATTTATTTATTTATTTATTTATTATACATAAGTACGCTGTAGCTGTCTTCAGACACACCAGAAGAGGGTGTCAGGTCTCATTACAGGTGGTTGTGAGCCACCATATGGTTGAGGGAATTTGAACTCAGTACCTTCGAAGAGCAATCAGTGTCCTTACCCGTTGAGCCATCTCACCAGCCCTGGTAGTTCTTTGTTATTCCTGATCTTACCAGCAATACTGGGTGTCTCTTCATTTGACACAATGTTCCAGCCTCTTCAGTGTTCCTTTCTCTTCAATATGGGAAGGGGAGAGAACTCCTGTGTTTCTTGACTCTCTCAGAGACTGGCTCTCCCAAGGGAGCACCTTTGTCTCTGGACAGTTCAGAGTCTCTTCAGGATGAAAAGGGAGAAGAGAAGGTTCCTGAAAGAACAGAAAACATTTCCCATGAGTCTGCCGTCCTTTAGAGCCATGGCTTCTCTCAGGCCTTGTTCTCTGCCCACACCCAACCTCTGTGACGTGTGACGTCAGTGGTGCTGAATCTCTGCCCTACCCAGACAGAAGCAGACTTCCCTTTTTGCCTCCTGGGACACATAGCTCCTCCTGGGCACAAGTTCTGGAATTTTCAGAGCATTGTATGTAACCTACTGGGGAAATTTGACCCTTGTTCCAGTCATTTCCTTCCCAGGTGGCCTCACAGACACTTCTGGAGTCACCAGGAAAGATATTTGATGCCCAAACTTTCCAACTCTTCTCCTCAG
Seq C2 exon
ATCCTCCAAAAACACACGTGACCCATCACCCCAGACCTGAAGGTTATGTCACCCTGAGATGCTGGGCCCTGCGCTTCTACCCTGCTGACATCACCCTGACCTGGCAGTTGAATGGGGAGGAATTGATTCAGGACACGGAGCTTGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGCAGCTGTGGTGGTGCCGCTTGGGAAGGAGCAGAAATACACATGTCATGTGTACCATGAGGGGCTGCCTGAGCCTCTCACCCTGAGATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054128:ENSMUST00000102675:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.035 A=NA C2=0.257
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(49.2=94.6)
A:
NA
C2:
PF0765410=C1-set=WD(100=90.3)
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGTGAGGTGGAGTTCTTCG
R:
GGGTGATGTCAGCAGGGTAGA
Band lengths:
345-1995
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