MmuINT0075677 @ mm9
Intron Retention
Gene
ENSMUSG00000054128 | H2-T3
Description
histocompatibility 2, T region locus 3 [Source:MGI Symbol;Acc:MGI:95959]
Coordinates
chr17:36324196-36326397:-
Coord C1 exon
chr17:36326122-36326397
Coord A exon
chr17:36324472-36326121
Coord C2 exon
chr17:36324196-36324471
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-H2-T3:NM_008208:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.043 A=NA C2=0.250
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(3.2=6.1),PF107444=Med1=FE(25.9=100)
A:
NA
C2:
PF107444=Med1=FE(49.7=100),PF0765410=C1-set=WD(100=90.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: