MmuINT0075540 @ mm10
Intron Retention
Gene
ENSMUSG00000061232 | H2-K1
Description
histocompatibility 2, K1, K region [Source:MGI Symbol;Acc:MGI:95904]
Coordinates
chr17:33996053-33996654:-
Coord C1 exon
chr17:33996616-33996654
Coord A exon
chr17:33996504-33996615
Coord C2 exon
chr17:33996053-33996503
Length
112 bp
Sequences
Splice sites
5' ss Seq
AAGGTGACA
5' ss Score
5.19
3' ss Seq
TTCGAATGTTGTCTTCACAGTGA
3' ss Score
6.1
Exon sequences
Seq C1 exon
GCTCCCAGACCTCTGATCTGTCTCTCCCAGATTGTAAAG
Seq A exon
GTGACACTCTAGGGTCTGATTGGGGAGGGGCAATGTGGACATGATTGGGTTTCAGGAACTCCCAGAATCCCCTGTGAGTGAGTGATGGGTTGTTCGAATGTTGTCTTCACAG
Seq C2 exon
TGATGGTTCATGACCCTCATTCTCTAGCGTGAAGACAGCTGCCTGGAGTGGACTTGGTGACAGACAATGTCTTCTCATATCTCCTGTGACATCCAGAGCCCTCAGTTCTCTTTAGTCAAGTGTCTGATGTTCCCTGTGAGCCTATGGACTCAATGTGAAGAACTGTGGAGCCCAGTCCACCCCTCTACACCAGGACCCTGTCCCTGCACTGCTCTGTCTTCCCTTCCACAGCCAACCTTGCTGGTTCAGCCAAACACTGAGGGACATCTGTAGCCTGTCAGCTCCATGCTACCCTGACCTGCAACTCCTCACTTCCACACTGAGAATAATAATTTGAATGTAACCTTGATTGTTATCATCTTGACCTAGGGCTGATTTCTTGTTAATTTCATGGATTGAGAATGCTTAGAGGTTTTGTTTGTTTGTTTGATTGATTTGTTTTTTTGAAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000061232:ENSMUST00000025181:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.143 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF066236=MHC_I_C=PD(46.2=85.7)
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:
ACCTCTGATCTGTCTCTCCCAG
R:
GAAGGGAAGACAGAGCAGTGC
Band lengths:
257-369
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