MmuINT0078019 @ mm9
Intron Retention
Gene
ENSMUSG00000020080 | Hkdc1
Description
hexokinase domain containing 1 [Source:MGI Symbol;Acc:MGI:2384910]
Coordinates
chr10:61861333-61861677:-
Coord C1 exon
chr10:61861538-61861677
Coord A exon
chr10:61861453-61861537
Coord C2 exon
chr10:61861333-61861452
Length
85 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
GCTCCGCTCTCTCCCTGCAGCTC
3' ss Score
12.78
Exon sequences
Seq C1 exon
AGAAAGGAAAGTTCCTTGCCCTGGATTTGGGGGGAACCAACTTCCGAGTCCTCCTGGTAAAGATCAGGCGGAGGTCTGTGCGCATGTACAACAAGATCTTCGCCATCCCTCTGGAGATCATGCAGGGCACTGGGGAGGAG
Seq A exon
GTGAGTGTCAGGGCTGGGGGTCGAGGTCGGGCAGCCACGCCCCCATCAGTGCACACCTTGCATGAGCTCCGCTCTCTCCCTGCAG
Seq C2 exon
CTCTTTGACCACATCGTACAGTGCATCGCTGACTTCCTGGACTACATGGGCCTCAAGGGCGCCCAGCTGCCTTTGGGCTTCACCTTCTCCTTCCCCTGCAGACAGACATGCATCGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020080-Hkdc1:NM_145419:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0034916=Hexokinase_1=FE(22.7=100)
A:
NA
C2:
PF0034916=Hexokinase_1=FE(19.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGTAAAGATCAGGCGGAGGT
R:
GGAGAAGGTGAAGCCCAAAGG
Band lengths:
176-261
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: