MmuINT0078027 @ mm10
Intron Retention
Gene
ENSMUSG00000020080 | Hkdc1
Description
hexokinase domain containing 1 [Source:MGI Symbol;Acc:MGI:2384910]
Coordinates
chr10:62411507-62411854:-
Coord C1 exon
chr10:62411706-62411854
Coord A exon
chr10:62411627-62411705
Coord C2 exon
chr10:62411507-62411626
Length
79 bp
Sequences
Splice sites
5' ss Seq
GAGGTACTG
5' ss Score
7.67
3' ss Seq
GCCTGTGTTCTCTCTGGCAGCTT
3' ss Score
10.64
Exon sequences
Seq C1 exon
AAAACGGGGAATTCCTTTCCCTGGATCTCGGAGGATCCAAGTTTCGGGTCTTGAAGGTGCAAGTCTCCCAAGAGGGCCAGCAAAATGTTCAGATGGAGAGCCAGTTCTACCCAATGCCCAATGAAATCACCCGTGGGAATGGCACGGAG
Seq A exon
GTACTGGCAGGAGGGGAAGACCTGGGTACCAGCCACGAGAGGCGGCACCTAAGCCTTGTGCCTGTGTTCTCTCTGGCAG
Seq C2 exon
CTTTTTGACTACGTAGCCGACTGCCTGGCAGATTTCATGAAGACCAAAAATCTGACACATAAGAAGCTGCCTCTGGGCTTCACCTTTTCTTTTCCCTGCAGACAGAATAAGTTGGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020080:ENSMUST00000020277:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.220 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0034916=Hexokinase_1=FE(23.8=100)
A:
NA
C2:
PF0034916=Hexokinase_1=FE(18.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGGTCTTGAAGGTGCAAGTC
R:
CCCAGAGGCAGCTTCTTATGTG
Band lengths:
182-261
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