MmuINT0078032 @ mm10
Intron Retention
Gene
ENSMUSG00000020080 | Hkdc1
Description
hexokinase domain containing 1 [Source:MGI Symbol;Acc:MGI:2384910]
Coordinates
chr10:62401724-62403647:-
Coord C1 exon
chr10:62403492-62403647
Coord A exon
chr10:62401958-62403491
Coord C2 exon
chr10:62401724-62401957
Length
1534 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGC
5' ss Score
6.16
3' ss Seq
TCATTCTTGTCTCTGGCTAGGAG
3' ss Score
8.91
Exon sequences
Seq C1 exon
GTTCGAGAAGATGATCAGCGGGCTGTACATGGGGGAGCTGGTCAGGCTTATCTTGCTGAAGATGGCCAAAGTTGGTCTCCTGTTTGGGGGTGCAAAATCCTCTGCTCTCCATACAAAGGGCAAGATCGAAACACAGCACGTGGCTGCCATGGAGAT
Seq A exon
GTAAGCTGCTGGGGTGTCCGTCCTCTTGCCTCTGTGGAGGGCTGGGTTGTCCCTCCTTCTTGACTCTGTGGAGGGTGGGGGTGTTTTACCTTGCCTCTGTGGAGGGCTGGGGTGTTTTGCCTTGCCTCTGTGGAGGGCTGGGGTGTTTGCCTTGCCTCTGTGGAGGGCTGGGGTGTCTCCTGCTGCCCTGACTGTGGAGGGCTGGGGTTGGTGGCCACAGTGCCGTGTACTTAGGTGATGGAGCAACAGTAGGGACCAGACCTTCCTCCCTCACAGGGAGTTTCAGTCCTGGGCTTGGCTTCAGACAAGCTAGAAGTCTCTGCTGTGGCTCAGTGTCACACCCTTGTGGGTCACTAACCAGGGACTGCACAAGTAGGTGTCAGAAAGCCACCTACTTGTCATGTTTTCCTGCCTTCTTCCTCCTTTGAATGGCACTAGTAATAATTTTGGGGTCACAGATCCCTTGGGGAATTTGAGTCAAGTCCTGGATACTTATCCCAAATTACACATTTGTGTATAGTTTTGCTGATGATATGGTTAGGCTGTTGTACCCTGTATGGTGCAGAGTCCCTGAGCCCTACTGTAGAAACTGAATCTTTTCCATTGGCTTCTGGAATGGCTGCCTTCAGATCTGCTGACTCGAGTCTTTACACCCAAAGCCCCACAATGGCATGATGAAGGAGCTTAGCTTTATCAGGCCAGGAACCTGCTCCTAGGCGTGGAACCCCTAGCCCTGCCCTGAGCTTTGCAGTCAGTCTAACATGCAGAGTCCATATCTACACAAGCTTGGCAGGGATGAACTGAGTGACAGGAGACCATGAGGTGCTTAAAAGCCTGGGCTCTAATATGTAACTGCCGGAGTCCAAACCGAGGTTTCAGGTCTGCGGAGCTTTGTGTGTGGAGAACAAGCCACTCACCCTCTGCCTCAGCCCTCTCACTTGCACCCTCTTCTAAGAGGTCCTTCCCTCGGGATTCTTTTTGTTTGTTTGTTTGTTTTTTTGTTTTTTTTGAGACAGGGTTTCTTTATAGCTCTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAATCCACCTGCCTCTGCTTCCTGAGTGCTGGGATTAAAGGCGTGTACCACCATGCCCGGCTCATTTATTTATTTTTTTTAAGATTTATTTATTTATTATATGTAAGTACACTGTAACTGTCCTCAGACACTCCAGAAGAGGGTGCCAGATCTCATTACGGATGGTTGTGAGCCACCATGTGGTTGTGGGATTTGAACTCAGGACCTTCGGAAGAGCAGTCAGTGCTCTTAACTGCTGAGCCATCTCTCCAGTCCCTCCCTCGGGATTCTTGTGGGGATCGGATGAGTTGACTTGCATGGCAGAGCCTTAGCAGGTACCTGCTGTGCGGTGGCACGTGGTAGTGGCTCTATTCAGTGCTGATGCTGTCTTTGGCACACAACCCCAAGGGCACACATCCCAGGAGGATACCCACAGCATGGAGAAGTGTGAGCCTCTCATTCTTGTCTCTGGCTAG
Seq C2 exon
GAGTAAAGAAGGCCTGGCCAACACTCGAGAGATCCTGGTGGATTTGGGCCTGGAGCCCTCTGAGTCAGACTGCATCGCTGTCCAGCACGTGTGCACCATCGTCTCTTTTCGCTCAGCCAATCTCTGCGCAGCGGCTCTGGCAACCATCCTGACTCGACTCCGAGAGAACAAGAAGCTGGCCCGGCTCCGCACCACAGTGGGCATGGATGGAACTCTCTACAAAACACACCCTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020080:ENSMUST00000020277:8
Average complexity
IR
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:
PF0372711=Hexokinase_2=FE(21.7=100)
A:
NA
C2:
PF0372711=Hexokinase_2=FE(32.5=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:
GGGAGCTGGTCAGGCTTATCT
R:
AGAGAGTTCCATCCATGCCCA
Band lengths:
342-1876
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