Hkdc1 (hexokinase domain containing 1) - Rat Genome Database

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Gene: Hkdc1 (hexokinase domain containing 1) Rattus norvegicus
Analyze
Symbol: Hkdc1
Name: hexokinase domain containing 1
RGD ID: 2321830
Description: Predicted to enable fructokinase activity and glucokinase activity. Predicted to be involved in several processes, including glucose 6-phosphate metabolic process; glycolytic process; and intracellular glucose homeostasis. Predicted to be located in cytoplasm and photoreceptor inner segment. Predicted to be active in cytosol and mitochondrion. Human ortholog(s) of this gene implicated in retinitis pigmentosa 92. Orthologous to human HKDC1 (hexokinase domain containing 1); INTERACTS WITH atrazine; glyphosate; 1,2-dimethylhydrazine (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: AABR07045032.1; hexokinase 1-like; hexokinase HKDC1; LOC100364027; putative hexokinase HKDC1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82030,878,037 - 30,917,044 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2030,878,319 - 30,916,704 (-)EnsemblGRCr8
mRatBN7.22030,335,322 - 30,373,792 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2030,335,628 - 30,373,867 (-)EnsemblmRatBN7.2
Rnor_6.02032,018,027 - 32,054,494 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2032,018,673 - 32,052,855 (-)NCBIrn6Rnor6.0
Rnor_5.02033,805,753 - 33,840,534 (-)NCBIRnor_5.0Rnor_5.0rn5
Celera2031,757,004 - 31,794,582 (-)NCBICelera
Cytogenetic Map20q11NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-palmitoylglycerol  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
aristolochic acid A  (ISO)
atrazine  (EXP)
Azaspiracid  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
beta-lapachone  (ISO)
bisphenol A  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
choline  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) chloride  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
dibenz[a,h]anthracene  (ISO)
diiodine  (ISO)
dioxygen  (ISO)
ethanol  (ISO)
folic acid  (ISO)
genistein  (ISO)
glucose  (ISO)
glyphosate  (EXP)
GW 4064  (ISO)
inulin  (ISO)
ivermectin  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
leflunomide  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N-Nitrosopyrrolidine  (ISO)
paracetamol  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
propanal  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sotorasib  (ISO)
sulforaphane  (ISO)
temozolomide  (ISO)
tetraphene  (ISO)
thiram  (ISO)
titanium dioxide  (ISO)
trametinib  (ISO)
tributylstannane  (ISO)
triptonide  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
valproic acid  (ISO)
Yessotoxin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:27459389   PMID:30517626   PMID:30543855   PMID:33309778  


Genomics

Comparative Map Data
Hkdc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82030,878,037 - 30,917,044 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2030,878,319 - 30,916,704 (-)EnsemblGRCr8
mRatBN7.22030,335,322 - 30,373,792 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2030,335,628 - 30,373,867 (-)EnsemblmRatBN7.2
Rnor_6.02032,018,027 - 32,054,494 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2032,018,673 - 32,052,855 (-)NCBIrn6Rnor6.0
Rnor_5.02033,805,753 - 33,840,534 (-)NCBIRnor_5.0Rnor_5.0rn5
Celera2031,757,004 - 31,794,582 (-)NCBICelera
Cytogenetic Map20q11NCBI
HKDC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381069,220,332 - 69,267,552 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1069,220,292 - 69,267,552 (+)Ensemblhg38GRCh38
GRCh371070,980,088 - 71,027,308 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361070,650,065 - 70,697,321 (+)NCBIBuild 36Build 36hg18NCBI36
Celera1064,255,904 - 64,303,168 (+)NCBICelera
Cytogenetic Map10q22.1NCBI
HuRef1064,980,307 - 65,027,150 (+)NCBIHuRef
CHM1_11071,261,818 - 71,308,763 (+)NCBICHM1_1
T2T-CHM13v2.01070,088,688 - 70,135,592 (+)NCBIT2T-CHM13v2.0
Hkdc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391062,218,916 - 62,259,490 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1062,218,916 - 62,258,270 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381062,383,137 - 62,423,711 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1062,383,137 - 62,422,491 (-)Ensemblmm10GRCm38
MGSCv371061,845,885 - 61,885,205 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361061,778,494 - 61,817,814 (-)NCBIMGSCv36mm8
Celera1063,486,364 - 63,525,623 (-)NCBICelera
Cytogenetic Map10B4NCBI
cM Map1032.4NCBI
Hkdc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543721,825,397 - 21,868,435 (-)Ensembl
ChiLan1.0NW_00495543721,825,647 - 21,873,698 (-)NCBIChiLan1.0ChiLan1.0
HKDC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2881,366,586 - 81,413,556 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11081,371,908 - 81,418,779 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01065,687,378 - 65,734,281 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11068,220,475 - 68,267,321 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1068,220,475 - 68,267,321 (+)EnsemblpanPan2panpan1.1
HKDC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1420,353,941 - 20,395,429 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl420,353,355 - 20,394,634 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha420,484,075 - 20,525,712 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0420,625,796 - 20,667,351 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl420,625,349 - 20,667,051 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1420,526,423 - 20,567,841 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0420,729,648 - 20,771,687 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0421,073,106 - 21,114,762 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Hkdc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721360,683,196 - 60,730,681 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365219,175,447 - 9,223,583 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365219,175,916 - 9,223,546 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HKDC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1472,283,845 - 72,335,886 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11472,285,941 - 72,343,990 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21478,302,927 - 78,353,257 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HKDC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1962,051,098 - 62,099,986 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl962,052,027 - 62,099,221 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604822,791,409 - 22,839,449 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hkdc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247543,511,730 - 3,556,184 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247543,511,947 - 3,556,131 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Hkdc1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11828,211,986 - 28,253,452 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Hkdc1
318 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:74
Count of miRNA genes:69
Interacting mature miRNAs:74
Transcripts:ENSRNOT00000074989
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202668936256021148Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)20418947649189476Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20133724594Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20153308346533083Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600300Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20134066551Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202074558556021148Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202668936256021148Rat
1598870Bp289Blood pressure QTL 2892.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)20821635953216359Rat
1598858Cm61Cardiac mass QTL 613.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)20821635953216359Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202679235356021148Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)201224324249189476Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202668936256021148Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578510Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600300Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202668936256021148Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
circulatory system
ectoderm
hemolymphoid system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
sensory system
visual system
7 5 21 2 44 10 3 21 27 28 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000074989   ⟹   ENSRNOP00000064051
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2030,878,319 - 30,916,704 (-)Ensembl
mRatBN7.2 Ensembl2030,335,628 - 30,373,867 (-)Ensembl
RefSeq Acc Id: XM_039099162   ⟹   XP_038955090
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82030,878,037 - 30,917,044 (-)NCBI
mRatBN7.22030,335,322 - 30,373,792 (-)NCBI
RefSeq Acc Id: XM_039099165   ⟹   XP_038955093
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82030,878,037 - 30,902,584 (-)NCBI
mRatBN7.22030,335,322 - 30,359,841 (-)NCBI
RefSeq Acc Id: XM_039099167   ⟹   XP_038955095
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82030,878,037 - 30,900,601 (-)NCBI
mRatBN7.22030,335,322 - 30,357,869 (-)NCBI
RefSeq Acc Id: XP_038955090   ⟸   XM_039099162
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955093   ⟸   XM_039099165
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038955095   ⟸   XM_039099167
- Peptide Label: isoform X3
Ensembl Acc Id: ENSRNOP00000064051   ⟸   ENSRNOT00000074989
Protein Domains
Hexokinase C-terminal   Hexokinase N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R3X7-F1-model_v2 AlphaFold M0R3X7 1-910 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2321830 AgrOrtholog
BioCyc Gene G2FUF-3694 BioCyc
BioCyc Pathway ANAGLYCOLYSIS-PWY [glycolysis III (from glucose)] BioCyc
  PWY-3861 [mannitol degradation II] BioCyc
  PWY-5941 [glycogen degradation II] BioCyc
  PWY3O-1743 [D-mannose degradation II] BioCyc
  UDPNACETYLGALSYN-PWY [UDP-N-acetyl-D-glucosamine biosynthesis II] BioCyc
BioCyc Pathway Image ANAGLYCOLYSIS-PWY BioCyc
  PWY-3861 BioCyc
  PWY-5941 BioCyc
  PWY3O-1743 BioCyc
  UDPNACETYLGALSYN-PWY BioCyc
Ensembl Genes ENSRNOG00000049045 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000074989 ENTREZGENE
  ENSRNOT00000074989.4 UniProtKB/TrEMBL
Gene3D-CATH 3.30.420.40 UniProtKB/TrEMBL
  3.40.367.20 UniProtKB/TrEMBL
InterPro ATPase_NBD UniProtKB/TrEMBL
  Hexokinase UniProtKB/TrEMBL
  Hexokinase_BS UniProtKB/TrEMBL
  Hexokinase_C UniProtKB/TrEMBL
  Hexokinase_N UniProtKB/TrEMBL
NCBI Gene 100364027 ENTREZGENE
PANTHER HEXOKINASE HKDC1 UniProtKB/TrEMBL
  PTHR19443 UniProtKB/TrEMBL
Pfam Hexokinase_1 UniProtKB/TrEMBL
  Hexokinase_2 UniProtKB/TrEMBL
PhenoGen Hkdc1 PhenoGen
PRINTS HEXOKINASE UniProtKB/TrEMBL
PROSITE HEXOKINASE_1 UniProtKB/TrEMBL
  HEXOKINASE_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000049045 RatGTEx
Superfamily-SCOP SSF53067 UniProtKB/TrEMBL
UniProt M0R3X7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Hkdc1  hexokinase domain containing 1  AABR07045032.1    Data merged from RGD:15005656 737654 PROVISIONAL
2019-11-08 AABR07045032.1        Symbol and Name status set to provisional 45752 PROVISIONAL
2017-05-24 Hkdc1  hexokinase domain containing 1  LOC100364027  hexokinase 1-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-06 LOC100364027  hexokinase 1-like      Symbol and Name status set to provisional 70820 PROVISIONAL