AGPHD1 Gene
protein-coding GIFtS: 43
GCID: GC15P078799
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aminoglycoside phosphotransferase domain containing 1
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Aliases
for AGPHD1 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| Aminoglycoside Phosphotransferase Domain Containing 11 2 | | 5-Hydroxylysine Kinase2 | | Aminoglycoside Phosphotransferase Domain-Containing Protein 12 3 | | Hydroxylysine Kinase2 | | 5-Hydroxy-L-Lysine Kinase2 3 | | EC 2.7.1.813 | | LOC1236881 | | |
Export aliases for AGPHD1 gene to outside databasesPrevious GC identifers: GC15P076587 GC15P055557 |
Summaries
for AGPHD1 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
UniProtKB/Swiss-Prot: AGPD1_HUMAN, A2RU49Function: Catalyzes the GTP-dependent phosphorylation of 5-hydroxy-L-lysine
|
Genomic Views
for AGPHD1 gene
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to
UCSC (hg19) and
Ensembl (release 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000015.9 NC_018926.1 NT_010194.17
Regulatory elements:
 Search SABiosciences Regulatory transcription factor binding sites for AGPHD1
Other transcription factors
Search SABiosciences Chromatin IP Primers for AGPHD1
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat AGPHD1 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 15q25.1 Ensembl cytogenetic band: 15q25.1 HGNC cytogenetic band: 15q25.1AGPHD1 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 15 GeneLoc Exon Structure GeneLoc location for GC15P078799: view genomic region
(about GC identifiers)
Start:
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78,799,906 bp from pter |
End:
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78,829,715 bp from pter |
Size:
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29,810 bases |
Orientation:
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plus strand |
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Proteins
for AGPHD1 gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
EMD Millipore,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological,
ProSpec, and/or
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
|
UniProtKB/Swiss-Prot: AGPD1_HUMAN, A2RU49 (See
protein sequence)Recommended Name: Hydroxylysine kinase Size: 373 amino acids; 41933 Da
Subcellular location: Cytoplasm (Potential)
Secondary accessions: B7ZMA5 Q6ZTN0Alternative splicing: 3 isoforms: A2RU49-1 A2RU49-2 A2RU49-3 (No experimental confirmation available)Explore the universe of human proteins at neXtProt for AGPHD1: NX_A2RU49
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_A2RU49
AGPHD1 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins (2 alternative transcripts):
NP_001013641.2 NP_001077081.1
ENSEMBL proteins: ENSP00000456614 ENSP00000457154 ENSP00000455459 ENSP00000454850 ENSP00000386197 ENSP00000373640 ENSP00000353710
Human Recombinant Protein Products for AGPHD1:
Gene Ontology (GO): 1 cellular component term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005737 | cytoplasm |
IEA | -- |
AGPHD1 for ontologies About GeneDecksing
AGPHD1 Antibody Products:
Assay Products for AGPHD1: |
Protein
Domains /
Families
for AGPHD1 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
AGPHD1 for domains About GeneDecksing
2 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry A2RU49ProtoNet protein and cluster: A2RU49 UniProtKB/Swiss-Prot: AGPD1_HUMAN, A2RU49Similarity: Belongs to the aminoglycoside phosphotransferase family |
Function
for AGPHD1 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
inGenious Targeting Laboratory,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase,
shRNA from
OriGene,
Sirion Biotech,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Sirion Biotech,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
Sirion Biotech,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Molecular Function:
UniProtKB/Swiss-Prot Summary: AGPD1_HUMAN, A2RU49Function: Catalyzes the GTP-dependent phosphorylation of 5-hydroxy-L-lysineCatalytic activity: GTP + 5-hydroxy-L-lysine = GDP + 5-phosphonooxy-L-lysineBiophysicochemical properties: Kinetic parameters: KM=280 uM for (5R)-5-hydroxy-L-lysine (in the presence of 2 mM ATP);KM=7.6 uM for (5R)-5-hydroxy-L-lysine (in the presence of 0.2 mM GTP); KM=810 uM for ATP (in the presence of 0.5 mM(5R)-5-hydroxy-L- lysine); KM=3.5 uM for GTP (in the presence of 0.5 mM (5R)-5-hydroxy-L- lysine); Vmax=4.95umol/min/mg enzyme toward (5R)-5-hydroxy-L-lysine (in the presence of 2 mM ATP); Vmax=0.49 umol/min/mg enzyme toward(5R)-5-hydroxy-L-lysine (in the presence of 0.2 mM GTP); Vmax=5.28 umol/min/mg enzyme toward ATP (in the presence of0.5 mM (5R)-5-hydroxy-L-lysine); Vmax=0.57 umol/min/mg enzyme toward GTP (in the presence of 0.5 mM(5R)-5-hydroxy-L-lysine); Enzyme Number (IUBMB): EC 2.7.1.811
Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0016301 | kinase activity |
-- | -- | | GO:0047992 | hydroxylysine kinase activity |
IEA | -- |
AGPHD1 for ontologies About GeneDecksing
Phenotypes:
1 GenomeRNAi human phenotype for AGPHD1:
Animal Models:
Clone
Products: |  | Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore | |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for AGPHD1 (see all 4)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for AGPHD1 (see all 2)
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
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In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for AGPHD1 |
|
Pathways & Interactions
for AGPHD1 gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
Reactome,
Tocris Bioscience,
GeneGo (Thomson Reuters),
QIAGEN,
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Interaction Networks according to
SABiosciences,
and/or STRING,
Interactions according to 1UniProtKB,
2MINT,
3I2D, and/or
4STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene).
About This Section
|
Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for AGPHD1
|
Drugs & Compounds
for AGPHD1 gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for AGPHD1
Search CenterWatch for drugs/clinical trials and news about AGPHD1 / AGPD1
|
Transcripts
for AGPHD1 gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
Sirion Biotech,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
REFSEQ mRNAs for AGPHD1 gene (2 alternative transcripts): NM_001013619.2 NM_001083612.1 Unigene Cluster for AGPHD1: Aminoglycoside phosphotransferase domain containing 1 Hs.307962 [show with all ESTs]Unigene Representative Sequence: BC1327537 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000566289(uc002bdt.3) ENST00000566332 ENST00000569878 ENST00000563233
ENST00000408962(uc010ble.3) ENST00000388988(uc010unc.2) ENST00000360519
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for AGPHD1 (see all 4)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for AGPHD1 (see all 2)
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector (see all 2): AGPHD1 (NM_001083612) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for AGPHD1 | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat AGPHD1 |
Additional cDNA sequence: BC132753.1 BC144383.1 3 DOTS entries: DT.408202 DT.97830952 DT.100738033 23 AceView cDNA sequences: AI092742 AA635871 N77676 CK820036 BX095433 CK820037 BF477719 BM354109 AI633355 BM354062 AI631501 BF679918 BM045979 AK126453 BQ919173 N58310 BM273151 AA707084 BM826406 AW236429 AW973177 BM273118 AA552191
GeneLoc Exon Structure
2 Alternative Splicing Database (ASD) splice patterns (SP) for AGPHD1 About this scheme
| ExUns: | 1 | ^ | 2a | · | 2b | ^ | 3 | ^ | 4 | ^ | 5a | · | 5b |
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| SP1: | | | | | | | | | | | | | | | |
| SP2: | | | | | | | | | - | | | | | |
ECgene alternative splicing isoforms for AGPHD1
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Expression
for AGPHD1 gene
(RNA expression data according to
H-InvDB,
NONCODE,
miRBase, and
RNAdb,
Expression images according to data from
BioGPS,
Illumina Human BodyMap, and
CGAP
SAGE,
Sets of similar genes according to GeneDecks,
in vivo and in vitro expression data from LifeMap Discovery™,
plus additional links to
Genevestigator, and/or
SOURCE, and/or
BioGPS, and/or
UniProtKB,
PCR Arrays from
SABiosciences,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN,
In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
| AGPHD1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: TCATTCATCT
About this image
See AGPHD1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for AGPHD1
SOURCE GeneReport for Unigene cluster: Hs.307962
SABiosciences Custom PCR Arrays for AGPHD1
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for AGPHD1
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse, rat AGPHD1 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat AGPHD1 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat AGPHD1 | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for AGPHD1 |
Orthologs
for AGPHD1 gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
,
5MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase,
and/or
6Ensembl pan taxonomic compara ,
Gene Trees according to Ensembl and
TreeFam)
About This Section
|
This gene was present in the common ancestor of animals.
Orthologs for AGPHD1 gene from 4/17 species (see all 17) About this table
ENSEMBL Gene Tree for AGPHD1 (if available)
TreeFam Gene Tree for AGPHD1 (if available) |
Paralogs
for AGPHD1 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| -- |
Genomic Variants
for AGPHD1 gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, and
DNA2.0,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene
Mutation Database (HGMD) and the Locus Specific Mutation
Databases (LSDB), Blood group antigen gene mutations by BGMUT,
Resequencing Primers from QIAGEN,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 15 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for AGPHD1 (78799906 - 78829715 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for AGPHD1
1 CNV: 5797 | SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing AGPHD1 |
|
Disorders
/ Diseases
for AGPHD1 gene
(in which this Gene is Involved, According to MalaCards,
OMIM, UniProtKB,
the University of Copenhagen DISEASES
database,
Genatlas, GeneTests,
GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
AGPHD1 for disorders About GeneDecksing
OMIM gene information: 614681
OMIM disorders: --
2  diseases for AGPHD1: About MalaCardslung cancer copd
Human Genome Epidemiology (HuGE) Navigator: AGPHD1 (1 document)
Export disorders for AGPHD1 gene to outside databases
|
Publications
for AGPHD1 gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6HMDB,
7DrugBank,
8UniProtKB/TrEMBL,
9 Novoseek, and/or
10fRNAdb)
About This Section
|
PubMed articles for AGPHD1 gene, integrated from 9 sources (see all 20):
(articles sorted by number of sources associating them with AGPHD1) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Molecular identification of hydroxylysine kinase and o f ammoniophospholyases acting on 5-phosphohydroxy-L-lysine and phosphoethanolami ne. (PubMed id 22241472)1, 2, 3 Veiga-da-Cunha M....Van Schaftingen E. (2012)
- Familial aggregation of common sequence variants on 15q24-25.1 in lung cancer. (PubMed id 18780872)1, 3 Liu P....You M. (2008)
- Strong association between two polymorphisms on 15q25. 1 and lung cancer risk: a meta-analysis. (PubMed id 22701590)1 Gu M....Niu W. (2012)
- Genome-wide association studies identify CHRNA5/3 and HTR4 in the development of airflow obstruction. (PubMed id 22837378)1 Wilk J.B....Stricker B.H. (2012)
- A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
- Genome-wide association study of smoking behaviours i n patients with COPD. (PubMed id 21685187)1 Siedlinski M....Silverman E.K. (2011)
- Nicotinic acetylcholine receptor region on chromosome 15q25 and lung cancer risk among African Americans: a case-control study. (PubMed id 20554942)1 Amos C.I....Spitz M.R. (2010)
- Replication of lung cancer susceptibility loci at chr omosomes 15q25, 5p15, and 6p21: a pooled analysis from the International Lung C ancer Consortium. (PubMed id 20548021)1 Truong T....Spitz M.R. (2010)
- Blood-based CHRNA3 single nucleotide polymorphism and outcome in advanced non-small-cell lung cancer patients. (PubMed id 19733931)1 Carcereny E....Rosell R. (2010)
- Fine mapping of chromosome 15q25.1 lung cancer suscep tibility in African-Americans. (PubMed id 20587604)1 Hansen H.M....Wiencke J.K. (2010)
|
External Searches for AGPHD1 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing AGPHD1 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing AGPHD1 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing AGPHD1 gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| Name | Description |
| PharmGKB entry for AGPHD1 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for AGPHD1 gene:
Search GeneIP for patents involving AGPHD1
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for AGPHD1 gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory)
About This Section
|
 | |
 | |
 |
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| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for AGPHD1 |
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