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ATP5F1D Gene(Protein Coding)

ATP Synthase F1 Subunit Delta

GCID:
GC19P001242
GIFtS:
36
Genes Participants
UDN Logo

Aliases for ATP5F1D Gene

Aliases for ATP5F1D Gene

  • ATP Synthase F1 Subunit Delta 2 3 4 5
  • ATP Synthase, H+ Transporting, Mitochondrial F1 Complex, Delta Subunit 2 3
  • F-ATPase Delta Subunit 3 4
  • ATP5D 3 4
  • Mitochondrial ATP Synthase Complex Delta-Subunit Precusor 3
  • ATP Synthase Subunit Delta, Mitochondrial 3
  • Mitochondrial ATP Synthase, Delta Subunit 3

External Ids for ATP5F1D Gene

Previous HGNC Symbols for ATP5F1D Gene

  • ATP5D

Summaries for ATP5F1D Gene

Entrez Gene Summary for ATP5F1D Gene

  • This gene encodes a subunit of mitochondrial ATP synthase. Mitochondrial ATP synthase catalyzes ATP synthesis, utilizing an electrochemical gradient of protons across the inner membrane during oxidative phosphorylation. ATP synthase is composed of two linked multi-subunit complexes: the soluble catalytic core, F1, and the membrane-spanning component, Fo, comprising the proton channel. The catalytic portion of mitochondrial ATP synthase consists of 5 different subunits (alpha, beta, gamma, delta, and epsilon) assembled with a stoichiometry of 3 alpha, 3 beta, and a single representative of the other 3. The proton channel consists of three main subunits (a, b, c). This gene encodes the delta subunit of the catalytic core. Alternatively spliced transcript variants encoding the same isoform have been identified. [provided by RefSeq, Jul 2008]

GeneCards Summary for ATP5F1D Gene

ATP5F1D (ATP Synthase F1 Subunit Delta) is a Protein Coding gene. Diseases associated with ATP5F1D include Mitochondrial Disorders. Among its related pathways are Metabolism and purine nucleotides de novo biosynthesis.

UniProtKB/Swiss-Prot for ATP5F1D Gene

  • Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core, and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP turnover in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F(1) domain and of the central stalk which is part of the complex rotary element. Rotation of the central stalk against the surrounding alpha(3)beta(3) subunits leads to hydrolysis of ATP in three separate catalytic sites on the beta subunits.

Gene Wiki entry for ATP5F1D Gene

Additional gene information for ATP5F1D Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ATP5F1D Gene

Genomics for ATP5F1D Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for ATP5F1D Gene

Promoters and enhancers for ATP5F1D Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH19J001236 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 659 +15.1 15113 41.1 CLOCK MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF416 CIRBP C19orf24 MIDN CBARP ATP5F1D SF3A2 TCF3 TMEM259 LOC100288123 MIER2
GH19J001202 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 4.7 -35.0 -34989 8 ZFP64 FEZF1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC ZC3H11A STK11 CIRBP TMEM259 DAZAP1 LOC100288123 TCF3 PTBP1 GRIN3B DOT1L POLRMT
GH19J001212 Enhancer 1.2 Ensembl ENCODE dbSUPER 8.2 -25.8 -25796 6.9 HDGF PKNOX1 RB1 KLF17 KLF14 ZNF2 RAD21 THRB ZSCAN5C SCRT2 CIRBP ATP5F1D WDR18 STK11 PIR41652 GC19M001234
GH19J001231 Enhancer 1 Ensembl ENCODE 8.6 -9.2 -9151 1.9 NFIB KLF17 ZNF2 ZEB1 GLIS2 SCRT2 ZNF398 PPARG NR2F2 ZFP69B SBNO2 TCF3 PTBP1 TMEM259 ENSG00000267317 STK11 LOC100288123 DAZAP1 GRIN3B MED16
GH19J001220 Enhancer 0.9 ENCODE dbSUPER 8 -20.1 -20056 1.7 ZBTB10 GATAD2A CTCF KLF1 ZBTB6 SAP130 ARID4B SMARCB1 RAD21 TGIF2 ATP5F1D STK11 PIR41652 GC19M001234
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ATP5F1D on UCSC Golden Path with GeneCards custom track

Genomic Locations for ATP5F1D Gene

Genomic Locations for ATP5F1D Gene
chr19:1,241,746-1,244,826
(GRCh38/hg38)
Size:
3,081 bases
Orientation:
Plus strand
chr19:1,241,749-1,244,824
(GRCh37/hg19)
Size:
3,076 bases
Orientation:
Plus strand

Genomic View for ATP5F1D Gene

Genes around ATP5F1D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATP5F1D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATP5F1D Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for ATP5F1D Gene

Proteins for ATP5F1D Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for ATP5F1D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P30049-ATPD_HUMAN
    Recommended name:
    ATP synthase subunit delta, mitochondrial
    Protein Accession:
    P30049
    Secondary Accessions:
    • D6W5Y3
    • Q6FG90

    Protein attributes for ATP5F1D Gene

    Size:
    168 amino acids
    Molecular mass:
    17490 Da
    Quaternary structure:
    • F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) seems to have nine subunits: a, b, c, d, e, f, g, F6 and 8 (or A6L). Component of an ATP synthase complex composed of ATP5F1, ATP5MC1, ATP5F1E, ATP5H, ATP5I, ATP5J, ATP5J2, MT-ATP6, MT-ATP8, ATP5F1A, ATP5F1B, ATP5F1D, ATP5F1C, ATP5O, ATP5L, USMG5 and MP68 (By similarity).

neXtProt entry for ATP5F1D Gene

Post-translational modifications for ATP5F1D Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ATP5F1D Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ATP5F1D Gene

Domains & Families for ATP5F1D Gene

Gene Families for ATP5F1D Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for ATP5F1D Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for ATP5F1D Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P30049

UniProtKB/Swiss-Prot:

ATPD_HUMAN :
  • Belongs to the ATPase epsilon chain family.
Family:
  • Belongs to the ATPase epsilon chain family.
genes like me logo Genes that share domains with ATP5F1D: view

Function for ATP5F1D Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for ATP5F1D Gene

UniProtKB/Swiss-Prot Function:
Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core, and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP turnover in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F(1) domain and of the central stalk which is part of the complex rotary element. Rotation of the central stalk against the surrounding alpha(3)beta(3) subunits leads to hydrolysis of ATP in three separate catalytic sites on the beta subunits.

Phenotypes From GWAS Catalog for ATP5F1D Gene

Gene Ontology (GO) - Molecular Function for ATP5F1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005215 transporter activity NAS 1531933
GO:0005524 contributes_to ATP binding NAS 12539966
GO:0016887 ATPase activity NAS 12539966
GO:0022857 transmembrane transporter activity IC 12110673
GO:0043531 contributes_to ADP binding NAS 12539966
genes like me logo Genes that share ontologies with ATP5F1D: view
genes like me logo Genes that share phenotypes with ATP5F1D: view

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ATP5F1D Gene

Localization for ATP5F1D Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATP5F1D Gene

Mitochondrion. Mitochondrion inner membrane.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ATP5F1D gene
Compartment Confidence
mitochondrion 5
cytoskeleton 1
nucleus 1

Gene Ontology (GO) - Cellular Components for ATP5F1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000275 mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) NAS 12539966
GO:0005739 mitochondrion NAS 12887009
GO:0005743 mitochondrial inner membrane ISS --
GO:0005753 mitochondrial proton-transporting ATP synthase complex NAS 1531933
GO:0005759 mitochondrial matrix TAS --
genes like me logo Genes that share ontologies with ATP5F1D: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for ATP5F1D Gene

Pathways & Interactions for ATP5F1D Gene

genes like me logo Genes that share pathways with ATP5F1D: view

Gene Ontology (GO) - Biological Process for ATP5F1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006119 oxidative phosphorylation NAS 12539966
GO:0006754 ATP biosynthetic process TAS --
GO:0006811 ion transport IEA --
GO:0015986 ATP synthesis coupled proton transport IBA,IEA --
GO:0042407 cristae formation TAS --
genes like me logo Genes that share ontologies with ATP5F1D: view

No data available for SIGNOR curated interactions for ATP5F1D Gene

Drugs & Compounds for ATP5F1D Gene

Products:

  1. Drug

(9) Drugs for ATP5F1D Gene - From: DrugBank, DGIdb, and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Desflurane Approved Pharma antagonist, Target, other/unknown 161
Enflurane Approved, Investigational, Vet_approved Pharma Target, other/unknown 2
Methoxyflurane Approved, Investigational, Vet_approved Pharma antagonist, Target, unknown 6
Sevoflurane Approved, Vet_approved Pharma antagonist, Target, other/unknown 556
Isoflurane Approved, Vet_approved Pharma Target, unknown 178

(3) Additional Compounds for ATP5F1D Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
 Full agonist, Agonist, Partial agonist, Antagonist, Gating inhibitor 58-64-0
Phosphate
  • [po(OH)3]
  • Acide phosphorique
  • Acidum phosphoricum
  • H3PO4
  • Orthophosphoric acid
 14265-44-2
trifluoroacetic acid
  • Acide trifluoroacetique
  • CF3COOH
  • Perfluoroacetic acid
  • Trifluoressigsaeure
  • Trifluoroacetate
 76-05-1
genes like me logo Genes that share compounds with ATP5F1D: view

Transcripts for ATP5F1D Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for ATP5F1D Gene

(2) REFSEQ mRNAs :
(278) Selected AceView cDNA sequences:
(9) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Alternative Splicing Database (ASD) splice patterns (SP) for ATP5F1D Gene

No ASD Table

Relevant External Links for ATP5F1D Gene

GeneLoc Exon Structure for
ATP5F1D
ECgene alternative splicing isoforms for
ATP5F1D

Expression for ATP5F1D Gene

Products:

  1. Primer

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of ATP5F1D Gene:

ATP5F1D

Evidence on tissue expression from TISSUES for ATP5F1D Gene

  • Liver(4.6)
  • Nervous system(4.6)
  • Lung(4.3)
  • Muscle(4.2)
  • Heart(3.9)
  • Kidney(3.2)
  • Stomach(3.1)
  • Intestine(2.7)
genes like me logo Genes that share expression patterns with ATP5F1D: view

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ATP5F1D Gene

Orthologs for ATP5F1D Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for ATP5F1D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia ATP5D 34 33
  • 99.21 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia ATP5D 34 33
  • 83.53 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia ATP5D 34 33
  • 83.33 (n)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Atp5d 33
  • 80.56 (n)
mouse
(Mus musculus)
 Mammalia Atp5d 16 34 33
  • 80.36 (n)
oppossum
(Monodelphis domestica)
 Mammalia ATP5D 34
  • 78 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia ATP5D 34
  • 78 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves ATP5D 34 33
  • 76.53 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia ATP5D 34
  • 60 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia atp5d 33
  • 65.44 (n)
Str.10780 33
African clawed frog
(Xenopus laevis)
 Amphibia Xl.23716 33
zebrafish
(Danio rerio)
 Actinopterygii atp5d 34 33
  • 70.96 (n)
 OneToOne
wufk58f09 33
rainbow trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.8822 33
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP007841 33
  • 59.4 (n)
fruit fly
(Drosophila melanogaster)
 Insecta l(1)G0230 34 33
  • 55.39 (n)
 OneToOne
worm
(Caenorhabditis elegans)
 Secernentea F58F12.1 34 33
  • 49.62 (n)
 OneToOne
A. gosspyii yeast
(Ashbya gossypii)
 Saccharomycetes AGOS_AEL008W 33
  • 52.42 (n)
K. lactis yeast
(Kluyveromyces lactis)
 Saccharomycetes KLLA0F14773g 33
  • 45.48 (n)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes ATP16 36 34 33
  • 43.17 (n)
thale cress
(Arabidopsis thaliana)
 eudicotyledons AT5G47030 33
  • 45.45 (n)
rice
(Oryza sativa)
 Liliopsida Os07g0495200 33
  • 48.74 (n)
bread mold
(Neurospora crassa)
 Ascomycetes NCU00385 33
  • 50.78 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.7960 34
  • 48 (a)
 OneToOne
fission yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes atp16 33
  • 42.49 (n)
Species where no ortholog for ATP5F1D was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for ATP5F1D Gene

ENSEMBL:
Gene Tree for ATP5F1D (if available)
TreeFam:
Gene Tree for ATP5F1D (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ATP5F1D: view image

Paralogs for ATP5F1D Gene

No data available for Paralogs for ATP5F1D Gene

Variants for ATP5F1D Gene

Sequence variations from dbSNP and Humsavar for ATP5F1D Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs867410737 pathogenic, Decreased activity of mitochondrial ATP synthase complex 1,242,559(+) C/T coding_sequence_variant, missense_variant
rs1000594236 -- 1,243,132(+) T/A intron_variant
rs1001115819 -- 1,242,288(+) A/G intron_variant
rs1001537027 -- 1,242,634(+) G/T intron_variant
rs1002251968 -- 1,241,968(+) T/C coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for ATP5F1D Gene

Variant ID Type Subtype PubMed ID
dgv136n111 CNV deletion 26073780
dgv6196n54 CNV loss 21841781
esv2758743 CNV gain+loss 17122850
nsv1058677 CNV loss 25217958
nsv1060536 CNV gain 25217958
nsv1160555 CNV deletion 26073780
nsv470103 CNV gain 18288195
nsv470104 CNV loss 18288195
nsv578268 CNV loss 21841781
nsv578272 CNV loss 21841781
nsv828368 CNV gain 20364138
nsv953941 CNV deletion 24416366
nsv9662 CNV gain 18304495

Variation tolerance for ATP5F1D Gene

Gene Damage Index Score: 1.20; 24.17% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ATP5F1D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ATP5F1D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ATP5F1D Gene

Disorders for ATP5F1D Gene

MalaCards: The human disease database

(1) MalaCards diseases for ATP5F1D Gene - From: ClinVar

Disorder Aliases PubMed IDs
mitochondrial disorders
  • mitochondrial encephalomyopathies
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for ATP5F1D

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with ATP5F1D: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ATP5F1D Gene

Publications for ATP5F1D Gene

  1. Molecular cloning of an import precursor of the delta-subunit of the human mitochondrial ATP synthase complex. (PMID: 1531933) Jordan EM … Breen GA (Biochimica et biophysica acta 1992) 2 3 4 58
  2. The DNA sequence and biology of human chromosome 19. (PMID: 15057824) Grimwood J … Lucas SM (Nature 2004) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Human liver protein map: a reference database established by microsequencing and gel comparison. (PMID: 1286669) Hochstrasser DF … Vargas R (Electrophoresis 1992) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for ATP5F1D Gene

Sources for ATP5F1D Gene

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