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APOD Gene(Protein Coding)

Apolipoprotein D

GCID:
GC03M195568
GIFtS:
61
Genes Participants
UDN Logo

Aliases for APOD Gene

Aliases for APOD Gene

  • Apolipoprotein D 2 3 5
  • Apo-D 3 4
  • ApoD 4

External Ids for APOD Gene

Previous GeneCards Identifiers for APOD Gene

  • GC03P194400
  • GC03M198737
  • GC03M9E0110
  • GC00M9Z0110
  • GC03M9G0110
  • GC03M196776
  • GC03M195295
  • GC03M192666

Summaries for APOD Gene

Entrez Gene Summary for APOD Gene

  • This gene encodes a component of high density lipoprotein that has no marked similarity to other apolipoprotein sequences. It has a high degree of homology to plasma retinol-binding protein and other members of the alpha 2 microglobulin protein superfamily of carrier proteins, also known as lipocalins. This glycoprotein is closely associated with the enzyme lecithin:cholesterol acyltransferase - an enzyme involved in lipoprotein metabolism. [provided by RefSeq, Aug 2008]

GeneCards Summary for APOD Gene

APOD (Apolipoprotein D) is a Protein Coding gene. Diseases associated with APOD include Breast Cyst and Niemann-Pick Disease. Among its related pathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds and Transport of vitamins, nucleosides, and related molecules. GO annotations related to this gene include transporter activity and cholesterol binding.

UniProtKB/Swiss-Prot for APOD Gene

  • APOD occurs in the macromolecular complex with lecithin-cholesterol acyltransferase. It is probably involved in the transport and binding of bilin. Appears to be able to transport a variety of ligands in a number of different contexts.

Gene Wiki entry for APOD Gene

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

Genomics for APOD Gene

Products:

  1. Regulatory Element

Regulatory Elements for APOD Gene

Enhancers for APOD Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03G195538 1.7 Ensembl ENCODE dbSUPER 10.6 +42.0 42049 6.4 CREB3L1 MLX ZFP64 FEZF1 DMAP1 YY1 ZNF143 SP3 NFYC ZNF610 ENSG00000223711 PPP1R2 ACAP2 APOD RPL24P6 MUC4 MUC20 RNU6ATAC24P
GH03G195539 1.6 FANTOM5 Ensembl ENCODE dbSUPER 10.6 +46.0 45957 1.0 YY1 RELA EED RELB IKZF2 CREM MTA2 BHLHE40 ZBED1 ZNF10 PPP1R2 ENSG00000223711 ACAP2 APOD RPL24P6 TNK2 RNU6ATAC24P
GH03G195547 1.4 Ensembl ENCODE dbSUPER 12.1 +34.0 34039 4.7 HDGF FOXA2 MLX DMAP1 SLC30A9 SP5 TBX21 PPARG KAT8 NFIL3 ENSG00000223711 PPP1R2 MUC4 APOD RPL24P6 ENSG00000271662 RN7SL73P
GH03G195557 1.1 Ensembl ENCODE 12.1 +25.9 25873 2.6 ELF3 SOX13 CTCF PKNOX1 EBF1 RAD21 ARID3A GATA2 ZSCAN5C SCRT2 PPP1R2 APOD ENSG00000223711 MUC4 GC03P195555 ENSG00000236425
GH03G196498 1.4 ENCODE dbSUPER 5.6 -917.7 -917657 5.9 HDGF PKNOX1 CREB3L1 MLX WRNIP1 SIN3A ARID4B DMAP1 YY1 SLC30A9 SDHAP2 RNF168 LINC00969 ENSG00000230732 ENSG00000271662 RNU6ATAC24P MUC20P1 UBXN7 ENSG00000231443 TM4SF19
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around APOD on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the APOD gene promoter:

Genomic Location for APOD Gene

Chromosome:
3
Start:
195,568,702 bp from pter
End:
195,584,205 bp from pter
Size:
15,504 bases
Orientation:
Minus strand

Genomic View for APOD Gene

Genes around APOD on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for APOD Gene

Proteins for APOD Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    P05090-APOD_HUMAN
    Recommended name:
    Apolipoprotein D
    Protein Accession:
    P05090
    Secondary Accessions:
    • B2R579
    • D3DNW6
    • Q6IBG6

    Protein attributes for APOD Gene

    Size:
    189 amino acids
    Molecular mass:
    21276 Da
    Quaternary structure:
    • Homodimer. In plasma, also exists as a disulfide-linked heterodimer with APOA2.
    Miscellaneous:
    • APOD is primarily localized in HDL (60-65%), with most of the remainder in VHDL and only trace amounts in VLDL and LDL.

    Three dimensional structures from OCA and Proteopedia for APOD Gene

neXtProt entry for APOD Gene

Protein Expression for APOD Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for APOD Gene

  • N-glycosylatd. N-glycan heterogeneity at Asn-65: Hex5HexNAc4 (major) and Hex6HexNAc5 (minor); at Asn-98: Hex5HexNAc4 (minor), dHex1Hex5HexNAc4 (major), dHex1Hex6HexNAc5 (minor) and dHex1Hex7HexNAc6 (minor).
  • Glycosylation at Asn65 and Asn98
  • Modification sites at PhosphoSitePlus

Other Protein References for APOD Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for APOD Gene

Domains & Families for APOD Gene

Gene Families for APOD Gene

HGNC:

Protein Domains for APOD Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for APOD Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P05090

UniProtKB/Swiss-Prot:

APOD_HUMAN :
  • Belongs to the calycin superfamily. Lipocalin family.
Family:
  • Belongs to the calycin superfamily. Lipocalin family.
genes like me logo Genes that share domains with APOD: view

Function for APOD Gene

Products:

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

Molecular function for APOD Gene

GENATLAS Biochemistry:
apolipoprotein D (lipocalin family,Kernel group),widely distributed,occuring in macromolecular complexes,predominantly with APOA2 in HDL and APOB-100 in LDL and VLDL,identical to gross-cystic disease fluid progesterone/pregnelonone binding protein representing overhalf of the protein component of breast cyst fluid
UniProtKB/Swiss-Prot Function:
APOD occurs in the macromolecular complex with lecithin-cholesterol acyltransferase. It is probably involved in the transport and binding of bilin. Appears to be able to transport a variety of ligands in a number of different contexts.

Gene Ontology (GO) - Molecular Function for APOD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005215 transporter activity IEA --
GO:0005319 lipid transporter activity NAS 3453108
GO:0005515 protein binding IPI 7918467
GO:0008289 lipid binding IEA --
GO:0015485 cholesterol binding IDA 9278274
genes like me logo Genes that share ontologies with APOD: view
genes like me logo Genes that share phenotypes with APOD: view

Animal Models for APOD Gene

MGI Knock Outs for APOD:

Animal Model Products

  • Taconic Biosciences Mouse Models for APOD

CRISPR Products

Inhibitory RNA Products

Clone Products

Cell Line Products

Flow Cytometry Products

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

Localization for APOD Gene

Subcellular locations from UniProtKB/Swiss-Prot for APOD Gene

Secreted.

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 APOD gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
cytosol 4
cytoskeleton 1
nucleus 1
lysosome 1

Gene Ontology (GO) - Cellular Components for APOD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region NAS,IEA 14718574
GO:0005615 extracellular space IDA 16502470
GO:0005622 intracellular IEA --
GO:0005783 endoplasmic reticulum ISS --
GO:0022626 cytosolic ribosome ISS --
genes like me logo Genes that share ontologies with APOD: view

Pathways & Interactions for APOD Gene

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

Gene Ontology (GO) - Biological Process for APOD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000302 response to reactive oxygen species IDA 18419796
GO:0001525 angiogenesis NAS 21705670
GO:0006006 glucose metabolic process IDA 19176353
GO:0006629 lipid metabolic process IDA 19176353
GO:0006810 transport IEA --
genes like me logo Genes that share ontologies with APOD: view

No data available for SIGNOR curated interactions for APOD Gene

Drugs & Compounds for APOD Gene

Products:

  1. Drug

(10) Drugs for APOD Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(12) Additional Compounds for APOD Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with APOD: view

Transcripts for APOD Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for APOD Gene

(1) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(525) Selected AceView cDNA sequences:
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for APOD Gene

Apolipoprotein D:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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

No ASD Table

Relevant External Links for APOD Gene

GeneLoc Exon Structure for
APOD
ECgene alternative splicing isoforms for
APOD

Expression for APOD Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for APOD Gene

mRNA expression in normal human tissues for APOD Gene
mRNA expression by BioGPS for APOD GenemRNA expression by GTEx for APOD Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for APOD Gene

This gene is overexpressed in Nerve - Tibial (x13.0).

Protein differential expression in normal tissues from HIPED for APOD Gene

This gene is overexpressed in Urine (15.5), Synovial fluid (8.8), and Cerebrospinal fluid (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for APOD Gene



Protein tissue co-expression partners for APOD Gene

NURSA nuclear receptor signaling pathways regulating expression of APOD Gene:

APOD

SOURCE GeneReport for Unigene cluster for APOD Gene:

Hs.522555

mRNA Expression by UniProt/SwissProt for APOD Gene:

P05090-APOD_HUMAN
Tissue specificity: Expressed in liver, intestine, pancreas, kidney, placenta, adrenal, spleen, fetal brain tissue and tears.

Evidence on tissue expression from TISSUES for APOD Gene

  • Nervous system(5)
  • Eye(4.9)
  • Skin(4.7)
  • Liver(4.4)
  • Bone marrow(4.1)
  • Muscle(2.9)
  • Heart(2.8)
  • Intestine(2.4)
  • Blood(2.1)
  • Gall bladder(2)
genes like me logo Genes that share expression patterns with APOD: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for APOD Gene

Orthologs for APOD Gene

This gene was present in the common ancestor of animals.

Orthologs for APOD Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia APOD 34 35
  • 99.12 (n)
cow
(Bos Taurus)
 Mammalia APOD 34 35
  • 87.05 (n)
dog
(Canis familiaris)
 Mammalia APOD 34 35
  • 84.62 (n)
mouse
(Mus musculus)
 Mammalia Apod 34 16 35
  • 78.74 (n)
rat
(Rattus norvegicus)
 Mammalia Apod 34
  • 77.2 (n)
oppossum
(Monodelphis domestica)
 Mammalia APOD 35
  • 72 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia APOD 35
  • 63 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves APOD 34 35
  • 64.34 (n)
zebrafish
(Danio rerio)
 Actinopterygii zgc:123339 34
  • 58.04 (n)
APOD (1 of 3) 35
  • 49 (a)
 OneToMany
apod 35
  • 45 (a)
 OneToMany
APOD (3 of 3) 35
  • 44 (a)
 OneToMany
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP009281 34
  • 52.61 (n)
fruit fly
(Drosophila melanogaster)
 Insecta NLaz 34 35
  • 49.9 (n)
GLaz 35
  • 25 (a)
 OneToMany
Species where no ortholog for APOD was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for APOD Gene

ENSEMBL:
Gene Tree for APOD (if available)
TreeFam:
Gene Tree for APOD (if available)

Paralogs for APOD Gene

No data available for Paralogs for APOD Gene

Variants for APOD Gene

Sequence variations from dbSNP and Humsavar for APOD Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs1000148184 -- 195,575,300(+) TTGAG(C/T)TCCCC intron-variant
rs1000535219 -- 195,573,758(+) GCAAG(A/G/T)TTCCC intron-variant
rs1000589318 -- 195,579,978(+) AGGGA(G/T)ATGCC intron-variant
rs1000750771 -- 195,585,781(+) TCTTC(A/C)TAGGT upstream-variant-2KB
rs1000897275 -- 195,570,415(+) CTTGT(A/T)CATGT intron-variant

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

Variant ID Type Subtype PubMed ID
dgv5014n100 CNV gain 25217958
dgv5015n100 CNV loss 25217958
dgv5016n100 CNV gain+loss 25217958
esv2759213 CNV gain+loss 17122850
esv2763776 CNV gain+loss 21179565
nsv1001387 CNV gain 25217958
nsv1006229 CNV gain 25217958
nsv428430 CNV gain+loss 18775914

Variation tolerance for APOD Gene

Residual Variation Intolerance Score: 74.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.08; 38.01% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for APOD Gene

Human Gene Mutation Database (HGMD)
APOD
SNPedia medical, phenotypic, and genealogical associations of SNPs for
APOD

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

Disorders for APOD Gene

MalaCards: The human disease database

(8) MalaCards diseases for APOD Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
breast cyst
  • cyst of the breast
niemann-pick disease
  • niemann-pick disease, type a
androgen insensitivity
  • androgen insensitivity syndrome
dermatofibrosarcoma protuberans
  • dfsp
niemann-pick disease, type c1
  • niemann-pick disease, type d
- elite association - COSMIC cancer census association via MalaCards
Search APOD in MalaCards View complete list of genes associated with diseases

Relevant External Links for APOD

Genetic Association Database (GAD)
APOD
Human Genome Epidemiology (HuGE) Navigator
APOD
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
APOD
genes like me logo Genes that share disorders with APOD: view

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

Publications for APOD Gene

  1. Apolipoprotein D is associated with long-term outcome in patients with schizophrenia. (PMID: 16402085) Hansen T. … Werge T. (Pharmacogenomics J. 2006) 3 22 46 64
  2. Genetic variation in apolipoprotein D and Alzheimer's disease. (PMID: 15316799) Helisalmi S. … Soininen H. (J. Neurol. 2004) 3 22 46 64
  3. Apolipoprotein D levels are elevated in prefrontal cortex of subjects with Alzheimer's disease: no relation to apolipoprotein E expression or genotype. (PMID: 12873803) Thomas E.A. … Martins R.N. (Biol. Psychiatry 2003) 3 22 46 64
  4. The human lacrimal gland synthesizes apolipoprotein D mRNA in addition to tear prealbumin mRNA, both species encoding members of the lipocalin superfamily. (PMID: 8549691) Holzfeind P. … Redl B. (Exp. Eye Res. 1995) 3 4 22 64
  5. Structure of human apolipoprotein D: locations of the intermolecular and intramolecular disulfide links. (PMID: 7918467) Yang C.-Y. … Pownall H.J. (Biochemistry 1994) 3 4 22 64

Products for APOD Gene

  • Cloud-Clone Corp. Antibodies for APOD
  • Cloud-Clone Corp. Proteins for APOD
  • Cloud-Clone Corp Assay Kits for APOD

Sources for APOD Gene

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