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Aliases & Descriptions for APOD
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc
, and/or 7Ensembl,
8miRBase) About This Section
|
| | | Descriptions |
|---|
| apolipoprotein D 2 |
|
| | Search outside databases for aliases for APOD genePrevious GC identifers: GC03P194400 GC03M198737 GC03M9E0110 GC00M9Z0110 GC03M9G0110 |
Summaries for APOD(According to Entrez Gene,
Wikipedia's
Gene Wiki,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
| EntrezGene summary for APOD: 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] UniProtKB/Swiss-Prot: APOD_HUMAN, P05090Function: 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 contextsGene Wiki entry for APOD (Apolipoprotein_D) |
Genomic Location for APOD
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to
UCSC and
Ensembl,
Transcription factor binding sites according to
SABiosciences) About This Section
| Genomic View: UCSC Golden Path with GeneCards custom track
Transcription factor binding sites upstream to the APOD gene 
Entrez Gene cytogenetic band: 3q26.2-qter Ensembl cytogenetic band: 3q29 HGNC cytogenetic band: 3q26.2-qterAPOD Gene in genomic location: bands according to Ensembl, locations according to
(and/or Entrez Gene and/or Ensembl if different)
 GeneLoc gene densities for chromosome 3 GeneLoc Exon Structure GeneLoc location for GC03M196776:
(about GC identifiers)
Start:
|
196,776,865 bp from pter |
End:
|
196,792,278 bp from pter |
Size:
|
15,414 bases |
Orientation:
|
minus strand |
RefSeq DNA sequence:- NC_000003.10 NT_005535.16
| Proteins for APOD
(According to
1UniProtKB,
and/or Ensembl,
Phosphorylation sites according to 2Phosphosite,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from Invitrogen,
Millipore,
Sigma-Aldrich,
R&D Systems,
Enzo Life Sciences,
Abnova,
OriGene and/or,
Abcam,
Biochemical Assays by
Invitrogen,
Millipore,
R&D Systems,
Cell Signaling Technology, and/or
Enzo Life Sciences,
Ontologies according to Gene
Ontology Consortium 01 Apr 2009 and
Entrez Gene,
Antibodies by Invitrogen,
Millipore,
Sigma-Aldrich,
R&D Systems,
Cell Signaling Technology,
Abcam,
Abnova, and/or
Novus Biologicals)
About This Section
| UniProtKB/Swiss-Prot: APOD_HUMAN, P05090 (See
protein sequence)Recommended Name: Apolipoprotein D precursor Size: 189 amino acids; 21276 Da
Subunit: Homodimer. In plasma, also exists as a disulfide-linked heterodimer with APOA2
Subcellular location: Secreted
Miscellaneous: APOD is primarily localized in HDL (60-65%), with most of the remainder in VHDL and only trace amounts in VLDL and LDL
PDB structures from and Proteopedia :2APD (3D)
 2HZQ (3D)
 2HZR (3D)
 
Secondary accessions: Q6IBG6REFSEQ proteins: NP_001638.1
ENSEMBL proteins: ENSP00000345179
Human Recombinant Proteins Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 
3 Gene Ontology (GO) cellular component terms (links to tree view): About this table
Antibodies for APOD: Assays for APOD: | Protein
Domains/ Families for APOD(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
| - Graphical View of Domain Structure for InterPro Entry P05090
ProtoNet protein and cluster: P05090 2 Blocks protein families: IPB002345 Lipocalin signature IPB002969 Apolipoprotein D signature
UniProtKB/Swiss-Prot: APOD_HUMAN, P05090Similarity: Belongs to the calycin superfamily. Lipocalin family | Gene Function for APOD
(According to MGI Jun 06 2009, UniProtKB,
IUBMB,and/or Genatlas,
shRNA from
OriGene,
Sigma-Aldrich, RNAi from
Sigma-Aldrich,
RNAi Products,
Clones, and
Q-PCR Products
from Invitrogen,
Millipore,
OriGene, and/or
Abnova,
siRNAs from
Applied Biosystems,
SYBR primers from OriGene,
Cell-based Assays from Millipore,
Ontologies according to Gene Ontology Consortium 01 Apr 2009 via
Entrez Gene.)
About This Section
|               OriGene 29mer shRNA kit in GFP-retroviral vector: NM_001647
Applied Biosystems Silencer® siRNAs for APOD
Sigma-Aldrich siRNA for APOD  Sigma-Aldrich shRNA for APOD  Explore Sigma-Aldrich super-pooled esiRNAs 
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_001647                                  Myc/DDK tagged cDNA clone in CMV expression vector: NM_001647                                  untagged cDNA clone in CMV expression vector: NM_001647 
Primers: Browse
Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers               OriGene genome-wide validated SYBR primer pairs: NM_001647
UniProtKB/Swiss-Prot: APOD_HUMAN, P05090Function: 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 contextsGenatlas biochemistry entry for APOD: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 fluid5 MGI mutant phenotypes (inferred from 3 alleles ) (MGI details for Apod):
5 Gene Ontology (GO) molecular function terms (links to tree view): About this table | Pathways & Interactions for APOD
(Pathways according to Invitrogen
(maps by GeneGo),
Millipore,
Cell Signaling Technology,
Sigma-Aldrich,
KEGG
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Proteins Network according to
SABiosciences,
Interactions according to 1UniProtKB,
2MINT, and/or
3STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Apr 2009 via
Entrez Gene.)
About This Section
|
5/55 Interacting proteins for APOD (P050901, 2 ENSP000003451793) via UniProtKB, MINT, and/or STRING (see all 55
)About this table
2 Gene Ontology (GO) biological process terms (links to tree view): About this table
|
Drugs & Compounds for APOD(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
Sigma-Aldrich, Tocris Bioscience, and/or
Novoseek and Drugs according to
Enzo Life Sciences and/or
PharmGKB)
About This Section
|
Browse Tocris compounds for APOD 10/12 Novoseek chemical compound relationships for APOD gene (see all 12
)
| Compound |
Score |
Articles |
PubMed IDs for Articles with Shared Sentences (# sentences) |
| arachidonic acid |
54.14 |
37 |
15560970 (7), 14623496 (4), 7789516 (3), 19429117 (2) (see all 13) |
| progesterone |
49.78 |
24 |
1868457 (1), 11058760 (1), 12021176 (1), 16850244 (1) (see all 16) |
| lipid |
43.79 |
27 |
19176353 (2), 11274430 (1), 11441143 (1), 12678535 (1) (see all 16) |
| cholesterol |
37.69 |
26 |
1582022 (3), 9422368 (3), 19429117 (2), 8549691 (2) (see all 11) |
| cyanogen bromide |
28.96 |
3 |
7918467 (1), 9659402 (1) |
| steroid |
27.97 |
14 |
1868457 (1), 7927949 (1), 7526888 (1), 11709627 (1) (see all 9) |
| agarose |
7.98 |
2 |
1628607 (1), 8905463 (1) |
| oligonucleotide |
0.00 |
1 |
8692868 (1) |
| prostaglandin |
0.00 |
1 |
7789516 (1) |
| phospholipid |
0.00 |
3 |
12942994 (1), 12363390 (1), 15560970 (1) |
About this table
|
Transcripts for APOD(GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 219 Homo sapiens; Jun 2 2009) or GenBank, RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
non coding RNAs according to
RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from Invitrogen,
Millipore, and/or
Abnova,
siRNAs from Applied Biosystems,
Sigma-Aldrich,
shRNA from
Sigma-Aldrich,
OriGene,
Tagged/untagged cDNA clones from
OriGene, Expression Assays from Applied Biosystems) About This Section
|               OriGene 29mer shRNA kit in GFP-retroviral vector: NM_001647
Sigma-Aldrich siRNA for APOD  Sigma-Aldrich shRNA for APOD  Explore Sigma-Aldrich super-pooled esiRNAs 
Applied Biosystems Silencer® siRNAs: NM_001647 REFSEQ mRNAs for APOD gene: NM_001647.3
Applied Biosystems TaqMan ® Gene Expression Assays: NM_001647               OriGene GFP tagged cDNA clone in CMV expression vector: NM_001647                                  Myc/DDK tagged cDNA clone in CMV expression vector: NM_001647                                  untagged cDNA clone in CMV expression vector: NM_001647  Additional cDNA sequence: AK294523.1 AK312090.1 BC007402.2 BT019860.1 BT019861.1 CR456838.1 CR541773.1 J02611.1 S80440.1 17 DOTS entries: DT.450718 DT.97761904 DT.99954896 DT.91774835 DT.91774833 DT.91805361 DT.100827291 DT.95166229 DT.95166241 DT.99943362 DT.120864927 DT.120864970 DT.120864975 DT.91774837 DT.95166228 DT.95166230 DT.100827294 24/525 AceView cDNA sequences (see all 525
):BE900773 BF724142 BQ270392 CA391995 BM688920 BU160982 CD514591 BU195270 AI379448 BM685383 AA411564 BU149134 BQ721355 BF475412 AW389748 BI496609 CD678334 CD679198 BI755710 BM687661 CA397281 CD677880 BQ678512 BM663178
highest scoring ESTs for APOD:AA131730 AA194561 AA317343 AA325694 AA364411 AA425640 AA457084 AL548966 AL548998 AU099589 Unigene Cluster for APOD: Apolipoprotein D Hs.522555 [show with all ESTs]Unigene Representative Sequence: BF790155
GeneLoc Exon Structure
1 Ensembl transcript including schematic representation: ENST00000343267
|
Expression for APOD
(Experimental results according to
1GeneNote
and GNF BioGPS,
probe sets-to-genes annotations according to
2GeneAnnot ,
3GeneTide ,
Sets of similar genes according to GeneDecks,
Electronic Northern calculations according to data from
UniGene (Build 219 Homo sapiens),
SAGE tags according to
CGAP,
plus additional links to
SOURCE, and/or
GNF
BioGPS, and/or
EXPOLDB, and/or
UniProtKB,
Expression Assays from
Applied Biosystems
)
About This Section
| APOD expression in normal and diseased human tissues
Applied Biosystems TaqMan ® Gene Expression Assays for APOD
1 / 2 / 3 3 probe-sets matching APOD gene Data from
(Publications) and GNF BioGPS About these images About these images
CGAP SAGE TAG: CCCTACCCTG
SOURCE GeneReport for Unigene cluster: Hs.522555
Expression variation in blood from EXPOLDB for APOD UniProtKB/Swiss-Prot: APOD_HUMAN, P05090Tissue specificity: Expressed in liver, intestine, pancreas, kidney, placenta, adrenal, spleen, fetal brain tissue and tears |
Orthologs for APOD
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
and/or
5MGI Jun 06 2009,
with possible further links to
Flybase
and/or
WormBase,
Gene Trees according to Ensembl)
About This Section
|
Orthologs for APOD gene from 5/9 species (see all 9
)
About this table Species with no ortholog for APOD
ENSEMBL Gene Tree for APOD | Paralogs for APOD(Paralogs according to 1HomoloGene and 2Ensembl, Pseudogenes according to 3Pseudogene.org) About This Section
| -- |
SNPs/Variants for APOD(According to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE, and
UniProtKB,
Linkage Disequilibrium by HapMap,
Genotyping Reagents from
Applied Biosystems)
About This Section
|
HapMap Linkage Disequilibrium images for APOD (up to first 250kb)
|
Disorders & Mutations for APOD
(in which this Gene is Involved, According to
OMIM, UniProtKB,
Novoseek, PharmGKB,
Genatlas, GeneTests,
Blood group antigen gene mutations by BGMUT,
HGMD, GAD,
HuGE Navigator,
BCGD,
and/or TGDB.)
About This Section
|
OMIM: 107740
10/38 Novoseek disease relationships for APOD gene (see all 38
)
| Disease |
Score |
Articles |
PubMed IDs for Articles with Shared Sentences (# sentences) |
| breast male carcinoma |
58.38 |
2 |
12678518 (1), 10504376 (1) |
| pilocytic astrocytoma |
55.78 |
7 |
11895042 (4), 16055749 (2) |
| breast cysts |
50.44 |
2 |
9075775 (2) |
| niemann-picks disease type c |
47.05 |
2 |
12646752 (1), 9422368 (1) |
| breast cancer |
42.79 |
52 |
8943263 (5), 17452772 (4), 19107621 (3), 12678530 (3) (see all 20) |
| breast diseases |
41.55 |
1 |
9293309 (1) |
| neuropathology |
41.54 |
12 |
9751198 (2), 11739619 (1), 14500696 (1), 18842892 (1) (see all 6) |
| breast carcinoma |
40.39 |
11 |
9307298 (2), 7929425 (1), 18505051 (1), 8943263 (1) (see all 7) |
| ganglioglioma |
39.57 |
2 |
16055749 (2) |
| malignant peripheral nerve sheath tumors |
38.88 |
3 |
15252314 (1), 16153462 (1) |
About this table
Human Gene Mutation Database: APOD Genetic Association Database: APOD Human Genome Epidemiology Navigator: APOD (9 documents)
|
Medical News for APOD(Possibly Related Articles in
Doctor's Guide)
About This Section
| -- |
Publications for APOD (in
PubMed.
Associations of this gene to articles via
1Novoseek,
2HGNC,
3Entrez Gene,
4UniProtKB/Swiss-Prot,
5UniProtKB/TrEMBL,
6GAD, and/or
7PharmGKB)
About This Section
| 10/169 PubMed articles for APOD gene (see all 169
):- Human apolipoprotein D gene: gene sequence, chromosome localization, and homology to the alpha 2u-globulin superfamily. (PubMed id 2439269)2, 3, 4 Drayna D.T....Lawn R.M. (1987)
- Cloning and expression of human apolipoprotein D cDNA. (PubMed id 3453108)2, 3, 4 Drayna D....Rhee L. (1986)
- Apolipoprotein D levels are elevated in prefrontal cortex of subjects with Alzheimer's disease: no relation to apolipoprotein E expression or genotype. (PubMed id 12873803)1, 3, 6 Thomas E.A....Martins R.N. (2003)
- The human lacrimal gland synthesizes apolipoprotein D mRNA in addition to tear prealbumin mRNA, both species encoding members of the lipocalin superfamily. (PubMed id 8549691)1, 3, 4 Holzfeind P.... Redl B. (1995)
- Structure of human apolipoprotein D: locations of the intermolecular and intramolecular disulfide links. (PubMed id 7918467)1, 3, 4 Yang C.-Y.... Pownall H.J. (1994)
- Genetic variation in apolipoprotein D and Alzheimer's disease. (PubMed id 15316799)1, 3, 6 Helisalmi S....Soininen H. (2004)
- Genetic variation in apolipoprotein D affects the risk of Alzheimer disease in African-Americans. (PubMed id 12497622)1, 3, 6 Desai P.P....Kamboh M.I. (2003)
- Apolipoprotein D is the major protein component in cyst fluid from women with human breast gross cystic disease. (PubMed id 2244881)1, 3, 4 Balbin M.... Lopez-Otin C. (1990)
- Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. (PubMed id 16335952)3, 4 Liu T.... Smith R.D. (2005)
- Screening for N-glycosylated proteins by liquid chromatography mass spectrometry. (PubMed id 14760718)3, 4 Bunkenborg J.... Wisniewski J.R. (2004)
|
Search for APOD
(in PubMed,
OMIM, and NCBI Bookshelf) About This Section
|
|
Genome Databases showing APOD
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
and/or
H-InvDB)
About This Section
|
| Other Databases showing APOD
(According to HUGE)
About This Section
| -- |
Specialized Databases showing APOD(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL, Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot) About This Section
|
| About This Section
| --
| Services for APOD(Reagents available from Applied Biosystems, Antibodies and assays by Cell
Signaling Technology, Abcam, Novus Biologicals, Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich, Enzo Life Sciences, and/or Tocris Bioscience) About This Section
| 
 Products for APOD:

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Incremental update: 13 Oct 2009
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