Human Gene APOM (ENST00000375920.8) from GENCODE V44
  Description: Homo sapiens apolipoprotein M (APOM), transcript variant 3, non-coding RNA. (from RefSeq NR_045828)
RefSeq Summary (NM_001256169): The protein encoded by this gene is an apolipoprotein and member of the lipocalin protein family. It is found associated with high density lipoproteins and to a lesser extent with low density lipoproteins and triglyceride-rich lipoproteins. The encoded protein is secreted through the plasma membrane but remains membrane-bound, where it is involved in lipid transport. Alternate splicing results in both coding and non-coding variants of this gene. [provided by RefSeq, Jan 2012].
Gencode Transcript: ENST00000375920.8
Gencode Gene: ENSG00000204444.11
Transcript (Including UTRs)
   Position: hg38 chr6:31,652,417-31,658,210 Size: 5,794 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg38 chr6:31,656,574-31,658,089 Size: 1,516 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:31,652,417-31,658,210)mRNA (may differ from genome)Protein (116 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: APOM_HUMAN
DESCRIPTION: RecName: Full=Apolipoprotein M; Short=Apo-M; Short=ApoM; AltName: Full=Protein G3a;
FUNCTION: Probably involved in lipid transport. Can bind sphingosine-1-phosphate, myristic acid, palmitic acid and stearic acid, retinol, all-trans-retinoic acid and 9-cis-retinoic acid.
SUBCELLULAR LOCATION: Secreted. Note=Present in high density lipoprotein (HDL) and to a lesser extent in triglyceride-rich lipoproteins (TGRLP) and low density lipoproteins (LDL).
TISSUE SPECIFICITY: Plasma protein. Expressed in liver and kidney.
SIMILARITY: Belongs to the calycin superfamily. Lipocalin family. Highly divergent.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: APOM
Diseases sorted by gene-association score: fetal macrosomia (6), arcus senilis (4)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 77.21 RPKM in Liver
Total median expression: 168.82 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -78.00237-0.329 Picture PostScript Text
3' UTR -35.10121-0.290 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR022734 - ApoM
IPR012674 - Calycin
IPR011038 - Calycin-like

Pfam Domains:
PF11032 - ApoM domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2WEW - X-ray MuPIT 2WEX - X-ray MuPIT 2YG2 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O95445
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005319 lipid transporter activity
GO:0005543 phospholipid binding
GO:0016209 antioxidant activity

Biological Process:
GO:0001523 retinoid metabolic process
GO:0006869 lipid transport
GO:0009749 response to glucose
GO:0033344 cholesterol efflux
GO:0034375 high-density lipoprotein particle remodeling
GO:0034380 high-density lipoprotein particle assembly
GO:0034384 high-density lipoprotein particle clearance
GO:0034445 negative regulation of plasma lipoprotein particle oxidation
GO:0042157 lipoprotein metabolic process
GO:0042632 cholesterol homeostasis
GO:0043691 reverse cholesterol transport
GO:0098869 cellular oxidant detoxification

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005887 integral component of plasma membrane
GO:0034361 very-low-density lipoprotein particle
GO:0034362 low-density lipoprotein particle
GO:0034364 high-density lipoprotein particle
GO:0034365 discoidal high-density lipoprotein particle
GO:0034366 spherical high-density lipoprotein particle


-  Descriptions from all associated GenBank mRNAs
  LF210797 - JP 2014500723-A/18300: Polycomb-Associated Non-Coding RNAs.
MA446374 - JP 2018138019-A/18300: Polycomb-Associated Non-Coding RNAs.
LF341251 - JP 2014500723-A/148754: Polycomb-Associated Non-Coding RNAs.
MA576828 - JP 2018138019-A/148754: Polycomb-Associated Non-Coding RNAs.
AF161454 - Homo sapiens HSPC336 mRNA, partial cds.
LF341250 - JP 2014500723-A/148753: Polycomb-Associated Non-Coding RNAs.
MA576827 - JP 2018138019-A/148753: Polycomb-Associated Non-Coding RNAs.
BC020683 - Homo sapiens apolipoprotein M, mRNA (cDNA clone MGC:22400 IMAGE:4733993), complete cds.
AJ245434 - Homo sapiens mRNA for G3a protein (G3a gene, located in the class III region of the major histocompatibility complex).
AF118393 - Homo sapiens apolipoprotein M mRNA, complete cds.
HQ447729 - Synthetic construct Homo sapiens clone IMAGE:100071060; CCSB013087_01 apolipoprotein M (APOM) gene, encodes complete protein.
KJ894289 - Synthetic construct Homo sapiens clone ccsbBroadEn_03683 APOM gene, encodes complete protein.
JD444645 - Sequence 425669 from Patent EP1572962.
JD236606 - Sequence 217630 from Patent EP1572962.
JD550496 - Sequence 531520 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O95445 (Reactome details) participates in the following event(s):

R-HSA-5246478 APOM binds retinoids
R-HSA-975634 Retinoid metabolism and transport
R-HSA-2187338 Visual phototransduction
R-HSA-6806667 Metabolism of fat-soluble vitamins
R-HSA-418594 G alpha (i) signalling events
R-HSA-196854 Metabolism of vitamins and cofactors
R-HSA-388396 GPCR downstream signalling
R-HSA-1430728 Metabolism
R-HSA-372790 Signaling by GPCR
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: APOM_HUMAN, B0UX98, ENST00000375920.1, ENST00000375920.2, ENST00000375920.3, ENST00000375920.4, ENST00000375920.5, ENST00000375920.6, ENST00000375920.7, G3A, HSPC336, NG20, NR_045828, O95445, Q9P046, Q9UMP6, uc003nvk.1, uc003nvk.2, uc003nvk.3, uc003nvk.4, uc003nvk.5
UCSC ID: ENST00000375920.8
RefSeq Accession: NM_001256169
Protein: O95445 (aka APOM_HUMAN)
CCDS: CCDS59004.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.