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AFM Gene

protein-coding   GIFtS: 54
GCID: GC04P074336

Afamin

  See AFM-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
afamin1 2     alpha-Alb2
ALB22 3 5     alpha-albumin2
ALBA2 3 5     Alpha-Alb3
ALF2     Alpha-albumin3

External Ids:    HGNC: 3161   Entrez Gene: 1732   Ensembl: ENSG000000795577   OMIM: 1041455   UniProtKB: P436523   

Export aliases for AFM gene to outside databases

Previous GC identifers: GC04P074587 GC04P074748 GC04P074813 GC04P074712 GC04P074566 GC04P070158


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for AFM Gene:
This gene is a member of the albumin gene family, which is comprised of four genes that localize to chromosome 4
in a tandem arrangement. These four genes encode structurally-related serum transport proteins that are known to
be evolutionarily related. The protein encoded by this gene is regulated developmentally, expressed in the liver
and secreted into the bloodstream. (provided by RefSeq, Jul 2008)

GeneCards Summary for AFM Gene:
AFM (afamin) is a protein-coding gene. Diseases associated with AFM include squamous papillomatosis, and trigonitis. GO annotations related to this gene include vitamin E binding. An important paralog of this gene is ALB.

UniProtKB/Swiss-Prot: AFAM_HUMAN, P43652
Function: Vitamin E binding protein. May transport vitamin E in body fluids under conditions where the lipoprotein
system is not sufficient. May be involved in the regulation and transport of vitamin E at the blood-brain barrier

Gene Wiki entry for AFM (Afamin) 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000004.11  NT_016354.20  NC_018915.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the AFM gene promoter:
         C/EBPbeta   FOXO3   CUTL1   FOXO3b   Evi-1   Nkx6-1   FOXO3a   MRF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidAFM promoter sequence
   Search Chromatin IP Primers for AFM

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat AFM


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 4q13.3   Ensembl cytogenetic band:  4q13.3   HGNC cytogenetic band: 4q13.3

AFM Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
AFM gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04P074336:  view genomic region     (about GC identifiers)

Start:
74,347,400 bp from pter      End:
74,369,718 bp from pter
Size:
22,319 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: AFAM_HUMAN, P43652 (See protein sequence)
Recommended Name: Afamin precursor  
Size: 599 amino acids; 69069 Da
Secondary accessions: A8K3E1 Q32MR3 Q4W5C5

Explore the universe of human proteins at neXtProt for AFM: NX_P43652

Explore proteomics data for AFM at MOPED

Post-translational modifications: 

  • N-glycosylated; more than 90% of the glycans are sialylated1
  • Glycosylation2 at Asn33, Asn109, Asn383, Asn402, Asn488
  • Modification sites at PhosphoSitePlus

  • See AFM Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001124.1  
    ENSEMBL proteins: 
     ENSP00000226355  

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    Cloud-Clone Corp. Proteins for AFM

     
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    antibodies-online proteins for AFM (10 products) 

     
    antibodies-online peptides for AFM

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    antibodies-online kits for AFM (11 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    Selected InterPro protein domains (see all 6):
     IPR000264 ALB/AFP/VDB
     IPR014760 Serum_albumin_N
     IPR020858 Serum_albumin-like
     IPR001703 Alpha-fetoprotein
     IPR020857 Serum_albumin_CS

    Graphical View of Domain Structure for InterPro Entry P43652

    ProtoNet protein and cluster: P43652

    1 Blocks protein domain: IPB000264 Serum albumin family

    UniProtKB/Swiss-Prot: AFAM_HUMAN, P43652
    Similarity: Belongs to the ALB/AFP/VDB family
    Similarity: Contains 3 albumin domains


    Find genes that share domains with AFM           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: AFAM_HUMAN, P43652
    Function: Vitamin E binding protein. May transport vitamin E in body fluids under conditions where the lipoprotein
    system is not sufficient. May be involved in the regulation and transport of vitamin E at the blood-brain barrier

         Genatlas biochemistry entry for AFM:
    afamin,87kDa,albumin superfamily

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008431vitamin E binding IDA15952736
         
    Find genes that share ontologies with AFM           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for AFM:
     Cell cycle / mitosis defect 

         4 MGI mutant phenotypes (inferred from 1 allele(MGI details for Afm):
     behavior/neurological  growth/size/body  nervous system  other 

    Find genes that share phenotypes with AFM           About GenesLikeMe

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for AFM

    miRNA
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    hsa-miR-137 hsa-miR-197
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    AFAM_HUMAN, P43652: Secreted
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    cytoskeleton1
    cytosol1
    golgi apparatus1
    peroxisome1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS7517938
    GO:0005615extracellular space IDA15952736
    GO:0072562blood microparticle IDA--

    Find genes that share ontologies with AFM           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for AFM
    Interactions:

        Search GeneGlobe Interaction Network for AFM

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0051180vitamin transport IDA19046407

    Find genes that share ontologies with AFM           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for AFM (AFAM)

    3 Novoseek inferred chemical compound relationships for AFM gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    vitamin-e 61.8 16 12463752 (3), 12456077 (3), 15952736 (2), 18094419 (1)
    vitamin d 52.1 9 10400926 (1), 16489915 (1), 19733224 (1), 17654119 (1) (see all 5)
    alpha tocopherol 50.4 18 19046407 (4), 12463752 (1), 12456077 (1)



    Find genes that share compounds with AFM           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for AFM gene: 
    NM_001133.2  

    Unigene Cluster for AFM:

    Afamin
    Hs.168718  [show with all ESTs]
    Unigene Representative Sequence: NM_001133
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000226355(uc003hhb.3) ENST00000505794
    miRNA
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    Inhib. RNA
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    Additional mRNA sequence: 

    AK290556.1 BC109020.1 BC109021.1 L35498.1 

    6 DOTS entries:

    DT.208928  DT.202804  DT.75100220  DT.91948823  DT.92422309  DT.92422310 

    Selected AceView cDNA sequences (see all 31):

    BX110719 CB157386 BF197337 AI247575 L35486 AW235536 L35497 BX103962 
    NM_001133 BF434245 T67570 L35498 AH003117 AW051948 CB162042 AA878846 
    AI492289 AA706914 AI671722 L32140 AI670879 T67409 AV694104 AA501625 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for AFM    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15 ^ 16
    SP1:                    -                                   -                                                               
    SP2:                                                                                                                        
    SP3:                                                                                                                        
    SP4:                                                                          -                                             


    ECgene alternative splicing isoforms for AFM

    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    AFM expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AACTCACAGA
    AFM Expression
    About this image


    AFM expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 3) fully expand
     
     Gut Tube (Gastrointestinal Tract)    fully expand to see all 2 entries
             Foregut
     
     Liver (Hepatobiliary System)
             Liver Lobule
     
     Kidney (Urinary System)
    AFM Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    AFM Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.168718

    UniProtKB/Swiss-Prot: AFAM_HUMAN, P43652
    Tissue specificity: High level detected in plasma but also in extravascular fluids such as follicular and
    cerebrospinal fluids (at protein level)

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    In Situ
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    (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)
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    This gene was present in the common ancestor of chordates.

    Orthologs for AFM gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Afm1 , 5 afamin1, 5 76.96(n)1
    67.78(a)1
      5 (44.78 cM)5
    2806621  NM_145146.21  NP_660128.21 
     905189325 
    chicken
    (Gallus gallus)
    Aves --
    Alpha-fetoprotein
    34(a)
    1 → many
    4(50277990-50289526)
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    Uncharacterized protein
    33(a)
    32(a)
    many ↔ many
    many ↔ many
    GL343253.1(493847-512660)
    GL343253.1(478702-490825)


    ENSEMBL Gene Tree for AFM (if available)
    TreeFam Gene Tree for AFM (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for AFM gene
    ALB2  GC2  AFP2  
    2 SIMAP similar genes for AFM using alignment to 1 protein entry:     AFAM_HUMAN:
    AFP    ALB

    Find genes that share paralogs with AFM           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for AFM (see all 585)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs46946191,2
    C,F,A,H--74345497(+) GATGTC/GTTTTG 1 -- us2k114Minor allele frequency- G:0.17NS EA NA WA CSA 556
    rs1466836501,2
    --74345538(+) TGATAA/TTTTGA 1 -- us2k10--------
    rs1406670831,2
    C--74345736(+) TATAGA/GTTCAT 1 -- us2k10--------
    rs46946201,2
    C,F,H--74345757(+) AAATTA/CCTGTG 1 -- us2k110Minor allele frequency- C:0.12NS EA WA NA 780
    rs728566141,2
    C,F--74345772(+) AATATA/GTTCCA 1 -- us2k14Minor allele frequency- G:0.03WA CSA NA 242
    rs1807200591,2
    C--74345811(+) TCATCA/GGCTTC 1 -- us2k10--------
    rs1458465541,2
    --74345854(+) GGCCTA/GGTGTG 1 -- us2k10--------
    rs131327121,2
    C,F--74345896(+) gaggcC/Tgaggt 1 -- us2k14Minor allele frequency- T:0.25WA NA CSA 8
    rs131504051,2
    C,F,A--74345939(+) tcctgG/Actaac 1 -- us2k14Minor allele frequency- A:0.27NA CSA EA 244
    rs1492277821,2
    --74345943(+) GGCTAA/GCACAG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for AFM (74347400 - 74369718 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for AFM: --
    Site Specific Mutation Identification with PCR Assays
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    (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.)
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    OMIM gene information: 104145    OMIM disorders: --

    2 diseases for AFM:    
    About MalaCards
    squamous papillomatosis    trigonitis

    2 diseases from the University of Copenhagen DISEASES database for AFM:
    Trigonitis     Squamous papillomatosis

    Find genes that share disorders with AFM           About GenesLikeMe

    Genetic Association Database (GAD): AFM

    Export disorders for AFM gene to outside databases

    (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)
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    PubMed articles for AFM gene, integrated from 10 sources (see all 44):
    (articles sorted by number of sources associating them with AFM)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Afamin is a new member of the albumin, alpha-fetoprotein, and vitamin D-binding protein gene family. (PubMed id 7517938)1, 2, 3, 9 Lichenstein H.S....Zukowski M.M. (J. Biol. Chem. 1994)
    2. Afamin is a novel human vitamin E-binding glycoprotein characterization and in vitro expression. (PubMed id 15952736)1, 2, 9 Jerkovic L.... Dieplinger H. (J. Proteome Res. 2005)
    3. Afamin is synthesized by cerebrovascular endothelial cells and mediates alpha-tocopherol transport across an in vitro model of the blood-brain barrier. (PubMed id 19046407)1, 2, 9 Kratzer I.... Sattler W. (J. Neurochem. 2009)
    4. Characterization of the vitamin E-binding properties of human plasma afamin. (PubMed id 12463752)1, 2, 9 Voegele A.F.... Dieplinger H. (Biochemistry 2002)
    5. Complete structure of the human alpha-albumin gene, a new member of the serum albumin multigene family. (PubMed id 8755513)1, 2, 9 Nishio H. and Dugaiczyk A. (Proc. Natl. Acad. Sci. U.S.A. 1996)
    6. Identification of rat alpha-albumin and cDNA cloning of its human ortholog. (PubMed id 7875606)1, 2, 9 Allard D.... Belanger L. (Gene 1995)
    7. Identification of N-linked glycoproteins in human saliva by glycoprotein capture and mass spectrometry. (PubMed id 16740002)1, 2 Ramachandran P....Loo J.A. (J. Proteome Res. 2006)
    8. Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. (PubMed id 16335952)1, 2 Liu T.... Smith R.D. (J. Proteome Res. 2005)
    9. Screening for N-glycosylated proteins by liquid chromatography mass spectrometry. (PubMed id 14760718)1, 2 Bunkenborg J.... Wisniewski J.R. (Proteomics 2004)
    10. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 173 HGNC: 316 AceView: AFM Ensembl:ENSG00000079557 euGenes: HUgn173
    ECgene: AFM H-InvDB: AFM

    (According to HUGE)
    About This Section

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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for AFM Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for AFM gene:
    Search GeneIP for patents involving AFM

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from genOway)
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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