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FAM3D FAM3 metabolism regulating signaling molecule D [ Homo sapiens (human) ]

Gene ID: 131177, updated on 2-Nov-2024

Summary

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Official Symbol
FAM3Dprovided by HGNC
Official Full Name
FAM3 metabolism regulating signaling molecule Dprovided by HGNC
Primary source
HGNC:HGNC:18665
See related
Ensembl:ENSG00000198643 MIM:608619; AllianceGenome:HGNC:18665
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
EF7; OIT1
Summary
Predicted to enable carbohydrate binding activity. Involved in negative regulation of insulin secretion. Predicted to be located in extracellular region and membrane. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in colon (RPKM 146.4), salivary gland (RPKM 60.2) and 6 other tissues See more
Orthologs
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Genomic context

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See FAM3D in Genome Data Viewer
Location:
3p14.2
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (58633946..58666774, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (58674325..58707258, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (58619673..58652501, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:58506479-58506996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:58512267-58512782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:58516141-58516641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:58517009-58517510 Neighboring gene uncharacterized LOC107984079 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58546021-58547021 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58547022-58547522 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58547523-58548023 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58548024-58549024 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58551949-58552472 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58551424-58551948 Neighboring gene Sharpr-MPRA regulatory region 12039 Neighboring gene ribosomal protein L27 pseudogene 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20013 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:58602944-58603149 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:58614585-58615086 Neighboring gene acyl-CoA oxidase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:58626659-58627159 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:58626158-58626658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:58634821-58635320 Neighboring gene family with sequence similarity 107 member A Neighboring gene FAM3D antisense RNA 1 Neighboring gene uncharacterized LOC105377109 Neighboring gene CFAP20 domain containing Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:58792456-58792956 Neighboring gene CFAP20DC antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58828169-58828785 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:58859831-58861030 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58876285-58876824 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:58884619-58885120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20014 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:58940883-58941482 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:58983704-58984903 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:59017398-59018230 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:59044085-59044335 Neighboring gene CFAP20DC divergent transcript Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:59113978-59114502 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:59114503-59115026 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20015 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14492 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14493 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20016 Neighboring gene SNRPB2 pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Targeting cytokine-like protein FAM3D lowers blood pressure in hypertension. Shen Y, et al. Cell Rep Med, 2023 Jun 20. PMID 37301198, Free PMC Article
  2. Oit1/Fam3D, a gut-secreted protein displaying nutritional status-dependent regulation. de Wit NJ, et al. J Nutr Biochem, 2012 Nov. PMID 22226334
  3. Hepatocyte-secreted FAM3D ameliorates hepatic steatosis by activating FPR1-hnRNP U-GR-SCAD pathway to enhance lipid oxidation. Hu Y, et al. Metabolism, 2023 Sep. PMID 37454871
  4. DNA methylation-driven gene FAM3D promotes colorectal cancer growth via the ATF4-SESN2-mTORC1 pathway. Zheng T, et al. Aging (Albany NY), 2024 Oct 10. PMID 39388305, Free PMC Article
  5. Identification of FAM3D as a new endogenous chemotaxis agonist for the formyl peptide receptors. Peng X, et al. J Cell Sci, 2016 May 1. PMID 26966188

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. DNA methylation-driven gene FAM3D promotes colorectal cancer growth via the ATF4-SESN2-mTORC1 pathway.
    Title: DNA methylation-driven gene FAM3D promotes colorectal cancer growth via the ATF4-SESN2-mTORC1 pathway.
  2. Hepatocyte-secreted FAM3D ameliorates hepatic steatosis by activating FPR1-hnRNP U-GR-SCAD pathway to enhance lipid oxidation.
    Title: Hepatocyte-secreted FAM3D ameliorates hepatic steatosis by activating FPR1-hnRNP U-GR-SCAD pathway to enhance lipid oxidation.
  3. Targeting cytokine-like protein FAM3D lowers blood pressure in hypertension.
    Title: Targeting cytokine-like protein FAM3D lowers blood pressure in hypertension.
  4. FAM3D plays a role in gastrointestinal homeostasis and inflammation through its receptors FPR1 and FPR2.
    Title: Identification of FAM3D as a new endogenous chemotaxis agonist for the formyl peptide receptors.
  5. Fam3D is a gut-derived protein that is expressed and secreted in a nutritional status-dependent manner
    Title: Oit1/Fam3D, a gut-secreted protein displaying nutritional status-dependent regulation.
  6. Statistical analysis indicated that six genes, NFATC2, SCP2, CACNA1C, TCRA, POLE, and FAM3D, were associated with narcolepsy.
    Title: An approach based on a genome-wide association study reveals candidate loci for narcolepsy.
  7. Observational study of gene-disease association. (HuGE Navigator)
    Title: An approach based on a genome-wide association study reveals candidate loci for narcolepsy.
  8. A cytokine-like protein found in placenta
    Title: Cloning, expression, and initial characterization of a novel cytokine-like gene family.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables carbohydrate binding IEA
Inferred from Electronic Annotation
more info
  
enables cytokine activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of insulin secretion IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in signal transduction IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in extracellular region NAS
Non-traceable Author Statement
more info
 PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
protein FAM3D
Names
Oncoprotein-induced transcript 1
cytokine-like protein EF-7
family with sequence similarity 3 member D

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_138805.3 → NP_620160.1  protein FAM3D precursor

    See identical proteins and their annotated locations for NP_620160.1

    Status: VALIDATED

    Source sequence(s)
    AY358677
    Consensus CDS
    CCDS2893.1
    UniProtKB/Swiss-Prot
    Q547G2, Q96BQ1
    UniProtKB/TrEMBL
    A0A0A8K9B4
    Related
    ENSP00000351632.2, ENST00000358781.7
    Conserved Domains (1) summary
    cd13940
    Location:50 → 220
    ILEI_FAM3C; Interleukin-like EMT inducer

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    58633946..58666774 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006712967.4 → XP_006713030.1  protein FAM3D isoform X6

    See identical proteins and their annotated locations for XP_006713030.1

    Conserved Domains (1) summary
    cd13940
    Location:13 → 183
    ILEI_FAM3C; Interleukin-like EMT inducer

  2. XM_011533352.3 → XP_011531654.1  protein FAM3D isoform X5

    See identical proteins and their annotated locations for XP_011531654.1

    Conserved Domains (1) summary
    cd13940
    Location:14 → 184
    ILEI_FAM3C; Interleukin-like EMT inducer

  3. XM_005264863.5 → XP_005264920.1  protein FAM3D isoform X4

    See identical proteins and their annotated locations for XP_005264920.1

    Conserved Domains (1) summary
    cd13940
    Location:49 → 219
    ILEI_FAM3C; Interleukin-like EMT inducer

  4. XM_011533350.3 → XP_011531652.1  protein FAM3D isoform X2

    Conserved Domains (1) summary
    cd13940
    Location:55 → 225
    ILEI_FAM3C; Interleukin-like EMT inducer

  5. XM_011533348.3 → XP_011531650.1  protein FAM3D isoform X1

    See identical proteins and their annotated locations for XP_011531650.1

    Conserved Domains (1) summary
    cd13940
    Location:56 → 226
    ILEI_FAM3C; Interleukin-like EMT inducer

  6. XM_047447435.1 → XP_047303391.1  protein FAM3D isoform X6

  7. XM_047447433.1 → XP_047303389.1  protein FAM3D isoform X5

  8. XM_011533351.3 → XP_011531653.1  protein FAM3D isoform X3

    See identical proteins and their annotated locations for XP_011531653.1

    UniProtKB/Swiss-Prot
    Q547G2, Q96BQ1
    UniProtKB/TrEMBL
    A0A0A8K9B4
    Conserved Domains (1) summary
    cd13940
    Location:50 → 220
    ILEI_FAM3C; Interleukin-like EMT inducer

  9. XM_047447431.1 → XP_047303387.1  protein FAM3D isoform X1

  10. XM_047447436.1 → XP_047303392.1  protein FAM3D isoform X6

  11. XM_047447434.1 → XP_047303390.1  protein FAM3D isoform X5

  12. XM_006712965.4 → XP_006713028.1  protein FAM3D isoform X3

    See identical proteins and their annotated locations for XP_006713028.1

    UniProtKB/Swiss-Prot
    Q547G2, Q96BQ1
    UniProtKB/TrEMBL
    A0A0A8K9B4
    Conserved Domains (1) summary
    cd13940
    Location:50 → 220
    ILEI_FAM3C; Interleukin-like EMT inducer

  13. XM_047447432.1 → XP_047303388.1  protein FAM3D isoform X1

  14. XM_011533354.3 → XP_011531656.1  protein FAM3D isoform X6

    See identical proteins and their annotated locations for XP_011531656.1

    Conserved Domains (1) summary
    cd13940
    Location:13 → 183
    ILEI_FAM3C; Interleukin-like EMT inducer

  15. XM_011533353.3 → XP_011531655.1  protein FAM3D isoform X5

    See identical proteins and their annotated locations for XP_011531655.1

    Conserved Domains (1) summary
    cd13940
    Location:14 → 184
    ILEI_FAM3C; Interleukin-like EMT inducer

  16. XM_005264864.5 → XP_005264921.1  protein FAM3D isoform X4

    See identical proteins and their annotated locations for XP_005264921.1

    Conserved Domains (1) summary
    cd13940
    Location:49 → 219
    ILEI_FAM3C; Interleukin-like EMT inducer

  17. XM_005264862.5 → XP_005264919.1  protein FAM3D isoform X3

    See identical proteins and their annotated locations for XP_005264919.1

    UniProtKB/Swiss-Prot
    Q547G2, Q96BQ1
    UniProtKB/TrEMBL
    A0A0A8K9B4
    Conserved Domains (1) summary
    cd13940
    Location:50 → 220
    ILEI_FAM3C; Interleukin-like EMT inducer

  18. XM_011533349.4 → XP_011531651.1  protein FAM3D isoform X1

    See identical proteins and their annotated locations for XP_011531651.1

    Conserved Domains (1) summary
    cd13940
    Location:56 → 226
    ILEI_FAM3C; Interleukin-like EMT inducer

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    58674325..58707258 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345204.1 → XP_054201179.1  protein FAM3D isoform X3

    UniProtKB/Swiss-Prot
    Q547G2, Q96BQ1
    UniProtKB/TrEMBL
    A0A0A8K9B4

  2. XM_054345209.1 → XP_054201184.1  protein FAM3D isoform X6

  3. XM_054345207.1 → XP_054201182.1  protein FAM3D isoform X5

  4. XM_054345205.1 → XP_054201180.1  protein FAM3D isoform X4

  5. XM_054345201.1 → XP_054201176.1  protein FAM3D isoform X2

  6. XM_054345199.1 → XP_054201174.1  protein FAM3D isoform X1

  7. XM_054345206.1 → XP_054201181.1  protein FAM3D isoform X4

  8. XM_054345203.1 → XP_054201178.1  protein FAM3D isoform X3

    UniProtKB/Swiss-Prot
    Q547G2, Q96BQ1
    UniProtKB/TrEMBL
    A0A0A8K9B4

  9. XM_054345202.1 → XP_054201177.1  protein FAM3D isoform X3

    UniProtKB/Swiss-Prot
    Q547G2, Q96BQ1
    UniProtKB/TrEMBL
    A0A0A8K9B4

  10. XM_054345210.1 → XP_054201185.1  protein FAM3D isoform X6

  11. XM_054345208.1 → XP_054201183.1  protein FAM3D isoform X5

  12. XM_054345200.1 → XP_054201175.1  protein FAM3D isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96BQ1.1 GenPept UniProtKB/Swiss-Prot:Q96BQ1

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