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    FAM3A FAM3 metabolism regulating signaling molecule A [ Homo sapiens (human) ]

    Gene ID: 60343, updated on 7-Apr-2024

    Summary

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    Official Symbol
    FAM3Aprovided by HGNC
    Official Full Name
    FAM3 metabolism regulating signaling molecule Aprovided by HGNC
    Primary source
    HGNC:HGNC:13749
    See related
    Ensembl:ENSG00000071889 MIM:300492; AllianceGenome:HGNC:13749
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DLD; 2.19; XAP-7; DXS560S
    Summary
    This gene encodes a cytokine-like protein. The expression of this gene may be regulated by peroxisome proliferator-activated receptor gamma, and the encoded protein may be involved in the regulation of glucose and lipid metabolism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
    Expression
    Ubiquitous expression in small intestine (RPKM 12.0), fat (RPKM 11.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See FAM3A in Genome Data Viewer
    Location:
    Xq28
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (154506171..154516232, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152742672..152752723, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153734502..153744556, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21112 Neighboring gene solute carrier family 10 member 3 Neighboring gene RNA, 7SL, cytoplasmic 697, pseudogene Neighboring gene uncharacterized LOC124905229 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153743824-153744447 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153744448-153745070 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:153745046-153745202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30065 Neighboring gene Sharpr-MPRA regulatory region 11639 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153762224-153762818 Neighboring gene glucose-6-phosphate dehydrogenase Neighboring gene G6PD and IKBKG intron CAGE-defined low expression enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153774097-153774640 Neighboring gene origin of replication in promoter of G6PD Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30067 Neighboring gene inhibitor of nuclear factor kappa B kinase regulatory subunit gamma Neighboring gene IKBKG recombination region Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153792215-153792716 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153792717-153793216 Neighboring gene IKBKG downstream recombination region Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153798001-153798800 Neighboring gene family with sequence similarity 223 member A

    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
    • 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. Case report: targeted whole exome sequencing enables the first prenatal diagnosis of the lethal skeletal dysplasia Osteocraniostenosis. Pemberton L, et al. BMC Med Genet, 2020 Jan 7. PMID 31910817, Free PMC Article
    2. Role of Family with Sequence Similarity 3A in High Glucose-induced Oxidative Damage of Human Umbilical Vein Endothelial Cells. Liao PZ, et al. Zhongguo Yi Xue Ke Xue Yuan Xue Bao, 2018 Feb 28. PMID 29532774
    3. Transcriptional regulation analysis of FAM3A gene and its effect on adipocyte differentiation. Kang T, et al. Gene, 2016 Dec 20. PMID 27688071
    4. FAM3A Protects HT22 Cells Against Hydrogen Peroxide-Induced Oxidative Stress Through Activation of PI3K/Akt but not MEK/ERK Pathway. Song Q, et al. Cell Physiol Biochem, 2015. PMID 26492522
    5. Endothelial FAM3A positively regulates post-ischaemic angiogenesis. Xu W, et al. EBioMedicine, 2019 May. PMID 31000420, Free PMC Article

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. FAM3A mediates the phenotypic switch of human aortic smooth muscle cells stimulated with oxidised low-density lipoprotein by influencing the PI3K-AKT pathway.
      Title: FAM3A mediates the phenotypic switch of human aortic smooth muscle cells stimulated with oxidised low-density lipoprotein by influencing the PI3K-AKT pathway.
    2. In this case prenatal ultrasound images were suggestive of a serious but non-lethal skeletal dysplasia. Due to the uncertain prognosis the parents were offered Whole Exome Sequencing (WES), which identified a specific gene mutation in the FAMIIIa gene
      Title: Case report: targeted whole exome sequencing enables the first prenatal diagnosis of the lethal skeletal dysplasia Osteocraniostenosis.
    3. our data demonstrate that FAM3A positively regulates angiogenesis through activation of VEGFA transcription, suggesting that FAM3A may constitute a novel molecular therapeutic target for ischaemic vascular disease.
      Title: Endothelial FAM3A positively regulates post-ischaemic angiogenesis.
    4. Fam3A may regulate high glucose-induced reactive oxygen species production in HUVECs via the p38 MAPK signaling pathway.
      Title: Role of Family with Sequence Similarity 3A in High Glucose-induced Oxidative Damage of Human Umbilical Vein Endothelial Cells.
    5. These results suggest that C/EBPbeta plays an important role in regulating FAM3A promoter activity and FAM3A inhibits adipocyte differentiation.
      Title: Transcriptional regulation analysis of FAM3A gene and its effect on adipocyte differentiation.
    6. In the present study, we report a putative human homologue of the antimicrobial Drosophila-derived drosomycin, designated drosomycin-like defensin (DLD), with specific antifungal activity.
      Title: Drosomycin-like defensin, a human homologue of Drosophila melanogaster drosomycin with antifungal activity.
    7. FAM3A plays crucial roles in the regulation of glucose and lipid metabolism in the liver, where it activates the PI3K-Akt signaling pathway by way of a Ca(2+) /CaM-dependent mechanism
      Title: FAM3A activates PI3K p110α/Akt signaling to ameliorate hepatic gluconeogenesis and lipogenesis.
    8. Upregulation of FAM3A by PPARgamma activation is correlated with increased pAkt level in liver cells
      Title: FAM3A is a target gene of peroxisome proliferator-activated receptor gamma.
    9. Expressed prominently in the vascular endothelium, particularly capillaries, also in islets of Langerhans.
      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

    EBI GWAS Catalog

    Description
    Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network.
    EBI GWAS Catalog

    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 molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in antifungal humoral response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in antimicrobial humoral immune response mediated by antimicrobial peptide IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of antifungal innate immune response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    protein FAM3A
    Names
    cytokine-like protein 2-19
    family with sequence similarity 3 member A

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_016401.2 RefSeqGene

      Range
      5121..15182
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001171132.3 → NP_001164603.1  protein FAM3A isoform 1 precursor

      See identical proteins and their annotated locations for NP_001164603.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1, 2 and 6 encode the same isoform (1).
      Source sequence(s)
      AL539139, AW612420, BC008912, BM457676, X87193
      Consensus CDS
      CCDS35453.1
      UniProtKB/Swiss-Prot
      A6QRH6, B2RBI7, B4DFI8, D3DWX4, P98173, Q5HY76, Q96H51
      Related
      ENSP00000352955.5, ENST00000359889.9
      Conserved Domains (1) summary
      cd13940
      Location:55 → 224
      ILEI_FAM3C; Interleukin-like EMT inducer

    2. NM_001171133.3 → NP_001164604.1  protein FAM3A isoform 2

      See identical proteins and their annotated locations for NP_001164604.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AL539139, AW612420, BC008912, BM457676, X87193
      Consensus CDS
      CCDS55542.1
      UniProtKB/Swiss-Prot
      P98173
      Related
      ENSP00000377202.1, ENST00000393572.5
      Conserved Domains (1) summary
      cd13940
      Location:17 → 186
      ILEI_FAM3C; Interleukin-like EMT inducer

    3. NM_001171134.3 → NP_001164605.1  protein FAM3A isoform 3

      See identical proteins and their annotated locations for NP_001164605.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AK314682, AL539139, AW612420, BM457676, X87193
      Consensus CDS
      CCDS55543.1
      UniProtKB/Swiss-Prot
      P98173
      Related
      ENSP00000393086.2, ENST00000419205.5
      Conserved Domains (1) summary
      cd13940
      Location:55 → 207
      ILEI_FAM3C; Interleukin-like EMT inducer

    4. NM_001282311.2 → NP_001269240.1  protein FAM3A isoform 4

      See identical proteins and their annotated locations for NP_001269240.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) contains an alternate exon in its 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (4) has a longer and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AL539139, AW612420, BC002934, BM457676, X87193
      Consensus CDS
      CCDS76060.1
      UniProtKB/TrEMBL
      D3DWX8
      Related
      ENSP00000320521.7, ENST00000322269.10
      Conserved Domains (1) summary
      cd13940
      Location:69 → 238
      ILEI_FAM3C; Interleukin-like EMT inducer

    5. NM_001282312.2 → NP_001269241.1  protein FAM3A isoform 1 precursor

      See identical proteins and their annotated locations for NP_001269241.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR, compared to variant 1. Variants 1, 2 and 6 encode the same isoform (1).
      Source sequence(s)
      AL539139, AW612420, BC008912, BM457676, X87193
      Consensus CDS
      CCDS35453.1
      UniProtKB/Swiss-Prot
      A6QRH6, B2RBI7, B4DFI8, D3DWX4, P98173, Q5HY76, Q96H51
      Related
      ENSP00000358657.1, ENST00000369643.5
      Conserved Domains (1) summary
      cd13940
      Location:55 → 224
      ILEI_FAM3C; Interleukin-like EMT inducer

    6. NM_001363822.2 → NP_001350751.1  protein FAM3A isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC244090
      Consensus CDS
      CCDS87800.1
      UniProtKB/TrEMBL
      Q5HY75
      Related
      ENSP00000358655.3, ENST00000369641.7
      Conserved Domains (1) summary
      cd13940
      Location:55 → 231
      ILEI_FAM3C; Interleukin-like EMT inducer

    7. NM_021806.4 → NP_068578.2  protein FAM3A isoform 1 precursor

      See identical proteins and their annotated locations for NP_068578.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform (1). Variants 1, 2 and 6 encode the same isoform (1).
      Source sequence(s)
      AK314682, AL539139, AW612420, BM457676, X87193
      Consensus CDS
      CCDS35453.1
      UniProtKB/Swiss-Prot
      A6QRH6, B2RBI7, B4DFI8, D3DWX4, P98173, Q5HY76, Q96H51
      Related
      ENSP00000416146.2, ENST00000447601.7
      Conserved Domains (1) summary
      cd13940
      Location:55 → 224
      ILEI_FAM3C; Interleukin-like EMT inducer

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      154506171..154516232 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005277879.5 → XP_005277936.1  protein FAM3A isoform X4

      See identical proteins and their annotated locations for XP_005277936.1

      UniProtKB/Swiss-Prot
      P98173
      Conserved Domains (1) summary
      cd13940
      Location:55 → 207
      ILEI_FAM3C; Interleukin-like EMT inducer

    2. XM_006724832.4 → XP_006724895.1  protein FAM3A isoform X2

      See identical proteins and their annotated locations for XP_006724895.1

      Conserved Domains (1) summary
      cd13940
      Location:55 → 232
      ILEI_FAM3C; Interleukin-like EMT inducer

    3. XM_024452418.2 → XP_024308186.1  protein FAM3A isoform X3

      Conserved Domains (1) summary
      cd13940
      Location:69 → 221
      ILEI_FAM3C; Interleukin-like EMT inducer

    4. XM_024452416.2 → XP_024308184.1  protein FAM3A isoform X1

      Conserved Domains (1) summary
      cd13940
      Location:69 → 245
      ILEI_FAM3C; Interleukin-like EMT inducer

    5. XM_047442293.1 → XP_047298249.1  protein FAM3A isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      152742672..152752723 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054327475.1 → XP_054183450.1  protein FAM3A isoform X4

    2. XM_054327473.1 → XP_054183448.1  protein FAM3A isoform X2

    3. XM_054327474.1 → XP_054183449.1  protein FAM3A isoform X3

    4. XM_054327472.1 → XP_054183447.1  protein FAM3A isoform X1

    5. XM_054327476.1 → XP_054183451.1  protein FAM3A isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P98173.2 GenPept UniProtKB/Swiss-Prot:P98173

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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