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    FNDC3A fibronectin type III domain containing 3A [ Homo sapiens (human) ]

    Gene ID: 22862, updated on 7-Apr-2024

    Summary

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    Official Symbol
    FNDC3Aprovided by HGNC
    Official Full Name
    fibronectin type III domain containing 3Aprovided by HGNC
    Primary source
    HGNC:HGNC:20296
    See related
    Ensembl:ENSG00000102531 MIM:615794; AllianceGenome:HGNC:20296
    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
    HUGO; FNDC3; bA203I16.1; bA203I16.5
    Summary
    Enables RNA binding activity. Predicted to act upstream of or within several processes, including Sertoli cell development; fertilization; and spermatid development. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in thyroid (RPKM 26.8), adrenal (RPKM 18.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    13q14.2
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (48975291..49209779)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (48193984..48431085)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (49550048..49783915)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene proteasome activator subunit 2 pseudogene 2 Neighboring gene uncharacterized LOC107984559 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:49447591-49448313 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr13:49449130-49449638 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:49449639-49450147 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7737 Neighboring gene NANOG hESC enhancer GRCh37_chr13:49531584-49532085 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7739 Neighboring gene H3K27ac hESC enhancers GRCh37_chr13:49549583-49550202 and GRCh37_chr13:49550203-49550822 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7741 Neighboring gene RNA, U6 small nuclear 60, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr13:49595218-49595767 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:49632061-49633260 Neighboring gene RAD17 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7743 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7744 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:49686954-49687458 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:49687459-49687962 Neighboring gene RNY3 pseudogene 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:49739489-49740046 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:49793904-49794160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5340 Neighboring gene COX7C pseudogene 1 Neighboring gene 2-oxoglutarate and iron dependent oxygenase domain containing 1 pseudogene 1 Neighboring gene motilin receptor

    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. Associations between single-nucleotide polymorphism in the FNDC3A and autism spectrum disorder in a Korean population. Ro M, et al. Psychiatry Res, 2013 Sep 30. PMID 23639254
    2. FAM46C and FNDC3A Are Multiple Myeloma Tumor Suppressors That Act in Concert to Impair Clearing of Protein Aggregates and Autophagy. Manfrini N, et al. Cancer Res, 2020 Nov 1. PMID 32963011
    3. HUGO (FNDC3A): a new gene overexpressed in human odontoblasts. Carrouel F, et al. J Dent Res, 2008 Feb. PMID 18218838
    4. The Interaction of the Tumor Suppressor FAM46C with p62 and FNDC3 Proteins Integrates Protein and Secretory Homeostasis. Fucci C, et al. Cell Rep, 2020 Sep 22. PMID 32966780
    5. The Penta-EF-Hand ALG-2 Protein Interacts with the Cytosolic Domain of the SOCE Regulator SARAF and Interferes with Ubiquitination. Zhang W, et al. Int J Mol Sci, 2020 Aug 31. PMID 32878247, Free PMC Article

    See all (50) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The Interaction of the Tumor Suppressor FAM46C with p62 and FNDC3 Proteins Integrates Protein and Secretory Homeostasis.
      Title: The Interaction of the Tumor Suppressor FAM46C with p62 and FNDC3 Proteins Integrates Protein and Secretory Homeostasis.
    2. FAM46C and FNDC3A Are Multiple Myeloma Tumor Suppressors That Act in Concert to Impair Clearing of Protein Aggregates and Autophagy.
      Title: FAM46C and FNDC3A Are Multiple Myeloma Tumor Suppressors That Act in Concert to Impair Clearing of Protein Aggregates and Autophagy.
    3. The results of this study concluded that FNDC3A influences the prevalence of autism spectrum disorder.
      Title: Associations between single-nucleotide polymorphism in the FNDC3A and autism spectrum disorder in a Korean population.
    4. We report the 1st characterization of new gene we named HUGO, and its associated deduced protein sequence. HUGO proteins are mainly composed of a proline-rich region at N-terminus, 8 type III-fibronectin modules, and transmembranous helix at C-terminus.
      Title: HUGO (FNDC3A): a new gene overexpressed in human odontoblasts.
    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

    Clone Names

    • FLJ31509, KIAA0970

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    Process Evidence Code Pubs
    involved_in Sertoli cell development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell-cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in fertilization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spermatid development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in acrosomal vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in intracellular membrane-bounded organelle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane HDA PubMed 
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    fibronectin type-III domain-containing protein 3A
    Names
    human gene expressed in odontoblasts

    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_001079673.2 → NP_001073141.1  fibronectin type-III domain-containing protein 3A isoform 1

      See identical proteins and their annotated locations for NP_001073141.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1). Variants 1 and 3 encode the same isoform.
      Source sequence(s)
      AJ749706, AL137000, BM973827
      Consensus CDS
      CCDS41886.1
      UniProtKB/Swiss-Prot
      B4DYG1, Q5HYC9, Q5JVF8, Q5JVF9, Q6EVH3, Q6EVH4, Q6N020, Q6P9D5, Q6ZME4, Q9H1W1, Q9Y2H6
      Related
      ENSP00000417257.1, ENST00000492622.6
      Conserved Domains (1) summary
      cd00063
      Location:371 → 462
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

    2. NM_001278438.2 → NP_001265367.1  fibronectin type-III domain-containing protein 3A isoform 1

      See identical proteins and their annotated locations for NP_001265367.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR exon, compared to variant 1. Variants 1 and 3 encode the same isoform (1).
      Source sequence(s)
      BC060816, BC132812, BM973827, DB460317
      Consensus CDS
      CCDS41886.1
      UniProtKB/Swiss-Prot
      B4DYG1, Q5HYC9, Q5JVF8, Q5JVF9, Q6EVH3, Q6EVH4, Q6N020, Q6P9D5, Q6ZME4, Q9H1W1, Q9Y2H6
      Related
      ENSP00000441831.1, ENST00000541916.5
      Conserved Domains (1) summary
      cd00063
      Location:371 → 462
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

    3. NM_014923.5 → NP_055738.3  fibronectin type-III domain-containing protein 3A isoform 2

      See identical proteins and their annotated locations for NP_055738.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AJ749707, BC051029, BM973827
      Consensus CDS
      CCDS9413.2
      Related
      ENSP00000381362.3, ENST00000398316.7
      Conserved Domains (1) summary
      cd00063
      Location:315 → 406
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

    RNA

    1. NR_103528.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) has an alternate 5' exon and an alternate splice site in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC051029, BM973827, DB460317
      Related
      ENST00000484074.5

    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_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      48975291..49209779
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017020440.3 → XP_016875929.1  fibronectin type-III domain-containing protein 3A isoform X1

      UniProtKB/Swiss-Prot
      B4DYG1, Q5HYC9, Q5JVF8, Q5JVF9, Q6EVH3, Q6EVH4, Q6N020, Q6P9D5, Q6ZME4, Q9H1W1, Q9Y2H6
      Conserved Domains (1) summary
      cd00063
      Location:371 → 462
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

    2. XM_017020443.2 → XP_016875932.1  fibronectin type-III domain-containing protein 3A isoform X3

      Conserved Domains (1) summary
      cd00063
      Location:371 → 462
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

    3. XM_011534997.4 → XP_011533299.1  fibronectin type-III domain-containing protein 3A isoform X2

      See identical proteins and their annotated locations for XP_011533299.1

      UniProtKB/Swiss-Prot
      Q9Y2H6
      Conserved Domains (1) summary
      cd00063
      Location:307 → 398
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      48193984..48431085
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054374243.1 → XP_054230218.1  fibronectin type-III domain-containing protein 3A isoform X1

      UniProtKB/Swiss-Prot
      B4DYG1, Q5HYC9, Q5JVF8, Q5JVF9, Q6EVH3, Q6EVH4, Q6N020, Q6P9D5, Q6ZME4, Q9H1W1, Q9Y2H6

    2. XM_054374245.1 → XP_054230220.1  fibronectin type-III domain-containing protein 3A isoform X3

    3. XM_054374244.1 → XP_054230219.1  fibronectin type-III domain-containing protein 3A isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y2H6.4 GenPept UniProtKB/Swiss-Prot:Q9Y2H6

    Gene LinkOut

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