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

Gene ID: 22862, updated on 3-Nov-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 be involved in spermatid development. Predicted to act upstream of or within Sertoli cell development; cell-cell adhesion; and fertilization. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in thyroid (RPKM 26.8), adrenal (RPKM 18.9) and 25 other tissues See more
Orthologs
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Genomic context

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See FNDC3A in Genome Data Viewer
Location:
13q14.2
Exon count:
31
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (48975291..49209779)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (48193984..48431085)
RS_2024_09 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. HUGO (FNDC3A): a new gene overexpressed in human odontoblasts. Carrouel F, et al. J Dent Res, 2008 Feb. PMID 18218838
  3. 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
  4. 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
  5. A chemical tool for blue light-inducible proximity photo-crosslinking in live cells. Mishra PK, et al. Chem Sci, 2022 Jan 26. PMID 35211260, Free PMC Article

See all (56) 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)

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_2024_08

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

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

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