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    C4orf46 chromosome 4 open reading frame 46 [ Homo sapiens (human) ]

    Gene ID: 201725, updated on 27-Nov-2024

    Summary

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    Official Symbol
    C4orf46provided by HGNC
    Official Full Name
    chromosome 4 open reading frame 46provided by HGNC
    Primary source
    HGNC:HGNC:27320
    See related
    Ensembl:ENSG00000205208 MIM:616210; AllianceGenome:HGNC:27320
    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
    RCDG1
    Summary
    This gene encodes a small, conserved protein of unknown function that is expressed in a variety of tissues. There are pseudogenes for this gene on chromosomes 6, 8, 16, and X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2013]
    Expression
    Broad expression in testis (RPKM 8.9), bone marrow (RPKM 5.4) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See C4orf46 in Genome Data Viewer
    Location:
    4q32.1
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (158666675..158672056, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (162017410..162022804, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (159587827..159593208, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene GC-rich promoter binding protein 1 pseudogene Neighboring gene uncharacterized LOC124900802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22084 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:159461287-159462486 Neighboring gene relaxin family peptide receptor 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:159501162-159501738 Neighboring gene Sharpr-MPRA regulatory region 15067 Neighboring gene NANOG hESC enhancer GRCh37_chr4:159577538-159578061 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:159580614-159581120 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:159592018-159592654 Neighboring gene H3K27ac hESC enhancers GRCh37_chr4:159592655-159593291 and GRCh37_chr4:159593295-159593796 Neighboring gene electron transfer flavoprotein dehydrogenase Neighboring gene small nucleolar RNA U3 Neighboring gene hESC enhancers GRCh37_chr4:159643958-159644541 and GRCh37_chr4:159644542-159645126 Neighboring gene peptidylprolyl isomerase D

    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. Expression and clinical significance of RCDG1 in renal cell carcinoma: a novel renal cancer‑associated gene. Yu Z, et al. Mol Med Rep, 2014 Sep. PMID 25059753
    2. Inactivation of testis-specific gene C4orf46 is dispensable for spermatogenesis and fertility in mouse. Shah B, et al. Mamm Genome, 2021 Oct. PMID 34076717
    3. Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. Otsuki T, et al. DNA Res, 2005. PMID 16303743
    4. The protein interaction landscape of the human CMGC kinase group. Varjosalo M, et al. Cell Rep, 2013 Apr 25. PMID 23602568
    5. Substrate-Trapped Interactors of PHD3 and FIH Cluster in Distinct Signaling Pathways. Rodriguez J, et al. Cell Rep, 2016 Mar 22. PMID 26972000, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A reduction in RCDG1 expression may be associated with the oncogenesis of renal cell carcinoma and the differentiation of clear cell renal cell carcinoma.
      Title: Expression and clinical significance of RCDG1 in renal cell carcinoma: a novel renal cancer‑associated gene.
    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

    • FLJ18760

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    renal cancer differentiation gene 1 protein

    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.

    Genomic

    1. NG_033150.1 RefSeqGene

      Range
      5369..10581
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001008393.4 → NP_001008394.1  renal cancer differentiation gene 1 protein

      See identical proteins and their annotated locations for NP_001008394.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the protein.
      Source sequence(s)
      AC107219, BC094775, BU688970
      Consensus CDS
      CCDS34088.1
      UniProtKB/Swiss-Prot
      B3KNH7, Q504U0
      Related
      ENSP00000368503.4, ENST00000379205.5
      Conserved Domains (1) summary
      pfam15725
      Location:5 → 87
      RCDG1; Renal cancer differentiation gene 1 protein

    RNA

    1. NR_077234.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
      Source sequence(s)
      AC107219, AK311718, BU688970

    2. NR_077235.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' exon and uses an alternate splice site in the 3' exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
      Source sequence(s)
      AC107219, BI823282, BU688970

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      158666675..158672056 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      162017410..162022804 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q504U0.1 GenPept UniProtKB/Swiss-Prot:Q504U0

    Gene LinkOut

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

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