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C19orf47 chromosome 19 open reading frame 47 [ Homo sapiens (human) ]

Gene ID: 126526, updated on 5-Mar-2024

Summary

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Official Symbol
C19orf47provided by HGNC
Official Full Name
chromosome 19 open reading frame 47provided by HGNC
Primary source
HGNC:HGNC:26723
See related
Ensembl:ENSG00000160392 AllianceGenome:HGNC:26723
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
Summary
Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in heart (RPKM 2.7), testis (RPKM 2.0) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
19q13.2
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (40292954..40348527, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (43113226..43169048, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (40825443..40854434, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene AKT serine/threonine kinase 2 Neighboring gene uncharacterized LOC107985289 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:40757528-40758152 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:40758153-40758776 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:40760793-40761294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:40761295-40761794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:40762167-40762909 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:40770063-40770648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:40770788-40771766 Neighboring gene Sharpr-MPRA regulatory region 4564 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:40774314-40775162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14642 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14644 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14647 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10619 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:40791573-40792404 Neighboring gene microRNA 641 Neighboring gene RNA, U6 small nuclear 945, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:40829016-40829516 Neighboring gene MPRA-validated peak3483 silencer Neighboring gene Sharpr-MPRA regulatory region 7250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14649 Neighboring gene phospholipase D family member 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:40873853-40874018 Neighboring gene Sharpr-MPRA regulatory region 12346 Neighboring gene microRNA 6796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:40895441-40895990 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:40895991-40896540 Neighboring gene homeodomain interacting protein kinase 4

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. Two-hybrid analysis identifies PSMD11, a non-ATPase subunit of the proteasome, as a novel interaction partner of AMP-activated protein kinase. Moreno D, et al. Int J Biochem Cell Biol, 2009 Dec. PMID 19616115
  2. MYC Protein Interactome Profiling Reveals Functionally Distinct Regions that Cooperate to Drive Tumorigenesis. Kalkat M, et al. Mol Cell, 2018 Dec 6. PMID 30415952
  3. CHD3 and CHD4 form distinct NuRD complexes with different yet overlapping functionality. Hoffmeister H, et al. Nucleic Acids Res, 2017 Oct 13. PMID 28977666, Free PMC Article
  4. The LIFEdb database in 2006. Mehrle A, et al. Nucleic Acids Res, 2006 Jan 1. PMID 16381901, Free PMC Article
  5. From ORFeome to biology: a functional genomics pipeline. Wiemann S, et al. Genome Res, 2004 Oct. PMID 15489336, Free PMC Article

See all (24) citations in PubMed

GeneRIFs: Gene References Into Functions

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

  • FLJ36888, DKFZp686P05129

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 nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
uncharacterized protein C19orf47

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_001256440.1 → NP_001243369.1  uncharacterized protein C19orf47 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001243369.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AI394044, AK094207, AL834131, CR936760
    Consensus CDS
    CCDS58662.1
    UniProtKB/Swiss-Prot
    Q8IZ33, Q8N0V9, Q8N9M1
    Related
    ENSP00000463159.1, ENST00000582783.5
    Conserved Domains (1) summary
    cd09531
    Location:45 → 109
    SAM_CS047; SAM domain of CS047 subfamily

  2. NM_001256441.2 → NP_001243370.1  uncharacterized protein C19orf47 isoform 2

    See identical proteins and their annotated locations for NP_001243370.1

    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 a downstream, in-frame start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC118344, AI394044, AL834131, BI916290, BM459040
    Consensus CDS
    CCDS92619.1
    UniProtKB/TrEMBL
    A0A804HLH2
    Related
    ENSP00000508349.1, ENST00000683109.1
    Conserved Domains (1) summary
    cd09531
    Location:8 → 72
    SAM_CS047; SAM domain of CS047 subfamily

RNA

  1. NR_046202.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has an alternate 5'-most exon and uses an alternate splice site in the 5' region, compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC118344, AI394044, AL834131, BI916290

  2. NR_156465.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in the 5' region, compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC118344

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    40292954..40348527 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011526460.3 → XP_011524762.1  uncharacterized protein C19orf47 isoform X9

    Conserved Domains (1) summary
    cd09531
    Location:45 → 109
    SAM_CS047; SAM domain of CS047 subfamily

  2. XM_047438176.1 → XP_047294132.1  uncharacterized protein C19orf47 isoform X7

  3. XM_024451364.2 → XP_024307132.1  uncharacterized protein C19orf47 isoform X6

    Conserved Domains (1) summary
    cd09531
    Location:8 → 72
    SAM_CS047; SAM domain of CS047 subfamily

  4. XM_005258520.3 → XP_005258577.1  uncharacterized protein C19orf47 isoform X2

    Conserved Domains (1) summary
    cd09531
    Location:45 → 109
    SAM_CS047; SAM domain of CS047 subfamily

  5. XM_017026291.2 → XP_016881780.1  uncharacterized protein C19orf47 isoform X1

    Conserved Domains (1) summary
    cd09531
    Location:8 → 72
    SAM_CS047; SAM domain of CS047 subfamily

  6. XM_024451365.2 → XP_024307133.1  uncharacterized protein C19orf47 isoform X8

    UniProtKB/TrEMBL
    A0A804HLH2
    Conserved Domains (1) summary
    cd09531
    Location:8 → 72
    SAM_CS047; SAM domain of CS047 subfamily

  7. XM_047438177.1 → XP_047294133.1  uncharacterized protein C19orf47 isoform X8

    UniProtKB/TrEMBL
    A0A804HLH2

  8. XM_047438178.1 → XP_047294134.1  uncharacterized protein C19orf47 isoform X10

    Related
    ENSP00000375889.2, ENST00000392035.6

  9. XM_047438179.1 → XP_047294135.1  uncharacterized protein C19orf47 isoform X11

  10. XM_047438175.1 → XP_047294131.1  uncharacterized protein C19orf47 isoform X5

  11. XM_017026293.3 → XP_016881782.1  uncharacterized protein C19orf47 isoform X4

  12. XM_017026292.3 → XP_016881781.1  uncharacterized protein C19orf47 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    43113226..43169048 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054319832.1 → XP_054175807.1  uncharacterized protein C19orf47 isoform X9

  2. XM_054319829.1 → XP_054175804.1  uncharacterized protein C19orf47 isoform X7

  3. XM_054319828.1 → XP_054175803.1  uncharacterized protein C19orf47 isoform X6

  4. XM_054319824.1 → XP_054175799.1  uncharacterized protein C19orf47 isoform X2

  5. XM_054319823.1 → XP_054175798.1  uncharacterized protein C19orf47 isoform X1

  6. XM_054319830.1 → XP_054175805.1  uncharacterized protein C19orf47 isoform X8

    UniProtKB/TrEMBL
    A0A804HLH2

  7. XM_054319831.1 → XP_054175806.1  uncharacterized protein C19orf47 isoform X8

    UniProtKB/TrEMBL
    A0A804HLH2

  8. XM_054319833.1 → XP_054175808.1  uncharacterized protein C19orf47 isoform X11

  9. XM_054319827.1 → XP_054175802.1  uncharacterized protein C19orf47 isoform X5

  10. XM_054319826.1 → XP_054175801.1  uncharacterized protein C19orf47 isoform X4

  11. XM_054319825.1 → XP_054175800.1  uncharacterized protein C19orf47 isoform X3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_178830.2: Suppressed sequence

    Description
    NM_178830.2: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N9M1.1 GenPept UniProtKB/Swiss-Prot:Q8N9M1

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