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    C12orf42 chromosome 12 open reading frame 42 [ Homo sapiens (human) ]

    Gene ID: 374470, updated on 17-Sep-2024

    Summary

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    Official Symbol
    C12orf42provided by HGNC
    Official Full Name
    chromosome 12 open reading frame 42provided by HGNC
    Primary source
    HGNC:HGNC:24729
    See related
    Ensembl:ENSG00000179088 AllianceGenome:HGNC:24729
    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
    Expression
    Biased expression in testis (RPKM 2.3), spleen (RPKM 0.3) and 2 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See C12orf42 in Genome Data Viewer
    Location:
    12q23.2-q23.3
    Exon count:
    42
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (103047624..103563790, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (103008475..103525054, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (103473418..103895283, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC112267865 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:103343731-103344658 Neighboring gene VISTA enhancer hs1122 Neighboring gene phenylalanine hydroxylase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:103351919-103352450 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:103352451-103352982 Neighboring gene VISTA enhancer hs1574 Neighboring gene VISTA enhancer hs1114 Neighboring gene VISTA enhancers hs998, hs1354 and hs1540 Neighboring gene achaete-scute family bHLH transcription factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4776 Neighboring gene VISTA enhancer hs967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6886 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6887 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4777 Neighboring gene U7 small nuclear RNA Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6889 Neighboring gene C12orf42 antisense RNA 1 Neighboring gene VISTA enhancer hs1575 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6890 Neighboring gene VISTA enhancer hs1723 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:103615579-103616560 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:103621893-103622473 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:103730647-103730806 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23171 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6891 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:103828343-103829043 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4778 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6892 Neighboring gene uncharacterized LOC105369945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4780 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4779 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6893 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6894 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6895 Neighboring gene glutaryl-CoA dehydrogenase, mitochondrial-like Neighboring gene Sharpr-MPRA regulatory region 5508 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:103954215-103955414 Neighboring gene long intergenic non-protein coding RNA 2401 Neighboring gene U8 small nucleolar RNA Neighboring gene uncharacterized LOC105369946 Neighboring gene stabilin 2

    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 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. Molecular characterization of a novel chromosomal translocation t(12;14)(q23;q11.2) in T-lymphoblastic lymphoma between the T-cell receptor delta-deleting elements (TRDREC and TRAJ61) and the hypothetical gene C12orf42. Przybylski GK, et al. Eur J Haematol, 2010 Nov. PMID 20659153
    2. A genome-wide association study identifies a region at chromosome 12 as a potential susceptibility locus for restenosis after percutaneous coronary intervention. Sampietro ML, et al. Hum Mol Genet, 2011 Dec 1. PMID 21878436, Free PMC Article
    3. Biological insights from 108 schizophrenia-associated genetic loci. Schizophrenia Working Group of the Psychiatric Genomics Consortium. Nature, 2014 Jul 24. PMID 25056061, Free PMC Article
    4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. Rose JE, et al. Mol Med, 2010 Jul-Aug. PMID 20379614, Free PMC Article
    5. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. deletional rearrangement of the TCR delta gene disrupted the hypothetical gene C12orf42 and brought the Achaete-scute complex homolog 1 gene into proximity of the TRA enhancer, which is overexpressed in thyroid and lung cancers
      Title: Molecular characterization of a novel chromosomal translocation t(12;14)(q23;q11.2) in T-lymphoblastic lymphoma between the T-cell receptor delta-deleting elements (TRDREC and TRAJ61) and the hypothetical gene C12orf42.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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
    A genome-wide association study identifies a region at chromosome 12 as a potential susceptibility locus for restenosis after percutaneous coronary intervention.
    EBI GWAS Catalog
    Biological insights from 108 schizophrenia-associated genetic loci.
    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

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ25323, MGC43592, MGC57409

    General protein information

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    Preferred Names
    uncharacterized protein C12orf42

    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_001099336.3 → NP_001092806.1  uncharacterized protein C12orf42 isoform 1

      See identical proteins and their annotated locations for NP_001092806.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) encodes the longer isoform (1). Variants 1 and 2 encode the same isoform 1.
      Source sequence(s)
      AC084364, AC090000, AC126176
      Consensus CDS
      CCDS44963.1
      UniProtKB/Swiss-Prot
      Q49A64, Q4G0S2, Q96LP6
      Related
      ENSP00000367353.2, ENST00000378113.7
      Conserved Domains (1) summary
      pfam15380
      Location:96 → 359
      DUF4607; Domain of unknown function (DUF4607)

    2. NM_001278419.3 → NP_001265348.1  uncharacterized protein C12orf42 isoform 2

      See identical proteins and their annotated locations for NP_001265348.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has an additional exon in the central region, which results in a downstream start codon, compared to variant 2. The resulting isoform (2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC084364, AC090000, AC126176
      UniProtKB/Swiss-Prot
      Q96LP6
      Conserved Domains (1) summary
      pfam15380
      Location:1 → 264
      DUF4607; Domain of unknown function (DUF4607)

    3. NM_001278420.3 → NP_001265349.1  uncharacterized protein C12orf42 isoform 2

      See identical proteins and their annotated locations for NP_001265349.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) has an alternate splice site in the 5' UTR and an additional exon in the central region, which results in a downstream start codon, compared to variant 2. The resulting isoform (2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AK058052, HY015666
      UniProtKB/Swiss-Prot
      Q96LP6
      Conserved Domains (1) summary
      pfam15380
      Location:1 → 264
      DUF4607; Domain of unknown function (DUF4607)

    4. NM_001386867.1 → NP_001373796.1  uncharacterized protein C12orf42 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC068642, AC068643, AC084364, AC090000

    5. NM_001386868.1 → NP_001373797.1  uncharacterized protein C12orf42 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC084364, AC090000, AC126176
      Conserved Domains (1) summary
      pfam15380
      Location:57 → 320
      DUF4607; Domain of unknown function (DUF4607)

    6. NM_001386869.1 → NP_001373798.1  uncharacterized protein C12orf42 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC090000, AC126176
      Consensus CDS
      CCDS91744.1
      UniProtKB/TrEMBL
      F8VV63
      Conserved Domains (1) summary
      pfam15380
      Location:29 → 292
      DUF4607; Domain of unknown function (DUF4607)

    7. NM_001386871.1 → NP_001373800.1  uncharacterized protein C12orf42 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC090000, AC126176
      Conserved Domains (1) summary
      pfam15380
      Location:1 → 264
      DUF4607; Domain of unknown function (DUF4607)

    8. NM_001386872.1 → NP_001373801.1  uncharacterized protein C12orf42 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC090000, AC126176
      Conserved Domains (1) summary
      pfam15380
      Location:19 → 168
      DUF4607; Domain of unknown function (DUF4607)

    9. NM_198521.5 → NP_940923.2  uncharacterized protein C12orf42 isoform 1

      See identical proteins and their annotated locations for NP_940923.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) has an alternate splice site in the 5' UTR, compared to variant 2. Variants 1 and 2 encode the same isoform 1.
      Source sequence(s)
      AK058052, HY015666
      Consensus CDS
      CCDS44963.1
      UniProtKB/Swiss-Prot
      Q49A64, Q4G0S2, Q96LP6
      Related
      ENSP00000447908.1, ENST00000548883.6
      Conserved Domains (1) summary
      pfam15380
      Location:96 → 359
      DUF4607; Domain of unknown function (DUF4607)

    RNA

    1. NR_103526.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) has an alternate splice site in the 5' region and lacks last two exons but has several alternate 3' terminal exons, compared to variant 2. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC039352, HY015666
      Related
      ENST00000547347.5

    2. NR_170332.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC068643, AC084364, AC090000

    3. NR_170333.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC090000, AC126176

    4. NR_170334.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC068643, AC090000

    5. NR_170335.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC068643, AC090000

    6. NR_170336.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC068642, AC068643, AC090000

    7. NR_170337.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC068643, AC090000

    8. NR_170338.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC068643, AC090000

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      103047624..103563790 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428807.1 → XP_047284763.1  uncharacterized protein C12orf42 isoform X12

    2. XM_017019281.2 → XP_016874770.1  uncharacterized protein C12orf42 isoform X9

    3. XM_011538312.3 → XP_011536614.1  uncharacterized protein C12orf42 isoform X8

    4. XM_047428806.1 → XP_047284762.1  uncharacterized protein C12orf42 isoform X11

    5. XM_011538315.3 → XP_011536617.1  uncharacterized protein C12orf42 isoform X10

    6. XM_047428808.1 → XP_047284764.1  uncharacterized protein C12orf42 isoform X13

    7. XM_047428803.1 → XP_047284759.1  uncharacterized protein C12orf42 isoform X2

      UniProtKB/Swiss-Prot
      Q49A64, Q4G0S2, Q96LP6

    8. XM_011538294.3 → XP_011536596.1  uncharacterized protein C12orf42 isoform X3

      Conserved Domains (1) summary
      pfam15380
      Location:92 → 355
      DUF4607; Domain of unknown function (DUF4607)

    9. XM_011538306.2 → XP_011536608.1  uncharacterized protein C12orf42 isoform X7

      Conserved Domains (1) summary
      pfam15380
      Location:105 → 254
      DUF4607; Domain of unknown function (DUF4607)

    10. XM_047428802.1 → XP_047284758.1  uncharacterized protein C12orf42 isoform X1

    11. XM_011538292.3 → XP_011536594.1  uncharacterized protein C12orf42 isoform X2

      See identical proteins and their annotated locations for XP_011536594.1

      UniProtKB/Swiss-Prot
      Q49A64, Q4G0S2, Q96LP6
      Conserved Domains (1) summary
      pfam15380
      Location:96 → 359
      DUF4607; Domain of unknown function (DUF4607)

    12. XM_017019276.2 → XP_016874765.1  uncharacterized protein C12orf42 isoform X2

      UniProtKB/Swiss-Prot
      Q49A64, Q4G0S2, Q96LP6
      Conserved Domains (1) summary
      pfam15380
      Location:96 → 359
      DUF4607; Domain of unknown function (DUF4607)

    13. XM_011538293.3 → XP_011536595.1  uncharacterized protein C12orf42 isoform X2

      See identical proteins and their annotated locations for XP_011536595.1

      UniProtKB/Swiss-Prot
      Q49A64, Q4G0S2, Q96LP6
      Conserved Domains (1) summary
      pfam15380
      Location:96 → 359
      DUF4607; Domain of unknown function (DUF4607)

    14. XM_011538305.2 → XP_011536607.1  uncharacterized protein C12orf42 isoform X6

      See identical proteins and their annotated locations for XP_011536607.1

      UniProtKB/TrEMBL
      F8VV63
      Conserved Domains (1) summary
      pfam15380
      Location:29 → 292
      DUF4607; Domain of unknown function (DUF4607)

    15. XM_047428804.1 → XP_047284760.1  uncharacterized protein C12orf42 isoform X5

    16. XM_011538300.2 → XP_011536602.1  uncharacterized protein C12orf42 isoform X5

      See identical proteins and their annotated locations for XP_011536602.1

      Conserved Domains (1) summary
      pfam15380
      Location:57 → 320
      DUF4607; Domain of unknown function (DUF4607)

    17. XM_011538295.2 → XP_011536597.1  uncharacterized protein C12orf42 isoform X4

      Conserved Domains (1) summary
      pfam15380
      Location:71 → 334
      DUF4607; Domain of unknown function (DUF4607)

    18. XM_017019278.2 → XP_016874767.1  uncharacterized protein C12orf42 isoform X5

      Conserved Domains (1) summary
      pfam15380
      Location:57 → 320
      DUF4607; Domain of unknown function (DUF4607)

    19. XM_017019280.2 → XP_016874769.1  uncharacterized protein C12orf42 isoform X6

      UniProtKB/TrEMBL
      F8VV63
      Related
      ENSP00000449362.1, ENST00000548048.5
      Conserved Domains (1) summary
      pfam15380
      Location:29 → 292
      DUF4607; Domain of unknown function (DUF4607)

    20. XM_017019279.2 → XP_016874768.1  uncharacterized protein C12orf42 isoform X6

      UniProtKB/TrEMBL
      F8VV63
      Conserved Domains (1) summary
      pfam15380
      Location:29 → 292
      DUF4607; Domain of unknown function (DUF4607)

    21. XM_017019277.2 → XP_016874766.1  uncharacterized protein C12orf42 isoform X5

      Conserved Domains (1) summary
      pfam15380
      Location:57 → 320
      DUF4607; Domain of unknown function (DUF4607)

    22. XM_011538297.3 → XP_011536599.1  uncharacterized protein C12orf42 isoform X5

      See identical proteins and their annotated locations for XP_011536599.1

      Conserved Domains (1) summary
      pfam15380
      Location:57 → 320
      DUF4607; Domain of unknown function (DUF4607)

    23. XM_047428805.1 → XP_047284761.1  uncharacterized protein C12orf42 isoform X5

    RNA

    1. XR_001748690.2 RNA Sequence

    2. XR_007063073.1 RNA Sequence

    3. XR_001748691.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      103008475..103525054 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371999.1 → XP_054227974.1  uncharacterized protein C12orf42 isoform X12

    2. XM_054371996.1 → XP_054227971.1  uncharacterized protein C12orf42 isoform X9

    3. XM_054371995.1 → XP_054227970.1  uncharacterized protein C12orf42 isoform X8

    4. XM_054371998.1 → XP_054227973.1  uncharacterized protein C12orf42 isoform X11

    5. XM_054371997.1 → XP_054227972.1  uncharacterized protein C12orf42 isoform X10

    6. XM_054372000.1 → XP_054227975.1  uncharacterized protein C12orf42 isoform X13

    7. XM_054371979.1 → XP_054227954.1  uncharacterized protein C12orf42 isoform X2

      UniProtKB/Swiss-Prot
      Q49A64, Q4G0S2, Q96LP6

    8. XM_054371983.1 → XP_054227958.1  uncharacterized protein C12orf42 isoform X3

    9. XM_054371994.1 → XP_054227969.1  uncharacterized protein C12orf42 isoform X7

    10. XM_054371978.1 → XP_054227953.1  uncharacterized protein C12orf42 isoform X1

    11. XM_054371981.1 → XP_054227956.1  uncharacterized protein C12orf42 isoform X2

      UniProtKB/Swiss-Prot
      Q49A64, Q4G0S2, Q96LP6

    12. XM_054371982.1 → XP_054227957.1  uncharacterized protein C12orf42 isoform X2

      UniProtKB/Swiss-Prot
      Q49A64, Q4G0S2, Q96LP6

    13. XM_054371980.1 → XP_054227955.1  uncharacterized protein C12orf42 isoform X2

      UniProtKB/Swiss-Prot
      Q49A64, Q4G0S2, Q96LP6

    14. XM_054371993.1 → XP_054227968.1  uncharacterized protein C12orf42 isoform X6

      UniProtKB/TrEMBL
      F8VV63

    15. XM_054371989.1 → XP_054227964.1  uncharacterized protein C12orf42 isoform X5

    16. XM_054371987.1 → XP_054227962.1  uncharacterized protein C12orf42 isoform X5

    17. XM_054371984.1 → XP_054227959.1  uncharacterized protein C12orf42 isoform X4

    18. XM_054371986.1 → XP_054227961.1  uncharacterized protein C12orf42 isoform X5

    19. XM_054371992.1 → XP_054227967.1  uncharacterized protein C12orf42 isoform X6

      UniProtKB/TrEMBL
      F8VV63

    20. XM_054371991.1 → XP_054227966.1  uncharacterized protein C12orf42 isoform X6

      UniProtKB/TrEMBL
      F8VV63

    21. XM_054371985.1 → XP_054227960.1  uncharacterized protein C12orf42 isoform X5

    22. XM_054371988.1 → XP_054227963.1  uncharacterized protein C12orf42 isoform X5

    23. XM_054371990.1 → XP_054227965.1  uncharacterized protein C12orf42 isoform X5

    RNA

    1. XR_008488580.1 RNA Sequence

    2. XR_008488581.1 RNA Sequence

    3. XR_008488582.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96LP6.2 GenPept UniProtKB/Swiss-Prot:Q96LP6

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