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    CNBP CCHC-type zinc finger nucleic acid binding protein [ Homo sapiens (human) ]

    Gene ID: 7555, updated on 17-Jun-2024

    Summary

    Official Symbol
    CNBPprovided by HGNC
    Official Full Name
    CCHC-type zinc finger nucleic acid binding proteinprovided by HGNC
    Primary source
    HGNC:HGNC:13164
    See related
    Ensembl:ENSG00000169714 MIM:116955; AllianceGenome:HGNC:13164
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DM2; ZNF9; CNBP1; PROMM; RNF163; ZCCHC22
    Summary
    This gene encodes a nucleic-acid binding protein with seven zinc-finger domains. The protein has a preference for binding single stranded DNA and RNA. The protein functions in cap-independent translation of ornithine decarboxylase mRNA, and may also function in sterol-mediated transcriptional regulation. A CCTG expansion from <30 repeats to 75-11000 repeats in the first intron of this gene results in myotonic dystrophy type 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2016]
    Expression
    Ubiquitous expression in ovary (RPKM 93.4), heart (RPKM 89.1) and 25 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See CNBP in Genome Data Viewer
    Location:
    3q21.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (129167827..129183896, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (131912733..131928791, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (128886670..128902739, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:128807293-128807837 Neighboring gene ISY1-RAB43 readthrough Neighboring gene RAB43, member RAS oncogene family Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:128831162-128831662 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:128838731-128839676 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14717 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14718 Neighboring gene ISY1 splicing factor homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20504 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20503 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20505 Neighboring gene myotonic dystrophy type 2 repeat instability region Neighboring gene uncharacterized LOC105374101 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20506 Neighboring gene NFE2L2 motif-containing MPRA enhancer 136 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:128931398-128931601 Neighboring gene ribosomal protein S27 pseudogene 12

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ11631

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables G-quadruplex DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA binding HDA PubMed 
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables single-stranded RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables translation regulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in endoplasmic reticulum ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    NOT located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    CCHC-type zinc finger nucleic acid binding protein
    Names
    cellular nucleic acid-binding protein
    erythroid differentiation-related
    sterol regulatory element-binding protein
    zinc finger protein 273
    zinc finger protein 9 (a cellular retroviral nucleic acid binding protein)

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_011902.1 RefSeqGene

      Range
      5072..21141
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001127192.2NP_001120664.1  CCHC-type zinc finger nucleic acid binding protein isoform 1

      See identical proteins and their annotated locations for NP_001120664.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC108673, AK292119, BU616793
      Consensus CDS
      CCDS46906.1
      UniProtKB/Swiss-Prot
      P62633
      Related
      ENSP00000410769.2, ENST00000441626.6
      Conserved Domains (1) summary
      PTZ00368
      Location:54173
      PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional
    2. NM_001127193.2NP_001120665.1  CCHC-type zinc finger nucleic acid binding protein isoform 2

      See identical proteins and their annotated locations for NP_001120665.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant, also known as alpha variant 1, uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in a shorter protein (isoform 2).
      Source sequence(s)
      AC108673, BU616793, DQ091187
      Consensus CDS
      CCDS46907.1
      UniProtKB/Swiss-Prot
      P62633
      Related
      ENSP00000399488.2, ENST00000451728.6
      Conserved Domains (1) summary
      PTZ00368
      Location:54172
      PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional
    3. NM_001127194.2NP_001120666.1  CCHC-type zinc finger nucleic acid binding protein isoform 4

      See identical proteins and their annotated locations for NP_001120666.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant, also known as beta variant 2, uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in a shorter protein (isoform 4).
      Source sequence(s)
      AC108673, BU616793, DQ092367
      Consensus CDS
      CCDS46908.1
      UniProtKB/Swiss-Prot
      P62633
      Related
      ENSP00000400444.2, ENST00000446936.6
      Conserved Domains (1) summary
      PTZ00368
      Location:47166
      PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional
    4. NM_001127195.2NP_001120667.1  CCHC-type zinc finger nucleic acid binding protein isoform 5

      See identical proteins and their annotated locations for NP_001120667.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant, also known as beta variant 1, uses two alternate in-frame splice sites in the 5' and central coding regions, compared to variant 1, resulting in a shorter protein (isoform 5).
      Source sequence(s)
      AC108673, BU616793, DQ092366
      UniProtKB/Swiss-Prot
      P62633
      Conserved Domains (1) summary
      PTZ00368
      Location:47165
      PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional
    5. NM_001127196.2NP_001120668.1  CCHC-type zinc finger nucleic acid binding protein isoform 6

      See identical proteins and their annotated locations for NP_001120668.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant uses two alternate in-frame splice sites in the 5' and central coding regions, compared to variant 1, resulting in a shorter protein (isoform 6).
      Source sequence(s)
      AC108673, BC014911, BU616793, DB027227
      Consensus CDS
      CCDS54637.1
      UniProtKB/TrEMBL
      A0A0S2Z4Q3
      Related
      ENSP00000421323.1, ENST00000502976.5
      Conserved Domains (1) summary
      PTZ00368
      Location:47164
      PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional
    6. NM_003418.5NP_003409.1  CCHC-type zinc finger nucleic acid binding protein isoform 3

      See identical proteins and their annotated locations for NP_003409.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in a shorter protein (isoform 3).
      Source sequence(s)
      AC108673, BC093058, BU616793, DB027227
      Consensus CDS
      CCDS3056.1
      UniProtKB/Swiss-Prot
      A8K7V4, B2RAV9, B4DP17, D3DNB9, D3DNC0, D3DNC1, E9PDR7, P20694, P62633, Q4JGY0, Q4JGY1, Q5QJR0, Q5U0E9, Q6PJI7, Q96NV3
      UniProtKB/TrEMBL
      A0A0S2Z4K2
      Related
      ENSP00000410619.3, ENST00000422453.7
      Conserved Domains (1) summary
      PTZ00368
      Location:54171
      PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      129167827..129183896 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      131912733..131928791 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)