Free for academic non-profit institutions. Other users need a Commercial license

Aliases for CNBP Gene

Aliases for CNBP Gene

  • CCHC-Type Zinc Finger Nucleic Acid Binding Protein 2 3 5
  • Zinc Finger Protein 9 (A Cellular Retroviral Nucleic Acid Binding Protein) 2 3
  • Zinc Finger Protein 9 2 4
  • RNF163 3 4
  • ZNF9 3 4
  • CCHC-Type Zinc Finger, Nucleic Acid Binding Protein 2
  • Sterol Regulatory Element-Binding Protein 3
  • Cellular Nucleic Acid-Binding Protein 3
  • Erythroid Differentiation-Related 3
  • Zinc Finger Protein 273 3
  • ZCCHC22 3
  • CNBP1 3
  • PROMM 3
  • DM2 3

External Ids for CNBP Gene

Previous HGNC Symbols for CNBP Gene

  • DM2
  • ZNF9

Previous GeneCards Identifiers for CNBP Gene

  • GC03M130372
  • GC03M128886
  • GC03M126273

Summaries for CNBP Gene

Entrez Gene Summary for CNBP Gene

  • 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]

GeneCards Summary for CNBP Gene

CNBP (CCHC-Type Zinc Finger Nucleic Acid Binding Protein) is a Protein Coding gene. Diseases associated with CNBP include Myotonic Dystrophy 2 and Myotonic Dystrophy. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and DNA binding transcription factor activity. An important paralog of this gene is ZCCHC13.

UniProtKB/Swiss-Prot for CNBP Gene

  • Single-stranded DNA-binding protein, with specificity to the sterol regulatory element (SRE). Involved in sterol-mediated repression.

Gene Wiki entry for CNBP Gene

Additional gene information for CNBP Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CNBP Gene

Genomics for CNBP Gene

GeneHancer (GH) Regulatory Elements for CNBP Gene

Promoters and enhancers for CNBP Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J129178 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 650.7 +1.4 1423 8.4 PKNOX1 SMAD1 FOXA2 MLX ZFP64 ARID4B NEUROD1 SIN3A FEZF1 DMAP1 CNBP LOC105374101 RPL32P3 ENSG00000244932 ISY1 H1FX-AS1 MBD4 RPS15AP16 H1FX COPG1
GH03J129223 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 17.8 -45.8 -45830 12 HDGF PKNOX1 FOXA2 MLX ARNT ZFP64 ARID4B DMAP1 IRF4 YY1 GC03M129230 LOC105374102 KIAA1257 RAB43 CNBP GP9 ISY1 HMCES MBD4 RPL32P3
GH03J129248 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 12.7 -65.6 -65620 2.6 HDGF ATF1 FOXA2 SMAD1 ARID4B SIN3A DMAP1 ZNF48 YY1 ETS1 PIR44075 COPG1 HMCES CNBP ISY1 RAB43 GP9 H1FX-AS1 MBD4 MIR6826
GH03J129159 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.4 +22.4 22413 4.4 PKNOX1 CLOCK ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 IRF4 YY1 ISY1 ISY1-RAB43 RPL32P3 ENSG00000244932 H1FX-AS1 CNBP MBD4 H1FX ENSG00000273437 GC03M129158
GH03J129024 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 11.6 +157.6 157592 2.9 CLOCK ATF1 SIN3A POLR2B GLIS2 ELK1 ZNF207 ZNF143 FOS ATF7 KIAA1257 EFCC1 GP9 CNBP RAB43 PIR62024
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CNBP on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CNBP gene promoter:

Genomic Locations for CNBP Gene

Genomic Locations for CNBP Gene
16,153 bases
Minus strand

Genomic View for CNBP Gene

Genes around CNBP on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CNBP Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CNBP Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CNBP Gene

Proteins for CNBP Gene

  • Protein details for CNBP Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Cellular nucleic acid-binding protein
    Protein Accession:
    Secondary Accessions:
    • A8K7V4
    • B2RAV9
    • B4DP17
    • D3DNB9
    • D3DNC0
    • D3DNC1
    • E9PDR7
    • P20694
    • Q4JGY0
    • Q4JGY1
    • Q5QJR0
    • Q5U0E9
    • Q6PJI7
    • Q96NV3

    Protein attributes for CNBP Gene

    177 amino acids
    Molecular mass:
    19463 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for CNBP Gene

neXtProt entry for CNBP Gene

Post-translational modifications for CNBP Gene

  • Arginine methylation by PRMT1 in the Arg/Gly-rich region impedes RNA binding.
  • Ubiquitination at posLast=152152, posLast=130130, Lys103, and Lys8
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CNBP Gene

Domains & Families for CNBP Gene

Gene Families for CNBP Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for CNBP Gene


Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CNBP: view

No data available for UniProtKB/Swiss-Prot for CNBP Gene

Function for CNBP Gene

Molecular function for CNBP Gene

UniProtKB/Swiss-Prot Function:
Single-stranded DNA-binding protein, with specificity to the sterol regulatory element (SRE). Involved in sterol-mediated repression.

Gene Ontology (GO) - Molecular Function for CNBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IDA 23774591
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA 23774591
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003697 single-stranded DNA binding IEA --
genes like me logo Genes that share ontologies with CNBP: view
genes like me logo Genes that share phenotypes with CNBP: view

Human Phenotype Ontology for CNBP Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CNBP Gene

MGI Knock Outs for CNBP:
  • Cnbp Cnbp<tm1b(KOMP)Wtsi>

Animal Model Products

CRISPR Products

miRNA for CNBP Gene

miRTarBase miRNAs that target CNBP

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CNBP

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for CNBP Gene

Localization for CNBP Gene

Subcellular locations from UniProtKB/Swiss-Prot for CNBP Gene

Cytoplasm. Endoplasmic reticulum.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CNBP gene
Compartment Confidence
nucleus 5
cytosol 5
endoplasmic reticulum 4
extracellular 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CNBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 NOT nucleus ISS --
GO:0005737 cytoplasm IEA --
GO:0005783 endoplasmic reticulum ISS --
GO:0005829 cytosol IEA,ISS --
genes like me logo Genes that share ontologies with CNBP: view

Pathways & Interactions for CNBP Gene

No Data Available

SIGNOR curated interactions for CNBP Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for CNBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 23774591
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated TAS 2562787
GO:0006695 cholesterol biosynthetic process TAS 2562787
GO:0008284 positive regulation of cell proliferation ISS,IEA --
genes like me logo Genes that share ontologies with CNBP: view

No data available for Pathways by source for CNBP Gene

Drugs & Compounds for CNBP Gene

(5) Drugs for CNBP Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(3) Additional Compounds for CNBP Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CNBP: view

Transcripts for CNBP Gene

Unigene Clusters for CNBP Gene

CCHC-type zinc finger, nucleic acid binding protein:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CNBP

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CNBP Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f ^ 2 ^ 3a · 3b · 3c · 3d ^ 4a · 4b ^ 5a · 5b · 5c · 5d ^ 6a · 6b ^ 7a · 7b · 7c · 7d · 7e · 7f · 7g ·
SP1: - - - -
SP2: - - -
SP3: - - - -
SP4: - - - -
SP5: - - - -
SP6: - - - -
SP7: - - -
SP8: - - - - -
SP9: - - - -
SP10: - - - -
SP11: - - - -
SP12: - -
SP13: - - -
SP14: - - - - - -
SP15: - -
SP17: - -

ExUns: 7h · 7i

Relevant External Links for CNBP Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CNBP Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CNBP Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CNBP Gene

This gene is overexpressed in Muscle - Skeletal (x4.3).

Protein differential expression in normal tissues from HIPED for CNBP Gene

This gene is overexpressed in Tlymphocyte (12.4), Urine (11.0), and Peripheral blood mononuclear cells (9.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CNBP Gene

Protein tissue co-expression partners for CNBP Gene

NURSA nuclear receptor signaling pathways regulating expression of CNBP Gene:


SOURCE GeneReport for Unigene cluster for CNBP Gene:


mRNA Expression by UniProt/SwissProt for CNBP Gene:

Tissue specificity: Present in all tissues examined.

Evidence on tissue expression from TISSUES for CNBP Gene

  • Nervous system(5)
  • Lung(4.8)
  • Liver(4.7)
  • Muscle(4.2)
  • Heart(3.7)
  • Intestine(3.6)
  • Eye(3.5)
  • Skin(3.4)
  • Stomach(3.1)
  • Blood(3)
  • Kidney(2.7)
  • Adrenal gland(2.3)
  • Pancreas(2.3)
  • Lymph node(2.2)
  • Spleen(2.2)
  • Thyroid gland(2.2)
  • Gall bladder(2.1)
  • Bone marrow(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CNBP Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • skeletal muscle
  • urinary
Head and neck:
  • brain
  • ear
  • eye
  • head
  • neck
  • pituitary gland
  • scalp
  • breast
  • heart
  • heart valve
  • kidney
  • pancreas
  • ovary
  • penis
  • prostate
  • testicle
  • uterus
  • vagina
  • vulva
  • lower limb
  • upper limb
  • blood
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with CNBP: view

Orthologs for CNBP Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for CNBP Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia CNBP 34
  • 100 (a)
(Pan troglodytes)
Mammalia CNBP 34 33
  • 99.25 (n)
(Monodelphis domestica)
Mammalia CNBP 34
  • 99 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 97 (a)
(Canis familiaris)
Mammalia CNBP 34 33
  • 96.61 (n)
(Rattus norvegicus)
Mammalia Cnbp 33
  • 95.48 (n)
(Mus musculus)
Mammalia Cnbp 16 34 33
  • 93.73 (n)
(Gallus gallus)
Aves CNBP 34 33
  • 90.64 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.6124 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.985 33
(Danio rerio)
Actinopterygii cnbpa 34
  • 74 (a)
cnbpb 34 33
  • 69.79 (n)
wufe36b09 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10040 33
fruit fly
(Drosophila melanogaster)
Insecta CG3800 34
  • 41 (a)
(Caenorhabditis elegans)
Secernentea K08D12.3 34
  • 36 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GIS2 34 33
  • 55.56 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C02805g 33
  • 54.28 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR646W 33
  • 51.8 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU05800 33
  • 48.21 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10180 34
  • 31 (a)
Species where no ortholog for CNBP was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CNBP Gene

Gene Tree for CNBP (if available)
Gene Tree for CNBP (if available)
Evolutionary constrained regions (ECRs) for CNBP: view image

Paralogs for CNBP Gene

Paralogs for CNBP Gene

(2) SIMAP similar genes for CNBP Gene using alignment to 3 proteins:

  • B4DP17_HUMAN
genes like me logo Genes that share paralogs with CNBP: view

Variants for CNBP Gene

Sequence variations from dbSNP and Humsavar for CNBP Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000112184 -- 129,177,190(-) A/C intron_variant
rs1000122624 -- 129,167,417(-) T/A downstream_transcript_variant
rs1000242482 -- 129,183,533(-) C/G intron_variant
rs1000546342 -- 129,177,455(-) G/T intron_variant
rs1000887652 -- 129,182,244(-) T/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CNBP Gene

Variant ID Type Subtype PubMed ID
nsv591650 CNV loss 21841781

Variation tolerance for CNBP Gene

Residual Variation Intolerance Score: 57.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.31; 6.87% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CNBP Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CNBP Gene

Disorders for CNBP Gene

MalaCards: The human disease database

(12) MalaCards diseases for CNBP Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
myotonic dystrophy 2
  • dm2
myotonic dystrophy
  • myotonic dystrophy 1
myotonia congenita
  • congenital myotonia, autosomal dominant form
deafness, autosomal dominant 18
  • dfna18
- elite association - COSMIC cancer census association via MalaCards
Search CNBP in MalaCards View complete list of genes associated with diseases


  • Dystrophia myotonica 2 (DM2) [MIM:602668]: A multisystem disease characterized by the association of proximal muscle weakness with myotonia, cardiac manifestations and cataract. Additional features can include hyperhidrosis, testicular atrophy, insulin resistance and diabetes and central nervous system anomalies in rare cases. Note=The disease is caused by mutations affecting the gene represented in this entry. The causative mutation is a CCTG expansion (mean approximately 5000 repeats) located in intron 1 of the CNBP gene.

Additional Disease Information for CNBP

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CNBP: view

No data available for Genatlas for CNBP Gene

Publications for CNBP Gene

  1. Myotonic dystrophy type 2 caused by a CCTG expansion in intron 1 of ZNF9. (PMID: 11486088) Liquori CL … Ranum LP (Science (New York, N.Y.) 2001) 2 3 4 22 58
  2. Organization of the gene encoding cellular nucleic acid-binding protein. (PMID: 7590281) Flink IL … Morkin E (Gene 1995) 3 4 22 58
  3. Mapping of the gene for CNBP, a finger protein, to human chromosome 3q13.3-q24. (PMID: 2249857) Lusis AJ … Sparkes RS (Genomics 1990) 2 3 22 58
  4. Arginine methylation of the cellular nucleic acid binding protein does not affect its subcellular localization but impedes RNA binding. (PMID: 24726729) Wei HM … Li C (FEBS letters 2014) 3 4 58
  5. Colocalization of ribonuclear inclusions with muscle blind like-proteins in a family with myotonic dystrophy type 2 associated with a short CCTG expansion. (PMID: 18804219) Lucchiari S … Meola G (Journal of the neurological sciences 2008) 3 22 58

Products for CNBP Gene

Sources for CNBP Gene

Loading form....