Human Gene CNBP (ENST00000422453.7) from GENCODE V44
  Description: Homo sapiens CCHC-type zinc finger nucleic acid binding protein (CNBP), transcript variant 3, mRNA. (from RefSeq NM_003418)
RefSeq Summary (NM_003418): 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].
Gencode Transcript: ENST00000422453.7
Gencode Gene: ENSG00000169714.17
Transcript (Including UTRs)
   Position: hg38 chr3:129,167,827-129,183,896 Size: 16,070 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg38 chr3:129,170,453-129,171,757 Size: 1,305 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:129,167,827-129,183,896)mRNA (may differ from genome)Protein (177 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCLynxMalacardsMGIneXtProtOMIM
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CNBP_HUMAN
DESCRIPTION: RecName: Full=Cellular nucleic acid-binding protein; Short=CNBP; AltName: Full=Zinc finger protein 9;
FUNCTION: Single stranded DNA-binding protein, with specificity to the sterol regulatory element (SRE). Involved in sterol-mediated repression.
SUBCELLULAR LOCATION: Cytoplasm (By similarity). Endoplasmic reticulum (By similarity).
TISSUE SPECIFICITY: Present in all tissues examined.
DISEASE: Defects in CNBP are the cause of dystrophia myotonica type 2 (DM2) [MIM:602668]; also known as proximal myotonic myopathy (PROMM). 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 causative mutation is a CCTG expansion (mean approximately 5000 repeats) located in intron 1 of the CNBP gene.
SIMILARITY: Contains 7 CCHC-type zinc fingers.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CNBP";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: CNBP
Diseases sorted by gene-association score: myotonic dystrophy 2* (1389), myotonic dystrophy (15), myotonia congenita (13), myotonia (12), deafness, autosomal dominant 18 (12), myotonic dystrophy 1 (10), myotonic disease (10), immature cataract (9), tinea unguium (8), deafness, autosomal recessive 15 (7), spinocerebellar ataxia 10 (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D010634 Phenobarbital
  • C517041 (4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)
  • C049325 1,2-dithiol-3-thione
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C049584 2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine
  • D015127 9,10-Dimethyl-1,2-benzanthracene
  • D000643 Ammonium Chloride
  • D001564 Benzo(a)pyrene
  • D020148 Butyric Acid
  • D002251 Carbon Tetrachloride
          more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 396.10 RPKM in Muscle - Skeletal
Total median expression: 9095.00 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -50.10135-0.371 Picture PostScript Text
3' UTR -728.502626-0.277 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001878 - Znf_CCHC

Pfam Domains:
PF00098 - Zinc knuckle

ModBase Predicted Comparative 3D Structure on P62633
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
MGIRGD   SGD
Protein SequenceProtein Sequence   Protein Sequence
AlignmentAlignment   Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003697 single-stranded DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003723 RNA binding
GO:0003727 single-stranded RNA binding
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0046872 metal ion binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006695 cholesterol biosynthetic process
GO:0008284 positive regulation of cell proliferation
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK021693 - Homo sapiens cDNA FLJ11631 fis, clone HEMBA1004267.
JD225394 - Sequence 206418 from Patent EP1572962.
JD345722 - Sequence 326746 from Patent EP1572962.
JD119918 - Sequence 100942 from Patent EP1572962.
JD081611 - Sequence 62635 from Patent EP1572962.
JD181043 - Sequence 162067 from Patent EP1572962.
JD414834 - Sequence 395858 from Patent EP1572962.
JD081610 - Sequence 62634 from Patent EP1572962.
JD311809 - Sequence 292833 from Patent EP1572962.
JD476733 - Sequence 457757 from Patent EP1572962.
JD070581 - Sequence 51605 from Patent EP1572962.
JD422137 - Sequence 403161 from Patent EP1572962.
BC014911 - Homo sapiens CCHC-type zinc finger, nucleic acid binding protein, mRNA (cDNA clone MGC:17190 IMAGE:3906502), complete cds.
DQ091187 - Homo sapiens cellular nucleic acid binding protein alpha variant 1 (CNBP) mRNA, complete cds, alternatively spliced.
DQ092366 - Homo sapiens cellular nucleic acid binding protein beta variant 1 (ZNF9) mRNA, complete cds, alternatively spliced.
DQ092367 - Homo sapiens cellular nucleic acid binding protein beta variant 2 (ZNF9) mRNA, complete cds, alternatively spliced.
AK298154 - Homo sapiens cDNA FLJ61146 complete cds, highly similar to Cellular nucleic acid-binding protein.
AK054592 - Homo sapiens cDNA FLJ30030 fis, clone 3NB692001339, highly similar to CELLULAR NUCLEIC ACID BINDING PROTEIN.
BC000288 - Homo sapiens CCHC-type zinc finger, nucleic acid binding protein, mRNA (cDNA clone MGC:8324 IMAGE:2819226), complete cds.
BC093058 - Homo sapiens CCHC-type zinc finger, nucleic acid binding protein, mRNA (cDNA clone MGC:111143 IMAGE:30721134), complete cds.
AY436367 - Homo sapiens cellular nucleic acid binding protein mRNA, partial cds.
M28372 - Homo sapiens sterol regulatory element-binding protein (CNBP) mRNA, complete cds.
JD378956 - Sequence 359980 from Patent EP1572962.
JD560180 - Sequence 541204 from Patent EP1572962.
JD546080 - Sequence 527104 from Patent EP1572962.
JD268098 - Sequence 249122 from Patent EP1572962.
AK292119 - Homo sapiens cDNA FLJ77718 complete cds.
JD284112 - Sequence 265136 from Patent EP1572962.
JD300294 - Sequence 281318 from Patent EP1572962.
JD298023 - Sequence 279047 from Patent EP1572962.
AK314380 - Homo sapiens cDNA, FLJ95153, Homo sapiens zinc finger protein 9 (a cellular retroviral nucleicacid binding protein) (ZNF9), mRNA.
KJ892400 - Synthetic construct Homo sapiens clone ccsbBroadEn_01794 CNBP gene, encodes complete protein.
BT019613 - Homo sapiens zinc finger protein 9 (a cellular retroviral nucleic acid binding protein) mRNA, complete cds.
CU674132 - Synthetic construct Homo sapiens gateway clone IMAGE:100017958 5' read CNBP mRNA.
KJ897754 - Synthetic construct Homo sapiens clone ccsbBroadEn_07148 CNBP gene, encodes complete protein.
KU178397 - Homo sapiens CCHC-type zinc finger nucleic acid binding protein isoform 1 (CNBP) mRNA, partial cds.
KU178398 - Homo sapiens CCHC-type zinc finger nucleic acid binding protein isoform 2 (CNBP) mRNA, complete cds, alternatively spliced.
KU178399 - Homo sapiens CCHC-type zinc finger nucleic acid binding protein isoform 3 (CNBP) mRNA, partial cds.
AB463471 - Synthetic construct DNA, clone: pF1KB7539, Homo sapiens CNBP gene for CCHC-type zinc finger, nucleic acid binding protein, without stop codon, in Flexi system.
JD059795 - Sequence 40819 from Patent EP1572962.
JD174494 - Sequence 155518 from Patent EP1572962.
JD265377 - Sequence 246401 from Patent EP1572962.
AY624556 - Homo sapiens ubiquitin-specific protease USP6 (ZNF9/USP6 fusion) mRNA, partial cds.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RAV9, CNBP_HUMAN, D3DNB9, D3DNC0, D3DNC1, ENST00000422453.1, ENST00000422453.2, ENST00000422453.3, ENST00000422453.4, ENST00000422453.5, ENST00000422453.6, NM_003418, P20694, P62633, Q4JGY0, Q5QJR0, Q5U0E9, Q6PJI7, Q96NV3, RNF163, uc003elq.1, uc003elq.2, uc003elq.3, uc003elq.4, uc003elq.5, uc003elq.6, ZNF9
UCSC ID: ENST00000422453.7
RefSeq Accession: NM_003418
Protein: P62633 (aka CNBP_HUMAN)
CCDS: CCDS3056.1, CCDS46906.1, CCDS46907.1, CCDS46908.1, CCDS54637.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CNBP:
myotonic-d2 (Myotonic Dystrophy Type 2)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.