Human Gene ZNF688 (ENST00000223459.11_7) from GENCODE V47lift37
  Description: zinc finger protein 688, transcript variant 1 (from RefSeq NM_145271.4)
Gencode Transcript: ENST00000223459.11_7
Gencode Gene: ENSG00000229809.9_11
Transcript (Including UTRs)
   Position: hg19 chr16:30,581,047-30,583,035 Size: 1,989 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr16:30,581,237-30,582,950 Size: 1,714 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:30,581,047-30,583,035)mRNA (may differ from genome)Protein (276 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ZN688_HUMAN
DESCRIPTION: RecName: Full=Zinc finger protein 688;
FUNCTION: May be involved in transcriptional regulation.
SUBCELLULAR LOCATION: Nucleus (Probable).
SIMILARITY: Belongs to the krueppel C2H2-type zinc-finger protein family.
SIMILARITY: Contains 2 C2H2-type zinc fingers.
SIMILARITY: Contains 1 KRAB domain.
SEQUENCE CAUTION: Sequence=AAC31673.1; Type=Erroneous gene model prediction; Note=The predicted gene has been split into 2 genes: ZNF688 and ZNF785;

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 17.83 RPKM in Testis
Total median expression: 247.89 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 -42.4085-0.499 Picture PostScript Text
3' UTR -57.70190-0.304 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
IPR001909 - Krueppel-associated_box
IPR007087 - Znf_C2H2
IPR015880 - Znf_C2H2-like
IPR013087 - Znf_C2H2/integrase_DNA-bd

Pfam Domains:
PF00096 - Zinc finger, C2H2 type
PF01352 - KRAB box

SCOP Domains:
109640 - KRAB domain (Kruppel-associated box)
57667 - beta-beta-alpha zinc fingers
57802 - Rubredoxin-like

ModBase Predicted Comparative 3D Structure on P0C7X2
FrontTopSide
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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003674 molecular_function
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0046872 metal ion binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0008150 biological_process

Cellular Component:
GO:0005575 cellular_component
GO:0005622 intracellular
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  BC018997 - Homo sapiens zinc finger protein 688, mRNA (cDNA clone MGC:20507 IMAGE:4336167), complete cds.
JD507252 - Sequence 488276 from Patent EP1572962.
AF085979 - Homo sapiens full length insert cDNA clone YT88C07.
AK122680 - Homo sapiens cDNA FLJ16133 fis, clone BRACE2043774, highly similar to Zinc finger protein 688.
JD214022 - Sequence 195046 from Patent EP1572962.
JD273917 - Sequence 254941 from Patent EP1572962.
KJ905001 - Synthetic construct Homo sapiens clone ccsbBroadEn_14395 ZNF688-like gene, encodes complete protein.
EU446577 - Synthetic construct Homo sapiens clone IMAGE:100069913; IMAGE:100011786; FLH257058.01L zinc finger protein 688 (ZNF688) gene, encodes complete protein.
KU178870 - Homo sapiens zinc finger protein 688 isoform 1 (ZNF688) mRNA, partial cds.
KU178871 - Homo sapiens zinc finger protein 688 isoform 2 (ZNF688) mRNA, complete cds, alternatively spliced.
KU178872 - Homo sapiens zinc finger protein 688 isoform 4 (ZNF688) mRNA, partial cds, alternatively spliced.
JC506937 - Sequence 305 from Patent EP2733220.
JC738049 - Sequence 305 from Patent WO2014075939.
JC506785 - Sequence 153 from Patent EP2733220.
JC737897 - Sequence 153 from Patent WO2014075939.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P0C7X2 (Reactome details) participates in the following event(s):

R-HSA-975040 KRAB-ZNF / KAP Interaction
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: A8MV39, B3KV51, ENST00000223459.1, ENST00000223459.10, ENST00000223459.2, ENST00000223459.3, ENST00000223459.4, ENST00000223459.5, ENST00000223459.6, ENST00000223459.7, ENST00000223459.8, ENST00000223459.9, NM_145271, O75701, P0C7X2, Q8IW91, Q8WV14, Q96MN0, uc317dhn.1, uc317dhn.2, ZN688_HUMAN
UCSC ID: ENST00000223459.11_7
RefSeq Accession: NM_145271.4
Protein: P0C7X2 (aka ZN688_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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