Human Gene ZKSCAN1 (uc003usj.3)
  Description: Homo sapiens zinc finger with KRAB and SCAN domains 1 (ZKSCAN1), mRNA.
RefSeq Summary (NM_003439): This gene encodes a member of the Kruppel C2H2-type zinc-finger family of proteins. This encoded protein may function as a transcription factor that regulates the expression of GABA type-A receptors in the brain. Transcripts from this gene have been shown to form stable and abundant circular RNAs. Elevated expression of this gene has been observed in gastric cancer and the encoded protein may stimulate migration and invasion of human gastric cancer cells. [provided by RefSeq, Oct 2016].
Transcript (Including UTRs)
   Position: hg19 chr7:99,613,219-99,622,583 Size: 9,365 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr7:99,621,133-99,621,953 Size: 821 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr7:99,613,219-99,622,583)mRNA (may differ from genome)Protein (199 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: SubName: Full=Zinc finger protein with KRAB and SCAN domains 1; Flags: Fragment;
SIMILARITY: Contains 1 SCAN box domain.
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  MalaCards Disease Associations
  MalaCards Gene Search: ZKSCAN1
Diseases sorted by gene-association score: split hand-foot malformation 1 (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • C029497 2,3-bis(3'-hydroxybenzyl)butyrolactone
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • C012796 2-butenal
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D000393 Air Pollutants
  • D001564 Benzo(a)pyrene
  • D019327 Copper Sulfate
  • D003375 Coumestrol
  • D004958 Estradiol
  • D058185 Magnetite Nanoparticles
          more ... click here to view the complete list

+  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: 20.49 RPKM in Liver
Total median expression: 543.84 RPKM

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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -73.50222-0.331 Picture PostScript Text
3' UTR -199.40630-0.317 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
IPR008916 - Retrov_capsid_C
IPR003309 - Tscrpt_reg_SCAN

Pfam Domains:
PF02023 - SCAN domain

ModBase Predicted Comparative 3D Structure on C9JRM9
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 Protein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003700 transcription factor activity, sequence-specific DNA binding

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

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  AL833578 - Homo sapiens mRNA; cDNA DKFZp686I0856 (from clone DKFZp686I0856).
AF454940 - Homo sapiens hypothetical protein mRNA, complete cds.
AY260738 - Homo sapiens truncated zinc finger protein 36 mRNA, complete cds.
AK054676 - Homo sapiens cDNA FLJ30114 fis, clone BNGH42000532, highly similar to Zinc finger with KRAB and SCAN domain-containing protein 1.
BC022378 - Homo sapiens zinc finger with KRAB and SCAN domains 1, mRNA (cDNA clone MGC:23963 IMAGE:4685873), complete cds.
BX640646 - Homo sapiens mRNA; cDNA DKFZp686L21110 (from clone DKFZp686L21110); complete cds.
AK091471 - Homo sapiens cDNA FLJ34152 fis, clone FCBBF3012901, highly similar to Zinc finger with KRAB and SCAN domain-containing protein 1.
AX747005 - Sequence 530 from Patent EP1308459.
AK074116 - Homo sapiens mRNA for FLJ00187 protein.
JD123865 - Sequence 104889 from Patent EP1572962.
BC112224 - Homo sapiens zinc finger with KRAB and SCAN domains 1, mRNA (cDNA clone MGC:138429 IMAGE:8327692), complete cds.
BC113697 - Homo sapiens zinc finger with KRAB and SCAN domains 1, mRNA (cDNA clone MGC:142257 IMAGE:8322749), complete cds.
KJ905952 - Synthetic construct Homo sapiens clone ccsbBroadEn_15622 ZKSCAN1 gene, encodes complete protein.
CU692588 - Synthetic construct Homo sapiens gateway clone IMAGE:100022259 5' read ZKSCAN1 mRNA.
EU446909 - Synthetic construct Homo sapiens clone IMAGE:100070027; IMAGE:100012118; FLH258279.01L zinc finger with KRAB and SCAN domains 1 (ZKSCAN1) gene, encodes complete protein.
HQ258578 - Synthetic construct Homo sapiens clone IMAGE:100073104 zinc finger with KRAB and SCAN domains 1 (ZKSCAN1) gene, encodes complete protein.
KJ892405 - Synthetic construct Homo sapiens clone ccsbBroadEn_01799 ZKSCAN1 gene, encodes complete protein.
AB384421 - Synthetic construct DNA, clone: pF1KSDF0187, Homo sapiens ZKSCAN1 gene for zinc finger protein with KRAB and SCAN domains 1, complete cds, without stop codon, in Flexi system.
JD452377 - Sequence 433401 from Patent EP1572962.
JD144556 - Sequence 125580 from Patent EP1572962.
JD496972 - Sequence 477996 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: AY260738, C9JRM9, C9JRM9_HUMAN, NM_003439, NP_003430
UCSC ID: uc003usj.3
RefSeq Accession: NM_003439
Protein: C9JRM9

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: AY260738.1
exon count: 3CDS single in 3' UTR: no RNA size: 1449
ORF size: 600CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1398.50frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 653# strange splices: 0
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.