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ZKSCAN1 zinc finger with KRAB and SCAN domains 1 [ Homo sapiens (human) ]

Gene ID: 7586, updated on 5-Mar-2024

Summary

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Official Symbol
ZKSCAN1provided by HGNC
Official Full Name
zinc finger with KRAB and SCAN domains 1provided by HGNC
Primary source
HGNC:HGNC:13101
See related
Ensembl:ENSG00000106261 MIM:601260; AllianceGenome:HGNC:13101
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
KOX18; ZNF36; PHZ-37; ZNF139; ZSCAN33
Summary
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]
Expression
Ubiquitous expression in stomach (RPKM 13.7), skin (RPKM 12.9) and 25 other tissues See more
Orthologs
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Genomic context

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See ZKSCAN1 in Genome Data Viewer
Location:
7q22.1
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (100015596..100045374)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (101255101..101284872)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (99613219..99642997)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene gap junction protein gamma 3 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:99591699-99592200 Neighboring gene uncharacterized LOC105375423 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26331 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26332 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:99601306-99601806 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99604826-99605326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99605327-99605827 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99607545-99608044 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99634953-99635454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99635455-99635954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99647299-99647918 Neighboring gene zinc finger and SCAN domain containing 21 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26333 Neighboring gene Sharpr-MPRA regulatory region 7718 Neighboring gene zinc finger protein 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26334 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99679591-99680572 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:99684712-99685405 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18414 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:99686990-99688189 Neighboring gene Sharpr-MPRA regulatory region 1952 Neighboring gene COP9 signalosome subunit 6

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. ZKSCAN1 gene and its related circular RNA (circZKSCAN1) both inhibit hepatocellular carcinoma cell growth, migration, and invasion but through different signaling pathways. Yao Z, et al. Mol Oncol, 2017 Apr. PMID 28211215, Free PMC Article
  2. Effects of ZNF139 on gastric cancer cells and mice with gastric tumors. Nie HF, et al. Oncol Lett, 2016 Oct. PMID 27698826, Free PMC Article
  3. Silencing of ZNF139-siRNA induces apoptosis in human gastric cancer cell line BGC823. Fan L, et al. Int J Clin Exp Pathol, 2015. PMID 26722429, Free PMC Article
  4. Zinc finger protein 139 expression in gastric cancer and its clinical significance. Li Y, et al. World J Gastroenterol, 2014 Dec 28. PMID 25561801, Free PMC Article
  5. Comparative proteomics in gastric cancer cell line BGC823 after ZNF139 gene inhibited with RNA interference. Fan LQ, et al. Hepatogastroenterology, 2014 Sep. PMID 25436386

See all (53) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A novel polypeptide encoded by the circular RNA ZKSCAN1 suppresses HCC via degradation of mTOR.
    Title: A novel polypeptide encoded by the circular RNA ZKSCAN1 suppresses HCC via degradation of mTOR.
  2. CircZKSCAN1 Suppresses Hepatocellular Carcinoma Tumorigenesis by Regulating miR-873-5p/Downregulation of Deleted in Liver Cancer 1.
    Title: CircZKSCAN1 Suppresses Hepatocellular Carcinoma Tumorigenesis by Regulating miR-873-5p/Downregulation of Deleted in Liver Cancer 1.
  3. The results revealed that ZKSCAN1 circular RNA exerted its inhibitive role by competitively binding FMRP, therefore, block the binding between FMRP and beta-catenin-binding protein-cell cycle and apoptosis regulator 1 (CCAR1) mRNA, and subsequently restrain the transcriptional activity of Wnt signaling.
    Title: Circular RNAs negatively regulate cancer stem cells by physically binding FMRP against CCAR1 complex in hepatocellular carcinoma.
  4. These results reveal that Circ-ZKSCAN1 acts as a tumor suppressor via a novel circ-ZKSCAN1/miR-1178-3p/p21 axis, which have the important role in the proliferation, migration and invasion ablitities of BCa cells and provide a novel perspective on circRNAs in BCa progression.
    Title: Circular RNA circ-ZKSCAN1 inhibits bladder cancer progression through miR-1178-3p/p21 axis and acts as a prognostic factor of recurrence.
  5. Dual luciferase activity assay demonstrated that ZNF139 inhibited transcriptional activities of miR-185's promoter in cells transfected with the reporter plasmid encompassing the upstream promoter region of miR-185 along with pcDNA-ZNF139. Our data reveal that ZNF139 might promote MDR gene MDR1/P-gp, MRP-1 and Bcl-2 by prohibiting miR-185
    Title: ZNF139 increases multidrug resistance in gastric cancer cells by inhibiting miR-185.
  6. High ZNF139 expression is associated with low chemosensitivity in gastric cancer.
    Title: miR‑195‑5p regulates multi‑drug resistance of gastric cancer cells via targeting ZNF139.
  7. ZKSCAN1, a zinc finger family gene, is expressed in both linear and circular (circZKSCAN1) forms of RNA in human hepatocellular carcinoma (HCC) tissues and cell lines.
    Title: ZKSCAN1 gene and its related circular RNA (circZKSCAN1) both inhibit hepatocellular carcinoma cell growth, migration, and invasion but through different signaling pathways.
  8. ZNF139 functions to promote apoptosis resistance of gastric cancer cells by regulating some apoptosis related genes.
    Title: Silencing of ZNF139-siRNA induces apoptosis in human gastric cancer cell line BGC823.
  9. ZNF139 expression is related to clinicopathologic characteristics and prognosis of gastric cancer. It is overexpressed and involved in apoptosis in GC tissues by regulating caspase-3.
    Title: Zinc finger protein 139 expression in gastric cancer and its clinical significance.
  10. ZNF139 was involved in GC MDR by promoting expressions of MDR1/P-gp, MRP1 and Bcl-2 and inhibiting Bax simultaneously.
    Title: Regulatory mechanism of ZNF139 in multi-drug resistance of gastric cancer cells.
Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC138429

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
zinc finger protein with KRAB and SCAN domains 1
Names
zinc finger protein 139
zinc finger protein 36 (KOX 18)

NCBI Reference Sequences (RefSeq)

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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_051950.1 RefSeqGene

    Range
    5045..31138
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001287054.3 → NP_001273983.1  zinc finger protein with KRAB and SCAN domains 1 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in its 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a. Both variants 2 and 5 encode isoform b.
    Source sequence(s)
    AA873735, AC004522, AC093619, AK054676, HY140376
    Consensus CDS
    CCDS69349.1
    UniProtKB/TrEMBL
    E9PC66
    Related
    ENSP00000409172.1, ENST00000426572.5
    Conserved Domains (7) summary
    smart00431
    Location:16 → 126
    SCAN; leucine rich region
    COG5048
    Location:320 → 501
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:399 → 419
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:341 → 363
    zf-C2H2; Zinc finger, C2H2 type
    pfam01352
    Location:191 → 226
    KRAB; KRAB box
    pfam02023
    Location:16 → 93
    SCAN; SCAN domain
    pfam13465
    Location:439 → 464
    zf-H2C2_2; Zinc-finger double domain

  2. NM_001287055.3 → NP_001273984.1  zinc finger protein with KRAB and SCAN domains 1 isoform c

    See identical proteins and their annotated locations for NP_001273984.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in its 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AA873735, AC093619, AK091471, HY140376
    Consensus CDS
    CCDS75640.1
    UniProtKB/TrEMBL
    B3KRF7
    Related
    ENSP00000443508.1, ENST00000535170.5
    Conserved Domains (5) summary
    COG5048
    Location:143 → 324
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:222 → 242
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:164 → 186
    zf-C2H2; Zinc finger, C2H2 type
    pfam01352
    Location:14 → 49
    KRAB; KRAB box
    pfam13465
    Location:262 → 287
    zf-H2C2_2; Zinc-finger double domain

  3. NM_001346579.2 → NP_001333508.1  zinc finger protein with KRAB and SCAN domains 1 isoform d

    Status: REVIEWED

    Source sequence(s)
    AC004522, AC093619

  4. NM_001346580.2 → NP_001333509.1  zinc finger protein with KRAB and SCAN domains 1 isoform b

    Status: REVIEWED

    Source sequence(s)
    AC004522, AC093619, CB250414
    Consensus CDS
    CCDS69349.1
    UniProtKB/TrEMBL
    E9PC66
    Related
    ENSP00000480305.1, ENST00000620510.1

  5. NM_001346581.2 → NP_001333510.1  zinc finger protein with KRAB and SCAN domains 1 isoform a

    Status: REVIEWED

    Source sequence(s)
    AC004522, AC093619, CB250414
    Consensus CDS
    CCDS34698.1
    UniProtKB/Swiss-Prot
    A4D294, P17029, P52745, Q2M1U1, Q8TBW5, Q8TEK7
    Conserved Domains (4) summary
    smart00431
    Location:52 → 162
    SCAN; leucine rich region
    cd07765
    Location:227 → 262
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
    COG5048
    Location:356 → 537
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:435 → 455
    ZF_C2H2; C2H2 Zn finger [structural motif]

  6. NM_003439.4 → NP_003430.1  zinc finger protein with KRAB and SCAN domains 1 isoform a

    See identical proteins and their annotated locations for NP_003430.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a). Both variants 1 and 6 encode isoform a.
    Source sequence(s)
    AA873735, AC093619, AK074116, HY140376
    Consensus CDS
    CCDS34698.1
    UniProtKB/Swiss-Prot
    A4D294, P17029, P52745, Q2M1U1, Q8TBW5, Q8TEK7
    Related
    ENSP00000323148.6, ENST00000324306.11
    Conserved Domains (4) summary
    smart00431
    Location:52 → 162
    SCAN; leucine rich region
    cd07765
    Location:227 → 262
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
    COG5048
    Location:356 → 537
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:435 → 455
    ZF_C2H2; C2H2 Zn finger [structural motif]

RNA

  1. NR_144477.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC004522, AC093619, CB250414

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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    100015596..100045374
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047420804.1 → XP_047276760.1  zinc finger protein with KRAB and SCAN domains 1 isoform X2

  2. XM_047420805.1 → XP_047276761.1  zinc finger protein with KRAB and SCAN domains 1 isoform X3

  3. XM_047420803.1 → XP_047276759.1  zinc finger protein with KRAB and SCAN domains 1 isoform X1

    UniProtKB/Swiss-Prot
    A4D294, P17029, P52745, Q2M1U1, Q8TBW5, Q8TEK7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    101255101..101284872
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054358949.1 → XP_054214924.1  zinc finger protein with KRAB and SCAN domains 1 isoform X2

  2. XM_054358948.1 → XP_054214923.1  zinc finger protein with KRAB and SCAN domains 1 isoform X1

    UniProtKB/Swiss-Prot
    A4D294, P17029, P52745, Q2M1U1, Q8TBW5, Q8TEK7
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P17029.3 GenPept UniProtKB/Swiss-Prot:P17029

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