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

    Gene ID: 7586, updated on 10-Dec-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (100015596..100045374)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (101255101..101284872)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Regulatory mechanism of ZNF139 in multi-drug resistance of gastric cancer cells. Li Y, et al. Mol Biol Rep, 2014 Jun. PMID 24515389
    2. ZNF139 promotes tumor metastasis by increasing migration and invasion in human gastric cancer cells. Li Y, et al. Neoplasma, 2014. PMID 24824930
    3. 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
    4. Comparative proteomics in gastric cancer cell line BGC823 after ZNF139 gene inhibited with RNA interference. Fan LQ, et al. Hepatogastroenterology, 2014 Sep. PMID 25436386
    5. 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

    See all (56) 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)

    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_2024_08

    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

    Gene LinkOut

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