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

    Gene ID: 7586, updated on 9-Dec-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    NEW Try the new Transcript table

    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_001287054.3NP_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:16126
      SCAN; leucine rich region
      COG5048
      Location:320501
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:399419
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:341363
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:191226
      KRAB; KRAB box
      pfam02023
      Location:1693
      SCAN; SCAN domain
      pfam13465
      Location:439464
      zf-H2C2_2; Zinc-finger double domain
    2. NM_001287055.3NP_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:143324
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:222242
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:164186
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:1449
      KRAB; KRAB box
      pfam13465
      Location:262287
      zf-H2C2_2; Zinc-finger double domain
    3. NM_001346579.2NP_001333508.1  zinc finger protein with KRAB and SCAN domains 1 isoform d

      Status: REVIEWED

      Source sequence(s)
      AC004522, AC093619
    4. NM_001346580.2NP_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_001346581.2NP_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:52162
      SCAN; leucine rich region
      cd07765
      Location:227262
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
      COG5048
      Location:356537
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:435455
      ZF_C2H2; C2H2 Zn finger [structural motif]
    6. NM_003439.4NP_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:52162
      SCAN; leucine rich region
      cd07765
      Location:227262
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
      COG5048
      Location:356537
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:435455
      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_047420804.1XP_047276760.1  zinc finger protein with KRAB and SCAN domains 1 isoform X2

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

    3. XM_047420803.1XP_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_054358949.1XP_054214924.1  zinc finger protein with KRAB and SCAN domains 1 isoform X2

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

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