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    ZNF189 zinc finger protein 189 [ Homo sapiens (human) ]

    Gene ID: 7743, updated on 5-Mar-2024

    Summary

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    Official Symbol
    ZNF189provided by HGNC
    Official Full Name
    zinc finger protein 189provided by HGNC
    Primary source
    HGNC:HGNC:12980
    See related
    Ensembl:ENSG00000136870 MIM:603132; AllianceGenome:HGNC:12980
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Kruppel-like zinc finger proteins such as ZNF189 contain a conserved stretch of 7 amino acids that connects a variable number of DNA-binding zinc finger repeats of the cys(2)his(2) (C2H2) type (summarized by Odeberg et al., 1998 [PubMed 9653648]). Approximately 30% of human Kruppel-like zinc finger proteins contain an N-terminal Kruppel-associated box (KRAB) domain. The KRAB domain consists of approximately 75 amino acids that may be subdivided into an A box, which is present in every KRAB domain and is essential for transcriptional repression, and a B box, which is not always present.[supplied by OMIM, May 2010]
    Expression
    Ubiquitous expression in gall bladder (RPKM 12.4), fat (RPKM 10.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    9q31.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (101398851..101410654)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (113570826..113582630)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (104161133..104172936)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene bile acid-CoA:amino acid N-acyltransferase Neighboring gene forty-two-three domain containing 1 pseudogene 1 Neighboring gene mitochondrial ribosomal protein L50 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:104160013-104160542 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:104160543-104161071 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:104169926-104171125 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28725 Neighboring gene aldolase, fructose-bisphosphate B Neighboring gene uncharacterized LOC105376184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20141 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20142

    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. Context-dependent Taq-polymerase-mediated nucleotide alterations, as revealed by direct sequencing of the ZNF189 gene: implications for mutation detection. Odeberg J, et al. Gene, 1999 Jul 22. PMID 10415338
    2. Cloning and characterization of ZNF189, a novel human Krüppel-like zinc finger gene localized to chromosome 9q22-q31. Odeberg J, et al. Genomics, 1998 Jun 1. PMID 9653648
    3. Protein interaction discovery using parallel analysis of translated ORFs (PLATO). Zhu J, et al. Nat Biotechnol, 2013 Apr. PMID 23503679, Free PMC Article
    4. Charting the molecular links between driver and susceptibility genes in colorectal cancer. Arroyo R, et al. Biochem Biophys Res Commun, 2014 Mar 21. PMID 24412244
    5. Image-based genome-wide siRNA screen identifies selective autophagy factors. Orvedahl A, et al. Nature, 2011 Dec 1. PMID 22020285, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Maternal genes FLNB, HIC1 and ZNF189 were strongly associated with risk of clefting.
      Title: Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia.
    Submit: New GeneRIF Correction

    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

    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
    		  
    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
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein 189

    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.

    mRNA and Protein(s)

    1. NM_001278231.2 → NP_001265160.1  zinc finger protein 189 isoform 3

      See identical proteins and their annotated locations for NP_001265160.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AK290163, AL353621, BC092425, BC126120
      Consensus CDS
      CCDS65096.1
      UniProtKB/Swiss-Prot
      O75820
      Related
      ENSP00000363995.3, ENST00000374861.7
      Conserved Domains (4) summary
      COG5048
      Location:124 → 510
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:332 → 352
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:10 → 40
      KRAB; KRAB box
      pfam13465
      Location:541 → 565
      zf-H2C2_2; Zinc-finger double domain

    2. NM_001278232.2 → NP_001265161.1  zinc finger protein 189 isoform 4

      See identical proteins and their annotated locations for NP_001265161.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AK290163, AL353621, BC092425, BC143877
      UniProtKB/TrEMBL
      B7ZLK9
      Conserved Domains (4) summary
      COG5048
      Location:123 → 509
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:331 → 351
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:12 → 39
      KRAB; KRAB box
      pfam13465
      Location:540 → 564
      zf-H2C2_2; Zinc-finger double domain

    3. NM_001278240.2 → NP_001265169.1  zinc finger protein 189 isoform 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) uses an alternate splice junction at the 5' end of an exon and contains an alternate 3' exon compared to variant 1. The resulting isoform (5) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform 1.
      Source sequence(s)
      AK290163, AL353621, BC092425, BX420042
      Consensus CDS
      CCDS75867.1
      UniProtKB/TrEMBL
      A0A087X0K2
      Related
      ENSP00000483461.1, ENST00000615466.1
      Conserved Domains (1) summary
      pfam01352
      Location:10 → 40
      KRAB; KRAB box

    4. NM_003452.4 → NP_003443.2  zinc finger protein 189 isoform 1

      See identical proteins and their annotated locations for NP_003443.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AK290163, AL353621, BC092425
      Consensus CDS
      CCDS6754.1
      UniProtKB/Swiss-Prot
      O75802, O75820, Q5T7D7, Q5T7D8, Q5T7D9, Q9UBL4, Q9UPE9, Q9UPF0, Q9UPF1
      Related
      ENSP00000342019.2, ENST00000339664.7
      Conserved Domains (4) summary
      COG5048
      Location:138 → 524
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:346 → 366
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:13 → 54
      KRAB; KRAB box
      pfam13465
      Location:555 → 579
      zf-H2C2_2; Zinc-finger double domain

    5. NM_197977.3 → NP_932094.1  zinc finger protein 189 isoform 2

      See identical proteins and their annotated locations for NP_932094.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate 5' exon and uses an alternate splice junction at the 5' end of an exon compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AK290163, AL353621, BC092425
      Consensus CDS
      CCDS6755.1
      UniProtKB/Swiss-Prot
      O75820
      Related
      ENSP00000259395.4, ENST00000259395.4
      Conserved Domains (3) summary
      COG5048
      Location:96 → 482
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:304 → 324
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:513 → 537
      zf-H2C2_2; Zinc-finger double domain

    RNA

    1. NR_103480.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) uses an alternate splice junction at the 5' end of an exon and contains an alternate 3' exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK290163, AL353621, BC092425, DB077406

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      101398851..101410654
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006717280.5 → XP_006717343.1  zinc finger protein 189 isoform X1

      See identical proteins and their annotated locations for XP_006717343.1

      UniProtKB/Swiss-Prot
      O75820
      Conserved Domains (3) summary
      COG5048
      Location:96 → 482
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:304 → 324
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:513 → 537
      zf-H2C2_2; Zinc-finger double domain

    2. XM_011518998.4 → XP_011517300.1  zinc finger protein 189 isoform X1

      See identical proteins and their annotated locations for XP_011517300.1

      UniProtKB/Swiss-Prot
      O75820
      Conserved Domains (3) summary
      COG5048
      Location:96 → 482
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:304 → 324
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:513 → 537
      zf-H2C2_2; Zinc-finger double domain

    3. XM_011518999.4 → XP_011517301.1  zinc finger protein 189 isoform X2

      See identical proteins and their annotated locations for XP_011517301.1

      Conserved Domains (3) summary
      COG5048
      Location:87 → 473
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:295 → 315
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:504 → 528
      zf-H2C2_2; Zinc-finger double domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      113570826..113582630
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363764.1 → XP_054219739.1  zinc finger protein 189 isoform X1

    2. XM_054363765.1 → XP_054219740.1  zinc finger protein 189 isoform X1

    3. XM_054363762.1 → XP_054219737.1  zinc finger protein 189 isoform X1

    4. XM_054363767.1 → XP_054219742.1  zinc finger protein 189 isoform X1

    5. XM_054363763.1 → XP_054219738.1  zinc finger protein 189 isoform X1

    6. XM_054363766.1 → XP_054219741.1  zinc finger protein 189 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75820.2 GenPept UniProtKB/Swiss-Prot:O75820

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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