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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
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Genomic context

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See ZNF189 in Genome Data Viewer
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

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