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ZNF439 zinc finger protein 439 [ Homo sapiens (human) ]

Gene ID: 90594, updated on 11-Apr-2024

Summary

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Official Symbol
ZNF439provided by HGNC
Official Full Name
zinc finger protein 439provided by HGNC
Primary source
HGNC:HGNC:20873
See related
Ensembl:ENSG00000171291 AllianceGenome:HGNC:20873
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
Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in lymph node (RPKM 4.2), skin (RPKM 4.0) and 25 other tissues See more
Orthologs
all
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Genomic context

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Location:
19p13.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (11848726..11869486)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (11976933..11997694)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (11959541..11980301)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10134 Neighboring gene zinc finger protein 440 Neighboring gene vomeronasal 2 receptor 13 pseudogene Neighboring gene Sharpr-MPRA regulatory region 10901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14036 Neighboring gene vomeronasal 2 receptor 14 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14037 Neighboring gene zinc finger protein 69 Neighboring gene zinc finger protein 440-like

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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GeneRIFs: Gene References Into Functions

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

  • DKFZp571K0837

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 transcription 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
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 439

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_001348718.2 → NP_001335647.1  zinc finger protein 439 isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AC008543, AC020951
    Conserved Domains (3) summary
    COG5048
    Location:321 → 492
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:392 → 412
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:26 → 67
    KRAB; KRAB box

  2. NM_001348719.2 → NP_001335648.1  zinc finger protein 439 isoform b

    Status: VALIDATED

    Source sequence(s)
    AC008543, AC020951
    Consensus CDS
    CCDS92520.1
    UniProtKB/TrEMBL
    A0A804HI69
    Related
    ENSP00000506930.1, ENST00000682736.1
    Conserved Domains (3) summary
    COG5048
    Location:318 → 489
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:389 → 409
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:23 → 64
    KRAB; KRAB box

  3. NM_001348720.2 → NP_001335649.1  zinc finger protein 439 isoform d

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4), as well as variant 5, encodes isoform d.
    Source sequence(s)
    AC008543, AC020951
    Conserved Domains (3) summary
    COG5048
    Location:300 → 471
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:371 → 391
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:5 → 46
    KRAB; KRAB box

  4. NM_001348721.2 → NP_001335650.1  zinc finger protein 439 isoform d

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5), as well as variant 4, encodes isoform d.
    Source sequence(s)
    AC008543, AC020951
    Conserved Domains (3) summary
    COG5048
    Location:300 → 471
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:371 → 391
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:5 → 46
    KRAB; KRAB box

  5. NM_001348722.2 → NP_001335651.1  zinc finger protein 439 isoform e

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6), as well as variant 7, encodes isoform e.
    Source sequence(s)
    AC008543, AC020951
    Conserved Domains (2) summary
    COG5048
    Location:277 → 437
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:337 → 357
    ZF_C2H2; C2H2 Zn finger [structural motif]

  6. NM_001348723.2 → NP_001335652.1  zinc finger protein 439 isoform e

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7), as well as variant 6, encodes isoform e.
    Source sequence(s)
    AC008543, AC020951
    Conserved Domains (2) summary
    COG5048
    Location:277 → 437
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:337 → 357
    ZF_C2H2; C2H2 Zn finger [structural motif]

  7. NM_001348724.2 → NP_001335653.1  zinc finger protein 439 isoform f

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8), as well as variant 9, encodes isoform f.
    Source sequence(s)
    AC008543, AC020951
    Consensus CDS
    CCDS86705.1
    UniProtKB/TrEMBL
    A0A0C4DG37
    Related
    ENSP00000395632.1, ENST00000455282.1
    Conserved Domains (2) summary
    COG5048
    Location:177 → 348
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:248 → 268
    ZF_C2H2; C2H2 Zn finger [structural motif]

  8. NM_001348725.2 → NP_001335654.1  zinc finger protein 439 isoform f

    Status: VALIDATED

    Description
    Transcript Variant: This variant (9), as well as variant 8, encodes isoform f.
    Source sequence(s)
    AC008543, AC020951
    Consensus CDS
    CCDS86705.1
    UniProtKB/TrEMBL
    A0A0C4DG37
    Conserved Domains (2) summary
    COG5048
    Location:177 → 348
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:248 → 268
    ZF_C2H2; C2H2 Zn finger [structural motif]

  9. NM_152262.3 → NP_689475.1  zinc finger protein 439 isoform c

    See identical proteins and their annotated locations for NP_689475.1

    Status: VALIDATED

    Source sequence(s)
    AC020951
    Consensus CDS
    CCDS12268.1
    UniProtKB/Swiss-Prot
    Q8IYZ7, Q8NDP4, Q96SU1
    Related
    ENSP00000305077.2, ENST00000304030.2
    Conserved Domains (5) summary
    smart00349
    Location:19 → 61
    KRAB; krueppel associated box
    COG5048
    Location:313 → 484
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:384 → 404
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:19 → 58
    KRAB; KRAB box
    pfam13465
    Location:368 → 393
    zf-H2C2_2; Zinc-finger double domain

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    11848726..11869486
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047439651.1 → XP_047295607.1  zinc finger protein 439 isoform X1

    UniProtKB/Swiss-Prot
    Q8IYZ7, Q8NDP4, Q96SU1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    11976933..11997694
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054322556.1 → XP_054178531.1  zinc finger protein 439 isoform X1

    UniProtKB/Swiss-Prot
    Q8IYZ7, Q8NDP4, Q96SU1
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NDP4.1 GenPept UniProtKB/Swiss-Prot:Q8NDP4

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