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ZNF419 zinc finger protein 419 [ Homo sapiens (human) ]

Gene ID: 79744, updated on 7-Apr-2024

Summary

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Official Symbol
ZNF419provided by HGNC
Official Full Name
zinc finger protein 419provided by HGNC
Primary source
HGNC:HGNC:20648
See related
Ensembl:ENSG00000105136 MIM:617410; AllianceGenome:HGNC:20648
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
Also known as
ZAPHIR; ZNF419A
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 5.2), spleen (RPKM 4.2) and 25 other tissues See more
Orthologs
all
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Genomic context

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Location:
19q13.43
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (57487750..57496098)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (60579865..60593144)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (57999118..58007466)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene vomeronasal 1 receptor 107 pseudogene Neighboring gene zinc finger protein 772 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr19:57988249-57989448 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:57998906-57999406 Neighboring gene zinc finger protein 773 Neighboring gene zinc finger protein 549

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. A polymorphism in the splice donor site of ZNF419 results in the novel renal cell carcinoma-associated minor histocompatibility antigen ZAPHIR. Broen K, et al. PLoS One, 2011. PMID 21738768, Free PMC Article
  2. Allele-specific splicing effects on DKKL1 and ZNF419 transcripts in HeLa cells. Martin G, et al. Gene, 2017 Jan 20. PMID 27826023
  3. Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. Suzuki Y, et al. Genome Res, 2004 Sep. PMID 15342556, Free PMC Article
  4. Cullin 3 Exon 9 Deletion in Familial Hyperkalemic Hypertension Impairs Cullin3-Ring-E3 Ligase (CRL3) Dynamic Regulation and Cycling. Kouranti I, et al. Int J Mol Sci, 2022 May 5. PMID 35563538, Free PMC Article
  5. Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. Haenig C, et al. Cell Rep, 2020 Aug 18. PMID 32814053

See all (18) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. previously unreported alternative splicing patterns in the genes ZNF419 and DKKL1
    Title: Allele-specific splicing effects on DKKL1 and ZNF419 transcripts in HeLa cells.
  2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
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

Clone Names

  • FLJ23233

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
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 419
Names
zinc finger protein 419A

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_054882.1 RefSeqGene

    Range
    5040..13388
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001098491.2 → NP_001091961.1  zinc finger protein 419 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC003005, AK026886, BC024259, DB004191
    Consensus CDS
    CCDS54325.1
    UniProtKB/Swiss-Prot
    Q96HQ0
    Related
    ENSP00000388864.1, ENST00000424930.6
    Conserved Domains (5) summary
    smart00349
    Location:28 → 88
    KRAB; krueppel associated box
    COG5048
    Location:262 → 418
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:262 → 282
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:28 → 67
    KRAB; KRAB box
    pfam13465
    Location:330 → 355
    zf-H2C2_2; Zinc-finger double domain

  2. NM_001098492.2 → NP_001091962.1  zinc finger protein 419 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.
    Source sequence(s)
    AC003005, AK026886, BC024259, DC315347
    Consensus CDS
    CCDS54327.1
    UniProtKB/Swiss-Prot
    Q96HQ0
    Related
    ENSP00000390916.1, ENST00000426954.6
    Conserved Domains (5) summary
    smart00349
    Location:15 → 75
    KRAB; krueppel associated box
    COG5048
    Location:249 → 405
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:249 → 269
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:15 → 54
    KRAB; KRAB box
    pfam13465
    Location:317 → 342
    zf-H2C2_2; Zinc-finger double domain

  3. NM_001098493.2 → NP_001091963.1  zinc finger protein 419 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (4) that is shorter than isoform 1.
    Source sequence(s)
    AC003005, AK026886, BC024259, DC392630
    Consensus CDS
    CCDS54328.1
    UniProtKB/Swiss-Prot
    Q96HQ0
    Related
    ENSP00000414709.2, ENST00000442920.6
    Conserved Domains (5) summary
    smart00349
    Location:14 → 74
    KRAB; krueppel associated box
    COG5048
    Location:248 → 404
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:248 → 268
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:14 → 53
    KRAB; KRAB box
    pfam13465
    Location:316 → 341
    zf-H2C2_2; Zinc-finger double domain

  4. NM_001098494.2 → NP_001091964.1  zinc finger protein 419 isoform 5

    See identical proteins and their annotated locations for NP_001091964.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (5) that is shorter than isoform 1.
    Source sequence(s)
    AC003005, AK026886, BC024259
    Consensus CDS
    CCDS42637.1
    UniProtKB/Swiss-Prot
    Q96HQ0
    Related
    ENSP00000299860.9, ENST00000347466.10
    Conserved Domains (5) summary
    smart00349
    Location:28 → 69
    KRAB; krueppel associated box
    COG5048
    Location:229 → 385
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:229 → 249
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:28 → 67
    KRAB; KRAB box
    pfam13465
    Location:297 → 322
    zf-H2C2_2; Zinc-finger double domain

  5. NM_001098495.2 → NP_001091965.1  zinc finger protein 419 isoform 6

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) lacks two alternate in-frame exons in the 5' coding region, compared to variant 1, resulting in an isoform (6) that is shorter than isoform 1.
    Source sequence(s)
    AC003005, AK026886, BC024259, BP336834, DC407547
    UniProtKB/Swiss-Prot
    Q96HQ0
    Conserved Domains (5) summary
    smart00349
    Location:15 → 56
    KRAB; krueppel associated box
    COG5048
    Location:216 → 372
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:216 → 236
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:15 → 54
    KRAB; KRAB box
    pfam13465
    Location:284 → 309
    zf-H2C2_2; Zinc-finger double domain

  6. NM_001098496.2 → NP_001091966.1  zinc finger protein 419 isoform 7

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) lacks two alternate in-frame exons and and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (7) that is shorter than isoform 1.
    Source sequence(s)
    AC003005, AK026886, BC024259, DC315347, DC425209
    Consensus CDS
    CCDS46211.1
    UniProtKB/Swiss-Prot
    Q96HQ0
    Related
    ENSP00000392129.2, ENST00000415379.6
    Conserved Domains (5) summary
    smart00349
    Location:14 → 55
    KRAB; krueppel associated box
    COG5048
    Location:215 → 371
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:215 → 235
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:14 → 53
    KRAB; KRAB box
    pfam13465
    Location:283 → 308
    zf-H2C2_2; Zinc-finger double domain

  7. NM_001291743.2 → NP_001278672.1  zinc finger protein 419 isoform 8

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8) uses an alternate in-frame splice site and lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (8) that is shorter than isoform 1.
    Source sequence(s)
    AC003005, AK026886, BC008297, CT002615, DC315347
    UniProtKB/Swiss-Prot
    Q96HQ0
    Conserved Domains (5) summary
    smart00349
    Location:27 → 68
    KRAB; krueppel associated box
    COG5048
    Location:228 → 384
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:228 → 248
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:27 → 66
    KRAB; KRAB box
    pfam13465
    Location:296 → 321
    zf-H2C2_2; Zinc-finger double domain

  8. NM_001291744.2 → NP_001278673.1  zinc finger protein 419 isoform 9

    Status: VALIDATED

    Description
    Transcript Variant: This variant (9) uses an alternate splice site and it thus differs in its 5' UTR and initiates translation at a downstream in-frame start codon, and it also lacks an in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (9) is shorter at the N-terminus, compared to isoform 1.
    Source sequence(s)
    AC003005, AK026886, BC008297, DA548110, DC315347
    UniProtKB/Swiss-Prot
    Q96HQ0
    Conserved Domains (3) summary
    COG5048
    Location:173 → 329
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:173 → 193
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:241 → 266
    zf-H2C2_2; Zinc-finger double domain

  9. NM_001291745.2 → NP_001278674.1  zinc finger protein 419 isoform 10

    Status: VALIDATED

    Description
    Transcript Variant: This variant (10) lacks an alternate in-frame exon in the 5' coding region, and it uses an alternate splice site in its 3' terminal exon and thus differs in the 3' coding region, compared to variant 1. The encoded isoform (10) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    BC008297, BF110540, DC315347
    UniProtKB/Swiss-Prot
    Q96HQ0
    Conserved Domains (2) summary
    smart00349
    Location:15 → 75
    KRAB; krueppel associated box
    pfam01352
    Location:15 → 54
    KRAB; KRAB box

  10. NM_024691.4 → NP_078967.3  zinc finger protein 419 isoform 2

    See identical proteins and their annotated locations for NP_078967.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
    Source sequence(s)
    AC003005, AK026886, BC024259, BP336834
    Consensus CDS
    CCDS54326.1
    UniProtKB/Swiss-Prot
    B4DXU7, B4E348, B7ZA41, E9PCP4, E9PED0, E9PET3, E9PFX9, Q96HQ0, Q9H5P0
    Related
    ENSP00000221735.7, ENST00000221735.12
    Conserved Domains (5) summary
    smart00349
    Location:27 → 87
    KRAB; krueppel associated box
    COG5048
    Location:261 → 417
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:261 → 281
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:27 → 66
    KRAB; KRAB box
    pfam13465
    Location:329 → 354
    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
    57487750..57496098
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    60579865..60593144
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054322177.1 → XP_054178152.1  zinc finger protein 419 isoform X3

  2. XM_054322176.1 → XP_054178151.1  zinc finger protein 419 isoform X3

  3. XM_054322178.1 → XP_054178153.1  zinc finger protein 419 isoform X4

  4. XM_054322175.1 → XP_054178150.1  zinc finger protein 419 isoform X2

  5. XM_054322174.1 → XP_054178149.1  zinc finger protein 419 isoform X1

  6. XM_054322179.1 → XP_054178154.1  zinc finger protein 419 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96HQ0.2 GenPept UniProtKB/Swiss-Prot:Q96HQ0

Gene LinkOut

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

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