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ZNF250 zinc finger protein 250 [ Homo sapiens (human) ]

Gene ID: 58500, updated on 7-Apr-2024

Summary

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Official Symbol
ZNF250provided by HGNC
Official Full Name
zinc finger protein 250provided by HGNC
Primary source
HGNC:HGNC:13044
See related
Ensembl:ENSG00000196150 AllianceGenome:HGNC:13044
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
ZFP647; ZNF647
Summary
Enables identical protein binding activity and sequence-specific double-stranded 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 3.2), ovary (RPKM 1.9) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
8q24.3
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (144876955..144902177, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (146050748..146075971, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (146102340..146127562, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100130027 Neighboring gene zinc finger protein 517 Neighboring gene hESC enhancers GRCh37_chr8:146052597-146053122 and GRCh37_chr8:146053123-146053648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:146053649-146054174 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:146064238-146064791 Neighboring gene zinc finger protein 7 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:146076290-146076441 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:146077648-146078496 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19714 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28107 Neighboring gene COMM domain containing 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28109 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:146126184-146126788 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:146126789-146127391 Neighboring gene uncharacterized LOC124902042 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:146127392-146127995 Neighboring gene zinc finger protein 16 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28110 Neighboring gene zinc finger protein 252, pseudogene Neighboring gene transmembrane p24 trafficking protein 10 pseudogene 1

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. The ancient mammalian KRAB zinc finger gene cluster on human chromosome 8q24.3 illustrates principles of C2H2 zinc finger evolution associated with unique expression profiles in human tissues. Lorenz P, et al. BMC Genomics, 2010 Mar 26. PMID 20346131, Free PMC Article
  2. Human ORFeome version 1.1: a platform for reverse proteomics. Rual JF, et al. Genome Res, 2004 Oct. PMID 15489335, Free PMC Article
  3. Network Analysis of UBE3A/E6AP-Associated Proteins Provides Connections to Several Distinct Cellular Processes. Martínez-Noël G, et al. J Mol Biol, 2018 Mar 30. PMID 29426014, Free PMC Article
  4. Pooled-matrix protein interaction screens using Barcode Fusion Genetics. Yachie N, et al. Mol Syst Biol, 2016 Apr 22. PMID 27107012, Free PMC Article
  5. A comprehensive SARS-CoV-2-human protein-protein interactome reveals COVID-19 pathobiology and potential host therapeutic targets. Zhou Y, et al. Nat Biotechnol, 2023 Jan. PMID 36217030, Free PMC Article

See all (29) citations in PubMed

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC9718, FLJ57354, MGC111123

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 sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
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 250
Names
zinc finger protein (clone 647)
zinc finger protein 647

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_001109689.4 → NP_001103159.1  zinc finger protein 250 isoform b

    See identical proteins and their annotated locations for NP_001103159.1

    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 a shorter protein (isoform b).
    Source sequence(s)
    AB208810, AF235103, AK054888, CA422363, DB272357
    Consensus CDS
    CCDS55282.1
    UniProtKB/Swiss-Prot
    P15622
    UniProtKB/TrEMBL
    B3KNS9
    Related
    ENSP00000393442.2, ENST00000417550.7
    Conserved Domains (3) summary
    smart00349
    Location:17 → 77
    KRAB; krueppel associated box
    COG5048
    Location:173 → 532
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:196 → 216
    ZF_C2H2; C2H2 Zn finger [structural motif]

  2. NM_001363098.2 → NP_001350027.1  zinc finger protein 250 isoform a

    Status: VALIDATED

    Source sequence(s)
    AF235103, BC017091, CA422363, DA496584, DB272357
    Consensus CDS
    CCDS34972.1
    UniProtKB/Swiss-Prot
    D3DWP1, P15622, Q59HE9, Q8N942, Q96AH9
    Conserved Domains (3) summary
    smart00349
    Location:22 → 82
    KRAB; krueppel associated box
    COG5048
    Location:178 → 537
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:201 → 221
    ZF_C2H2; C2H2 Zn finger [structural motif]

  3. NM_001363099.2 → NP_001350028.1  zinc finger protein 250 isoform a

    Status: VALIDATED

    Source sequence(s)
    AF235103, BC017091, BI820228, CA422363, DB272357
    Consensus CDS
    CCDS34972.1
    UniProtKB/Swiss-Prot
    D3DWP1, P15622, Q59HE9, Q8N942, Q96AH9
    Conserved Domains (3) summary
    smart00349
    Location:22 → 82
    KRAB; krueppel associated box
    COG5048
    Location:178 → 537
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:201 → 221
    ZF_C2H2; C2H2 Zn finger [structural motif]

  4. NM_001363100.2 → NP_001350029.1  zinc finger protein 250 isoform b

    Status: VALIDATED

    Source sequence(s)
    AF235103, BC017091, BI820228, CA422363, CV022909, DB272357
    Consensus CDS
    CCDS55282.1
    Conserved Domains (3) summary
    smart00349
    Location:17 → 77
    KRAB; krueppel associated box
    COG5048
    Location:173 → 532
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:196 → 216
    ZF_C2H2; C2H2 Zn finger [structural motif]

  5. NM_001363101.2 → NP_001350030.1  zinc finger protein 250 isoform b

    Status: VALIDATED

    Source sequence(s)
    AF235103, BC017091, BI820228, CA422363, CV022909, DA496584, DB272357
    Consensus CDS
    CCDS55282.1
    Conserved Domains (3) summary
    smart00349
    Location:17 → 77
    KRAB; krueppel associated box
    COG5048
    Location:173 → 532
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:196 → 216
    ZF_C2H2; C2H2 Zn finger [structural motif]

  6. NM_001363102.2 → NP_001350031.1  zinc finger protein 250 isoform b

    Status: VALIDATED

    Source sequence(s)
    AF235103, AK054888, BC017091, CA422363, CV022909, DA782437, DB272357
    Consensus CDS
    CCDS55282.1
    Conserved Domains (3) summary
    smart00349
    Location:17 → 77
    KRAB; krueppel associated box
    COG5048
    Location:173 → 532
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:196 → 216
    ZF_C2H2; C2H2 Zn finger [structural motif]

  7. NM_001363103.2 → NP_001350032.1  zinc finger protein 250 isoform b

    Status: VALIDATED

    Source sequence(s)
    AF235103, BC017091, BI820228, CA422363, CV022909, DB272357, R53168
    Consensus CDS
    CCDS55282.1
    Conserved Domains (3) summary
    smart00349
    Location:17 → 77
    KRAB; krueppel associated box
    COG5048
    Location:173 → 532
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:196 → 216
    ZF_C2H2; C2H2 Zn finger [structural motif]

  8. NM_001363104.2 → NP_001350033.1  zinc finger protein 250 isoform c

    Status: VALIDATED

    Source sequence(s)
    AF235103, AK054888, BC017091, CA422363, DB272357
    Conserved Domains (3) summary
    smart00349
    Location:22 → 82
    KRAB; krueppel associated box
    COG5048
    Location:157 → 516
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:180 → 200
    ZF_C2H2; C2H2 Zn finger [structural motif]

  9. NM_001363105.2 → NP_001350034.1  zinc finger protein 250 isoform d

    Status: VALIDATED

    Source sequence(s)
    AF235103, BC017091, BI820228, CA422363, DB272357
    Conserved Domains (3) summary
    smart00349
    Location:17 → 77
    KRAB; krueppel associated box
    COG5048
    Location:152 → 511
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:175 → 195
    ZF_C2H2; C2H2 Zn finger [structural motif]

  10. NM_001363106.2 → NP_001350035.1  zinc finger protein 250 isoform d

    Status: VALIDATED

    Source sequence(s)
    AF235103, AK054888, BC017091, CA422363, DB272357, DR000625
    Conserved Domains (3) summary
    smart00349
    Location:17 → 77
    KRAB; krueppel associated box
    COG5048
    Location:152 → 511
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:175 → 195
    ZF_C2H2; C2H2 Zn finger [structural motif]

  11. NM_001363107.2 → NP_001350036.1  zinc finger protein 250 isoform d

    Status: VALIDATED

    Source sequence(s)
    AF235103, BC017091, CA422363, DA496584, DB272357, DR000625
    Conserved Domains (3) summary
    smart00349
    Location:17 → 77
    KRAB; krueppel associated box
    COG5048
    Location:152 → 511
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:175 → 195
    ZF_C2H2; C2H2 Zn finger [structural motif]

  12. NM_021061.5 → NP_066405.1  zinc finger protein 250 isoform a

    See identical proteins and their annotated locations for NP_066405.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AF235103, AK054888, BC017091, CA422363, DB272357
    Consensus CDS
    CCDS34972.1
    UniProtKB/Swiss-Prot
    D3DWP1, P15622, Q59HE9, Q8N942, Q96AH9
    Related
    ENSP00000292579.7, ENST00000292579.11
    Conserved Domains (3) summary
    smart00349
    Location:22 → 82
    KRAB; krueppel associated box
    COG5048
    Location:178 → 537
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:201 → 221
    ZF_C2H2; C2H2 Zn finger [structural motif]

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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    144876955..144902177 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047422065.1 → XP_047278021.1  zinc finger protein 250 isoform X2

  2. XM_047422064.1 → XP_047278020.1  zinc finger protein 250 isoform X1

    UniProtKB/Swiss-Prot
    D3DWP1, P15622, Q59HE9, Q8N942, Q96AH9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    146050748..146075971 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P15622.3 GenPept UniProtKB/Swiss-Prot:P15622

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