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

    Gene ID: 58500, updated on 10-Dec-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, Dec 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 3.2), ovary (RPKM 1.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZNF250 in Genome Data Viewer
    Location:
    8q24.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (144876955..144902177, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (146050748..146075971, complement)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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. Analysis of Ku70 S155 Phospho-Specific BioID2 Interactome Identifies Ku Association with TRIP12 in Response to DNA Damage. Abbasi S, et al. Int J Mol Sci, 2023 Apr 11. PMID 37108203, Free PMC Article
    5. Acetylation-Mimic Mutation of TRIM28-Lys304 to Gln Attenuates the Interaction with KRAB-Zinc-Finger Proteins and Affects Gene Expression in Leukemic K562 Cells. Chang YJ, et al. Int J Mol Sci, 2023 Jun 6. PMID 37372979, Free PMC Article

    See all (34) 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)

    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 identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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_2024_08

    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

    Gene LinkOut

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

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