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    ZNF550 zinc finger protein 550 [ Homo sapiens (human) ]

    Gene ID: 162972, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ZNF550provided by HGNC
    Official Full Name
    zinc finger protein 550provided by HGNC
    Primary source
    HGNC:HGNC:28643
    See related
    Ensembl:ENSG00000251369 AllianceGenome:HGNC:28643
    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 factor activity, RNA polymerase II-specific and RNA polymerase II transcription 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, Dec 2024]
    Expression
    Ubiquitous expression in ovary (RPKM 3.7), lymph node (RPKM 3.2) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See ZNF550 in Genome Data Viewer
    Location:
    19q13.43
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (57541838..57561395, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (60638766..60658323, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (58053206..58071231, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein 773 Neighboring gene zinc finger protein 549 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15144 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:58070497-58071361 Neighboring gene uncharacterized LOC124904781 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr19:58071339-58072538 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11076 Neighboring gene zinc finger protein 416 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:58095022-58095553 Neighboring gene zinc finger protein interacting with K protein 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. 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
    2. The DNA sequence and biology of human chromosome 19. Grimwood J, et al. Nature, 2004 Apr 1. PMID 15057824
    3. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Rush J, et al. Nat Biotechnol, 2005 Jan. PMID 15592455
    4. A proteome-scale map of the human interactome network. Rolland T, et al. Cell, 2014 Nov 20. PMID 25416956, Free PMC Article
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

    See all (11) 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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC41917

    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 550

    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_001277090.2 → NP_001264019.1  zinc finger protein 550 isoform a

      See identical proteins and their annotated locations for NP_001264019.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1, 2 and 3 all encode isoform a.
      Source sequence(s)
      AC003682, AK122867, BC034810, BC053858
      Consensus CDS
      CCDS35500.2
      UniProtKB/Swiss-Prot
      B3KVF6, O43337, Q7Z398, Q7Z6D7, Q8NE45
      Related
      ENSP00000469580.1, ENST00000447310.5
      Conserved Domains (4) summary
      smart00349
      Location:12 → 72
      KRAB; krueppel associated box
      COG5048
      Location:200 → 357
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:205 → 225
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:357 → 382
      zf-H2C2_2; Zinc-finger double domain

    2. NM_001277091.2 → NP_001264020.1  zinc finger protein 550 isoform a

      See identical proteins and their annotated locations for NP_001264020.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 3' UTR, compared to variant 1. Variants 1, 2 and 3 all encode isoform a.
      Source sequence(s)
      AC003682, AI114826, AK122867, BC034810
      Consensus CDS
      CCDS35500.2
      UniProtKB/Swiss-Prot
      B3KVF6, O43337, Q7Z398, Q7Z6D7, Q8NE45
      Related
      ENSP00000469537.1, ENST00000376230.7
      Conserved Domains (4) summary
      smart00349
      Location:12 → 72
      KRAB; krueppel associated box
      COG5048
      Location:200 → 357
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:205 → 225
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:357 → 382
      zf-H2C2_2; Zinc-finger double domain

    3. NM_001277092.2 → NP_001264021.1  zinc finger protein 550 isoform a

      See identical proteins and their annotated locations for NP_001264021.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an exon in the 3' UTR, compared to variant 1. Variants 1, 2 and 3 all encode isoform a.
      Source sequence(s)
      AI114826, AK122867, BC034810, BX538032
      Consensus CDS
      CCDS35500.2
      UniProtKB/Swiss-Prot
      B3KVF6, O43337, Q7Z398, Q7Z6D7, Q8NE45
      Related
      ENSP00000469679.1, ENST00000457177.5
      Conserved Domains (4) summary
      smart00349
      Location:12 → 72
      KRAB; krueppel associated box
      COG5048
      Location:200 → 357
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:205 → 225
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:357 → 382
      zf-H2C2_2; Zinc-finger double domain

    4. NM_001277093.2 → NP_001264022.1  zinc finger protein 550 isoform b

      See identical proteins and their annotated locations for NP_001264022.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains alternate 3' exon structure and it thus differs in the 3' coding region, compared to variant 1. The encoded isoform (b) has a distinct and shorter C-terminus, compared to isoform a.
      Source sequence(s)
      AK122867, BC034810, CX756948
      UniProtKB/Swiss-Prot
      Q7Z398
      Conserved Domains (2) summary
      smart00349
      Location:12 → 72
      KRAB; krueppel associated box
      pfam01352
      Location:12 → 51
      KRAB; KRAB box

    5. NM_001397372.1 → NP_001384301.1  zinc finger protein 550 isoform a

      Status: VALIDATED

      Source sequence(s)
      AC003682
      Consensus CDS
      CCDS35500.2
      UniProtKB/Swiss-Prot
      B3KVF6, O43337, Q7Z398, Q7Z6D7, Q8NE45
      Related
      ENSP00000514306.1, ENST00000699333.1
      Conserved Domains (4) summary
      smart00349
      Location:12 → 72
      KRAB; krueppel associated box
      COG5048
      Location:200 → 357
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:205 → 225
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:357 → 382
      zf-H2C2_2; Zinc-finger double domain

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      57541838..57561395 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047438311.1 → XP_047294267.1  zinc finger protein 550 isoform X1

    2. XM_047438312.1 → XP_047294268.1  zinc finger protein 550 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      60638766..60658323 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054320051.1 → XP_054176026.1  zinc finger protein 550 isoform X1

    2. XM_054320052.1 → XP_054176027.1  zinc finger protein 550 isoform X1

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001039654.1: Suppressed sequence

      Description
      NM_001039654.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

    2. NM_153231.2: Suppressed sequence

      Description
      NM_153231.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z398.2 GenPept UniProtKB/Swiss-Prot:Q7Z398

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