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

Gene ID: 162972, updated on 11-Apr-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 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 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_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (57541838..57561395, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (60638766..60658323, complement)
105.20220307 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. The DNA sequence and biology of human chromosome 19. Grimwood J, et al. Nature, 2004 Apr 1. PMID 15057824
  2. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Rush J, et al. Nat Biotechnol, 2005 Jan. PMID 15592455
  3. A proteome-scale map of the human interactome network. Rolland T, et al. Cell, 2014 Nov 20. PMID 25416956, Free PMC Article
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
  5. Architecture of the human interactome defines protein communities and disease networks. Huttlin EL, et al. Nature, 2017 May 25. PMID 28514442, Free PMC Article

See all (10) 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

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_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
    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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