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    ZNF48 zinc finger protein 48 [ Homo sapiens (human) ]

    Gene ID: 197407, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ZNF48provided by HGNC
    Official Full Name
    zinc finger protein 48provided by HGNC
    Primary source
    HGNC:HGNC:13114
    See related
    Ensembl:ENSG00000180035 AllianceGenome:HGNC:13114
    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
    ZNF553
    Summary
    Enables identical protein 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, Nov 2024]
    Expression
    Broad expression in appendix (RPKM 1.0), fat (RPKM 0.8) and 15 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZNF48 in Genome Data Viewer
    Location:
    16p11.2
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (30378312..30400108)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (30764515..30786312)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (30389633..30411429)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene CD2BP2 divergent transcript Neighboring gene TBC1 domain family member 10B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7363 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7364 Neighboring gene myosin light chain 11 Neighboring gene Sharpr-MPRA regulatory region 9884 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7365 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10700 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30390133-30390690 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30390691-30391248 Neighboring gene septin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30404661-30405161 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7367 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7368 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:30407163-30407759 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30410094-30410637 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:30418651-30418830 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7369 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7370 Neighboring gene zinc finger protein 771 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7371 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7372 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7373 Neighboring gene small nucleolar RNA, H/ACA box 80C

    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 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. Clustering of C2-H2 zinc finger motif sequences within telomeric and fragile site regions of human chromosomes. Lichter P, et al. Genomics, 1992 Aug. PMID 1505991
    2. Characterization and mapping of human genes encoding zinc finger proteins. Bray P, et al. Proc Natl Acad Sci U S A, 1991 Nov 1. PMID 1946370, Free PMC Article
    3. SARS-CoV-2 N Protein Antagonizes Stress Granule Assembly and IFN Production by Interacting with G3BPs to Facilitate Viral Replication. Liu H, et al. J Virol, 2022 Jun 22. PMID 35652658, Free PMC Article
    4. Acetylation of ELF5 suppresses breast cancer progression by promoting its degradation and targeting CCND1. Li X, et al. NPJ Precis Oncol, 2021 Mar 19. PMID 33742100, Free PMC Article
    5. Mutual regulation between OGT and XIAP to control colon cancer cell growth and invasion. Seo HG, et al. Cell Death Dis, 2020 Sep 29. PMID 32994395, Free PMC Article

    See all (23) 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

    • FLJ31751, MGC43952, DKFZp762K013

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator 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 
    Process Evidence Code Pubs
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 48
    Names
    zinc finger protein 553

    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_050732.1 RefSeqGene

      Range
      22109..26797
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001214906.1 → NP_001201835.1  zinc finger protein 48 isoform 1

      See identical proteins and their annotated locations for NP_001201835.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has an alternate 5' UTR, compared to variant 1. Variants 1, 2 and 3 all encode the same isoform (1).
      Source sequence(s)
      AC116348, AK056313, CA434624, DA492655, DA508718
      Consensus CDS
      CCDS10679.1
      UniProtKB/Swiss-Prot
      Q15920, Q4G0R3, Q69YP3, Q96IL9, Q96MX3
      Conserved Domains (5) summary
      COG5048
      Location:114 → 499
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:114 → 134
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:573 → 593
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:451 → 473
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:557 → 580
      zf-H2C2_2; Zinc-finger double domain

    2. NM_001214907.1 → NP_001201836.1  zinc finger protein 48 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) has an alternate 5' exon, resulting in a downstream AUG start codon, compared to variant 1. The resulting isoform (2) is shorter at the N-terminus, compared to isoform 1. Variants 4 and 5 both encode the same isoform (2).
      Source sequence(s)
      AC116348, CA434624, DA492655
      Consensus CDS
      CCDS73868.1
      UniProtKB/TrEMBL
      A0A087WVT1
      Related
      ENSP00000479658.1, ENST00000622647.3
      Conserved Domains (5) summary
      COG5048
      Location:67 → 476
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:19 → 39
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:450 → 470
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:328 → 350
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:434 → 457
      zf-H2C2_2; Zinc-finger double domain

    3. NM_001214909.2 → NP_001201838.1  zinc finger protein 48 isoform 1

      See identical proteins and their annotated locations for NP_001201838.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has an alternate 5' UTR, compared to variant 1. Variants 1, 2 and 3 all encode the same isoform (1).
      Source sequence(s)
      AC116348, BU854776, CA434624, CF594347
      Consensus CDS
      CCDS10679.1
      UniProtKB/Swiss-Prot
      Q15920, Q4G0R3, Q69YP3, Q96IL9, Q96MX3
      Related
      ENSP00000480262.1, ENST00000613509.2
      Conserved Domains (5) summary
      COG5048
      Location:114 → 499
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:114 → 134
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:573 → 593
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:451 → 473
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:557 → 580
      zf-H2C2_2; Zinc-finger double domain

    4. NM_001324494.2 → NP_001311423.1  zinc finger protein 48 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) and variant 4 both encode the same isoform (2).
      Source sequence(s)
      AC116348
      Consensus CDS
      CCDS73868.1
      UniProtKB/TrEMBL
      A0A087WVT1
      Conserved Domains (5) summary
      COG5048
      Location:67 → 476
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:19 → 39
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:450 → 470
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:328 → 350
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:434 → 457
      zf-H2C2_2; Zinc-finger double domain

    5. NM_152652.3 → NP_689865.2  zinc finger protein 48 isoform 1

      See identical proteins and their annotated locations for NP_689865.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1). Variants 1, 2 and 3 all encode the same isoform (1).
      Source sequence(s)
      AC116348, AK056313, CA434624
      Consensus CDS
      CCDS10679.1
      UniProtKB/Swiss-Prot
      Q15920, Q4G0R3, Q69YP3, Q96IL9, Q96MX3
      Related
      ENSP00000324056.2, ENST00000320159.2
      Conserved Domains (5) summary
      COG5048
      Location:114 → 499
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:114 → 134
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:573 → 593
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:451 → 473
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:557 → 580
      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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      30378312..30400108
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      30764515..30786312
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96MX3.2 GenPept UniProtKB/Swiss-Prot:Q96MX3

    Gene LinkOut

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

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