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

Gene ID: 197407, updated on 27-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
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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
  • 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)

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

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