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    ZNF541 zinc finger protein 541 [ Homo sapiens (human) ]

    Gene ID: 84215, updated on 5-Mar-2024

    Summary

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    Official Symbol
    ZNF541provided by HGNC
    Official Full Name
    zinc finger protein 541provided by HGNC
    Primary source
    HGNC:HGNC:25294
    See related
    Ensembl:ENSG00000118156 MIM:619942; AllianceGenome:HGNC:25294
    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 transcription corepressor activity. Predicted to be involved in histone deacetylation; negative regulation of transcription, DNA-templated; and regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be part of histone deacetylase complex and transcription regulator complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in testis (RPKM 7.8) and ovary (RPKM 0.4) See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    19q13.33
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (47520690..47573309, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (50351494..50404109, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (48023947..48076405, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene hESC enhancers GRCh37_chr19:47931091-47931659 and GRCh37_chr19:47931660-47932227 Neighboring gene Sharpr-MPRA regulatory region 169 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:47939851-47940352 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:47945299-47945446 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10853 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:47949904-47950829 Neighboring gene solute carrier family 8 member A2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:47971701-47972200 Neighboring gene Sharpr-MPRA regulatory region 3844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14866 Neighboring gene NAPA antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48003933-48004487 Neighboring gene kaptin, actin binding protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14867 Neighboring gene NSF attachment protein alpha Neighboring gene Sharpr-MPRA regulatory region 13246 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14868 Neighboring gene RNA, 7SL, cytoplasmic 322, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10857 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14869 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10858 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10859 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10861 Neighboring gene BICRA antisense RNA 2 Neighboring gene BRD4 interacting chromatin remodeling complex associated protein

    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. 19q13.32 microdeletion syndrome: three new cases. Castillo A, et al. Eur J Med Genet, 2014 Nov-Dec. PMID 25230004
    2. Meiosis-specific ZFP541 repressor complex promotes developmental progression of meiotic prophase towards completion during mouse spermatogenesis. Horisawa-Takada Y, et al. Nat Commun, 2021 Jun 1. PMID 34075040, Free PMC Article
    3. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. Wiemann S, et al. Genome Res, 2001 Mar. PMID 11230166, Free PMC Article
    4. A census of human transcription factors: function, expression and evolution. Vaquerizas JM, et al. Nat Rev Genet, 2009 Apr. PMID 19274049
    5. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article

    See all (9) 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

    • MGC119518, MGC119519, MGC119521, DKFZp434I1930

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription corepressor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in male meiotic nuclear division ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of histone deacetylase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of histone deacetylase complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of transcription regulator complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein 541

    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_054911.1 RefSeqGene

      Range
      5091..57549
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001277075.3 → NP_001264004.1  zinc finger protein 541

      See identical proteins and their annotated locations for NP_001264004.1

      Status: VALIDATED

      Source sequence(s)
      AC010331, AL136846, DT932577, HY033195
      Consensus CDS
      CCDS46133.2
      UniProtKB/Swiss-Prot
      Q8NDK8, Q9H0D2
      Related
      ENSP00000375770.3, ENST00000391901.8
      Conserved Domains (7) summary
      smart00717
      Location:1165 → 1209
      SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
      COG5048
      Location:150 → 319
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:142 → 162
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:142 → 162
      zf-C2H2; Zinc finger, C2H2 type
      pfam01448
      Location:1055 → 1110
      ELM2; ELM2 domain
      pfam13465
      Location:154 → 179
      zf-H2C2_2; Zinc-finger double domain
      cl21498
      Location:1165 → 1208
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...

    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
      47520690..47573309 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047439506.1 → XP_047295462.1  zinc finger protein 541 isoform X2

      UniProtKB/Swiss-Prot
      Q8NDK8, Q9H0D2

    2. XM_011527369.3 → XP_011525671.1  zinc finger protein 541 isoform X1

      See identical proteins and their annotated locations for XP_011525671.1

      Conserved Domains (7) summary
      smart00717
      Location:1170 → 1214
      SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
      COG5048
      Location:150 → 324
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:142 → 162
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:142 → 162
      zf-C2H2; Zinc finger, C2H2 type
      pfam01448
      Location:1060 → 1115
      ELM2; ELM2 domain
      pfam13465
      Location:154 → 179
      zf-H2C2_2; Zinc-finger double domain
      cl21498
      Location:1170 → 1213
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...

    3. XM_011527368.3 → XP_011525670.1  zinc finger protein 541 isoform X1

      See identical proteins and their annotated locations for XP_011525670.1

      Conserved Domains (7) summary
      smart00717
      Location:1170 → 1214
      SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
      COG5048
      Location:150 → 324
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:142 → 162
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:142 → 162
      zf-C2H2; Zinc finger, C2H2 type
      pfam01448
      Location:1060 → 1115
      ELM2; ELM2 domain
      pfam13465
      Location:154 → 179
      zf-H2C2_2; Zinc-finger double domain
      cl21498
      Location:1170 → 1213
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...

    4. XM_017027351.3 → XP_016882840.1  zinc finger protein 541 isoform X3

    5. XM_011527372.4 → XP_011525674.1  zinc finger protein 541 isoform X4

      Conserved Domains (6) summary
      COG5048
      Location:150 → 324
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:142 → 162
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:142 → 162
      zf-C2H2; Zinc finger, C2H2 type
      pfam01448
      Location:1060 → 1115
      ELM2; ELM2 domain
      pfam13465
      Location:154 → 179
      zf-H2C2_2; Zinc-finger double domain
      cl21498
      Location:1140 → 1158
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...

    6. XM_011527373.4 → XP_011525675.1  zinc finger protein 541 isoform X5

      Conserved Domains (7) summary
      smart00717
      Location:1112 → 1156
      SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
      COG5048
      Location:150 → 324
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:142 → 162
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:142 → 162
      zf-C2H2; Zinc finger, C2H2 type
      pfam01448
      Location:1002 → 1057
      ELM2; ELM2 domain
      pfam13465
      Location:154 → 179
      zf-H2C2_2; Zinc-finger double domain
      cl21498
      Location:1112 → 1155
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...

    7. XM_047439505.1 → XP_047295461.1  zinc finger protein 541 isoform X1

    8. XM_011527374.4 → XP_011525676.1  zinc finger protein 541 isoform X6

      Conserved Domains (7) summary
      smart00717
      Location:1108 → 1152
      SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
      COG5048
      Location:88 → 262
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:80 → 100
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:80 → 100
      zf-C2H2; Zinc finger, C2H2 type
      pfam01448
      Location:998 → 1053
      ELM2; ELM2 domain
      pfam13465
      Location:92 → 117
      zf-H2C2_2; Zinc-finger double domain
      cl21498
      Location:1108 → 1151
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...

    9. XM_005259311.6 → XP_005259368.1  zinc finger protein 541 isoform X2

      See identical proteins and their annotated locations for XP_005259368.1

      UniProtKB/Swiss-Prot
      Q8NDK8, Q9H0D2
      Conserved Domains (7) summary
      smart00717
      Location:1165 → 1209
      SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
      COG5048
      Location:150 → 319
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:142 → 162
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:142 → 162
      zf-C2H2; Zinc finger, C2H2 type
      pfam01448
      Location:1055 → 1110
      ELM2; ELM2 domain
      pfam13465
      Location:154 → 179
      zf-H2C2_2; Zinc-finger double domain
      cl21498
      Location:1165 → 1208
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...

    10. XM_005259314.5 → XP_005259371.1  zinc finger protein 541 isoform X9

      Conserved Domains (6) summary
      smart00717
      Location:527 → 571
      SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
      sd00017
      Location:142 → 162
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:142 → 162
      zf-C2H2; Zinc finger, C2H2 type
      pfam01448
      Location:417 → 472
      ELM2; ELM2 domain
      pfam13465
      Location:154 → 179
      zf-H2C2_2; Zinc-finger double domain
      cl21498
      Location:527 → 570
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...

    11. XM_011527371.3 → XP_011525673.1  zinc finger protein 541 isoform X1

      See identical proteins and their annotated locations for XP_011525673.1

      Conserved Domains (7) summary
      smart00717
      Location:1170 → 1214
      SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
      COG5048
      Location:150 → 324
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:142 → 162
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:142 → 162
      zf-C2H2; Zinc finger, C2H2 type
      pfam01448
      Location:1060 → 1115
      ELM2; ELM2 domain
      pfam13465
      Location:154 → 179
      zf-H2C2_2; Zinc-finger double domain
      cl21498
      Location:1170 → 1213
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...

    12. XM_047439507.1 → XP_047295463.1  zinc finger protein 541 isoform X7

    13. XM_047439508.1 → XP_047295464.1  zinc finger protein 541 isoform X8

    14. XM_011527375.3 → XP_011525677.1  zinc finger protein 541 isoform X8

      Conserved Domains (4) summary
      COG5048
      Location:150 → 324
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:142 → 162
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:142 → 162
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:154 → 179
      zf-H2C2_2; Zinc-finger double domain

    RNA

    1. XR_935865.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      50351494..50404109 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322322.1 → XP_054178297.1  zinc finger protein 541 isoform X2

    2. XM_054322319.1 → XP_054178294.1  zinc finger protein 541 isoform X1

    3. XM_054322318.1 → XP_054178293.1  zinc finger protein 541 isoform X1

    4. XM_054322323.1 → XP_054178298.1  zinc finger protein 541 isoform X3

    5. XM_054322325.1 → XP_054178300.1  zinc finger protein 541 isoform X5

    6. XM_054322324.1 → XP_054178299.1  zinc finger protein 541 isoform X4

    7. XM_054322317.1 → XP_054178292.1  zinc finger protein 541 isoform X1

    8. XM_054322326.1 → XP_054178301.1  zinc finger protein 541 isoform X6

    9. XM_054322321.1 → XP_054178296.1  zinc finger protein 541 isoform X2

    10. XM_054322330.1 → XP_054178305.1  zinc finger protein 541 isoform X9

    11. XM_054322320.1 → XP_054178295.1  zinc finger protein 541 isoform X1

    12. XM_054322327.1 → XP_054178302.1  zinc finger protein 541 isoform X7

    13. XM_054322329.1 → XP_054178304.1  zinc finger protein 541 isoform X8

    14. XM_054322328.1 → XP_054178303.1  zinc finger protein 541 isoform X8

    RNA

    1. XR_008485208.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001101419.1: Suppressed sequence

      Description
      NM_001101419.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

    2. NM_032255.1: Suppressed sequence

      Description
      NM_032255.1: This RefSeq was permanently suppressed because the CDS was partial.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H0D2.3 GenPept UniProtKB/Swiss-Prot:Q9H0D2

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

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