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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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See ZNF541 in Genome Data Viewer
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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