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ZNF540 zinc finger protein 540 [ Homo sapiens (human) ]

Gene ID: 163255, updated on 11-Jun-2021

Summary

Official Symbol
ZNF540provided by HGNC
Official Full Name
zinc finger protein 540provided by HGNC
Primary source
HGNC:HGNC:25331
See related
Ensembl:ENSG00000171817 MIM:613903
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
Nbla10512
Expression
Ubiquitous expression in brain (RPKM 3.9), thyroid (RPKM 3.7) and 23 other tissues See more
Orthologs
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Genomic context

See ZNF540 in Genome Data Viewer
Location:
19q13.12
Exon count:
6
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (37551374..37614179)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (38042276..38105080)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein 569 Neighboring gene zinc finger protein 570 Neighboring gene ZNF793 antisense RNA 1 (head to head) Neighboring gene zinc finger protein 793 Neighboring gene ZNF571 antisense RNA 1 Neighboring gene MT-ND4 pseudogene 41 Neighboring gene zinc finger protein 571 Neighboring gene MT-ND5 pseudogene 45 Neighboring gene MT-CO1 pseudogene 41 Neighboring gene ZFP30 zinc finger protein Neighboring gene zinc finger protein 781

Genomic regions, transcripts, and products

Expression

  • 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

General gene information

Markers

Homology

Clone Names

  • FLJ16004, DKFZp313K2238, DKFZp547B0714

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
zinc finger protein 540
Names
CTD-3064H18.6
putative protein product of Nbla10512

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_001172225.3NP_001165696.1  zinc finger protein 540 isoform a

    See identical proteins and their annotated locations for NP_001165696.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform a. Both variants 1 and 2 encode the same isoform (a), which is longer than isoform b.
    Source sequence(s)
    AL832315, BC017940, BE464266
    Consensus CDS
    CCDS12506.1
    UniProtKB/Swiss-Prot
    Q8NDQ6
    Related
    ENSP00000324598.3, ENST00000316433.9
    Conserved Domains (4) summary
    smart00349
    Location:666
    KRAB; krueppel associated box
    COG5048
    Location:241620
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:581601
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:621646
    zf-H2C2_2; Zinc-finger double domain
  2. NM_001172226.3NP_001165697.1  zinc finger protein 540 isoform b

    See identical proteins and their annotated locations for NP_001165697.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the coding region, compared to variant 1. The resulting isoform (b) lacks an internal segment, compared to isoform a.
    Source sequence(s)
    AL832100, AL832315, BC017940, BE464266
    Consensus CDS
    CCDS54258.1
    UniProtKB/Swiss-Prot
    Q8NDQ6
    Related
    ENSP00000467118.1, ENST00000589117.5
    Conserved Domains (5) summary
    smart00349
    Location:647
    KRAB; krueppel associated box
    COG5048
    Location:209614
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:549569
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:645
    KRAB; KRAB box
    pfam13465
    Location:561584
    zf-H2C2_2; Zinc-finger double domain
  3. NM_152606.5NP_689819.1  zinc finger protein 540 isoform a

    See identical proteins and their annotated locations for NP_689819.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has an alternate 5' UTR exon compared to variant 1, and represents a read-through transcript between the upstream non-coding LOC100507433 locus (GeneID 100507433) and the downstream ZNF540 locus (GeneID 163255).Both variants 1 and 2 encode the same isoform (a), which is longer than isoform b.
    Source sequence(s)
    AC022148, AL832315, BE464266
    Consensus CDS
    CCDS12506.1
    UniProtKB/Swiss-Prot
    Q8NDQ6
    Related
    ENSP00000466274.1, ENST00000592533.5
    Conserved Domains (4) summary
    smart00349
    Location:666
    KRAB; krueppel associated box
    COG5048
    Location:241620
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:581601
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:621646
    zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

    Range
    37551374..37614179
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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