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Zfp40 zinc finger protein 40 [ Rattus norvegicus (Norway rat) ]

Gene ID: 690661, updated on 4-Jan-2025

Summary

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Official Symbol
Zfp40provided by RGD
Official Full Name
zinc finger protein 40provided by RGD
Primary source
RGD:1593410
See related
EnsemblRapid:ENSRNOG00000011675 AllianceGenome:RGD:1593410
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA 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, Jan 2025]
Expression
Biased expression in Brain (RPKM 115.5), Lung (RPKM 61.7) and 9 other tissues See more
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Genomic context

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See Zfp40 in Genome Data Viewer
Location:
1q12
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (71395819..71658824, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (62962456..62985007, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (62555186..62577750, complement)

Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene zinc finger protein 945 Neighboring gene uncharacterized LOC134482877 Neighboring gene vomeronasal 2 receptor, 80 Neighboring gene vomeronasal 2, receptor 116 like, pseudogene 18 Neighboring gene vomeronasal 2 receptor, pseudogene 30 Neighboring gene vomeronasal 2 receptor, pseudogene 31

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
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 DNA-templated transcription 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
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
zinc finger protein 40

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_001395138.1 → NP_001382067.1  zinc finger protein 40

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000001
    UniProtKB/TrEMBL
    F1LYD5
    Related
    ENSRNOP00000015520.6, ENSRNOT00000015520.7
    Conserved Domains (4) summary
    smart00349
    Location:42 → 84
    KRAB; krueppel associated box
    COG5048
    Location:278 → 678
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:645 → 665
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:685 → 710
    zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086019.1 Reference GRCr8

    Range
    71395819..71658824 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063274800.1 → XP_063130870.1  zinc finger protein 40 isoform X1

    UniProtKB/TrEMBL
    A0A8I5ZKZ9

  2. XM_063274809.1 → XP_063130879.1  zinc finger protein 40 isoform X1

    UniProtKB/TrEMBL
    A0A8I5ZKZ9

  3. XM_063274810.1 → XP_063130880.1  zinc finger protein 40 isoform X1

    UniProtKB/TrEMBL
    A0A8I5ZKZ9

  4. XM_063274802.1 → XP_063130872.1  zinc finger protein 40 isoform X1

    UniProtKB/TrEMBL
    A0A8I5ZKZ9

  5. XM_063274801.1 → XP_063130871.1  zinc finger protein 40 isoform X1

    UniProtKB/TrEMBL
    A0A8I5ZKZ9

  6. XM_063274806.1 → XP_063130876.1  zinc finger protein 40 isoform X1

    UniProtKB/TrEMBL
    A0A8I5ZKZ9

  7. XM_063274808.1 → XP_063130878.1  zinc finger protein 40 isoform X1

    UniProtKB/TrEMBL
    A0A8I5ZKZ9

  8. XM_063274815.1 → XP_063130885.1  zinc finger protein 40 isoform X1

    UniProtKB/TrEMBL
    A0A8I5ZKZ9

  9. XM_063274811.1 → XP_063130881.1  zinc finger protein 40 isoform X1

    UniProtKB/TrEMBL
    A0A8I5ZKZ9

  10. XM_063274813.1 → XP_063130883.1  zinc finger protein 40 isoform X1

    UniProtKB/TrEMBL
    A0A8I5ZKZ9

  11. XM_039091489.2 → XP_038947417.1  zinc finger protein 40 isoform X2

    UniProtKB/TrEMBL
    A0A8I6A5R9
    Conserved Domains (4) summary
    smart00349
    Location:67 → 109
    KRAB; krueppel associated box
    COG5048
    Location:303 → 703
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:670 → 690
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:710 → 735
    zf-H2C2_2; Zinc-finger double domain

  12. XM_039091495.2 → XP_038947423.1  zinc finger protein 40 isoform X3

    Conserved Domains (4) summary
    smart00349
    Location:38 → 80
    KRAB; krueppel associated box
    COG5048
    Location:274 → 674
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:641 → 661
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:681 → 706
    zf-H2C2_2; Zinc-finger double domain

  13. XM_063274817.1 → XP_063130887.1  zinc finger protein 40 isoform X4

RNA

  1. XR_010057955.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001168642.1: Suppressed sequence

    Description
    NM_001168642.1: This RefSeq record was removed by NCBI staff. Contact [email protected] for further information.
Nucleotide Protein Strain
Heading Accession and Version

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