U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 690661, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    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 activity; catalytic activity; and metal ion binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 115.5), Lung (RPKM 61.7) and 9 other tissues See more
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    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

    Go to the top of the page Help

    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

    Go to the top of the page Help
    Preferred Names
    zinc finger protein 40

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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

    Gene LinkOut

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

    Molecular Biology Databases
    Research Materials
    Tools