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    Zkscan3 zinc finger with KRAB and SCAN domains 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 306977, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Zkscan3provided by RGD
    Official Full Name
    zinc finger with KRAB and SCAN domains 3provided by RGD
    Primary source
    RGD:1305753
    See related
    EnsemblRapid:ENSRNOG00000055000 AllianceGenome:RGD:1305753
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Zfp307
    Summary
    Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Predicted to be involved in several processes, including negative regulation of autophagy; negative regulation of cellular senescence; and regulation of DNA-templated transcription. Predicted to be located in cytoplasm and nucleoplasm. Orthologous to human ZKSCAN3 (zinc finger with KRAB and SCAN domains 3) and ZKSCAN4 (zinc finger with KRAB and SCAN domains 4). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Heart (RPKM 68.3), Adrenal (RPKM 65.3) and 9 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Zkscan3 in Genome Data Viewer
    Location:
    17p11
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 17 NC_086035.1 (47912816..47928553)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 17 NC_051352.1 (43217168..43232828)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 17 NC_005116.4 (45247724..45263422)

    Chromosome 17 - NC_086035.1Genomic Context describing neighboring genes Neighboring gene zinc finger and SCAN domain containing 26 Neighboring gene microRNA 1896 Neighboring gene piggyBac transposable element derived 1 Neighboring gene uncharacterized LOC120097923 Neighboring gene zinc finger and SCAN domain containing 12 Neighboring gene uncharacterized LOC120097820

    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. ZKSCAN3 is a master transcriptional repressor of autophagy. Chauhan S, et al. Mol Cell, 2013 Apr 11. PMID 23434374, Free PMC Article
    2. Unbiased screening for transcriptional targets of ZKSCAN3 identifies integrin beta 4 and vascular endothelial growth factor as downstream targets. Yang L, et al. J Biol Chem, 2008 Dec 12. PMID 18940803, Free PMC Article
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    4. 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

    Clone Names

    • MGC108865

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in lysosome organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of autophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of cellular senescence ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein with KRAB and SCAN domains 3
    Names
    zinc finger protein 307

    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_001012053.2 → NP_001012053.2  zinc finger protein with KRAB and SCAN domains 3

      See identical proteins and their annotated locations for NP_001012053.2

      Status: PROVISIONAL

      Source sequence(s)
      BC089847, CK602433
      UniProtKB/TrEMBL
      A6KN76, F7DP88, Q5FVP7
      Conserved Domains (6) summary
      smart00431
      Location:47 → 159
      SCAN; leucine rich region
      COG5048
      Location:367 → 514
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:371 → 391
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:507 → 529
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:328 → 350
      zf-H2C2_2; Zinc-finger double domain
      cl02581
      Location:213 → 271
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

    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_086035.1 Reference GRCr8

      Range
      47912816..47928553
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063276457.1 → XP_063132527.1  zinc finger protein with KRAB and SCAN domains 3 isoform X3

    2. XM_063276451.1 → XP_063132521.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

      UniProtKB/TrEMBL
      A6KN76, F7DP88, Q5FVP7

    3. XM_063276453.1 → XP_063132523.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

      UniProtKB/TrEMBL
      A6KN76, F7DP88, Q5FVP7

    4. XM_006254101.5 → XP_006254163.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

      See identical proteins and their annotated locations for XP_006254163.1

      UniProtKB/TrEMBL
      A6KN76, F7DP88, Q5FVP7
      Conserved Domains (6) summary
      smart00431
      Location:47 → 159
      SCAN; leucine rich region
      COG5048
      Location:367 → 514
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:371 → 391
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:507 → 529
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:328 → 350
      zf-H2C2_2; Zinc-finger double domain
      cl02581
      Location:213 → 271
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

    5. XM_063276456.1 → XP_063132526.1  zinc finger protein with KRAB and SCAN domains 3 isoform X3

    6. XM_063276455.1 → XP_063132525.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

      UniProtKB/TrEMBL
      A6KN76, F7DP88, Q5FVP7

    7. XM_006254099.5 → XP_006254161.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

      See identical proteins and their annotated locations for XP_006254161.1

      UniProtKB/TrEMBL
      A6KN76, F7DP88, Q5FVP7
      Conserved Domains (6) summary
      smart00431
      Location:47 → 159
      SCAN; leucine rich region
      COG5048
      Location:367 → 514
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:371 → 391
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:507 → 529
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:328 → 350
      zf-H2C2_2; Zinc-finger double domain
      cl02581
      Location:213 → 271
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

    8. XM_063276449.1 → XP_063132519.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

      UniProtKB/TrEMBL
      A6KN76, F7DP88, Q5FVP7

    9. XM_063276448.1 → XP_063132518.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

      UniProtKB/TrEMBL
      A6KN76, F7DP88, Q5FVP7

    10. XM_063276452.1 → XP_063132522.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

      UniProtKB/TrEMBL
      A6KN76, F7DP88, Q5FVP7

    11. XM_063276454.1 → XP_063132524.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

      UniProtKB/TrEMBL
      A6KN76, F7DP88, Q5FVP7

    12. XM_039095714.2 → XP_038951642.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

      UniProtKB/TrEMBL
      A6KN76, F7DP88, Q5FVP7
      Conserved Domains (6) summary
      smart00431
      Location:47 → 159
      SCAN; leucine rich region
      COG5048
      Location:367 → 514
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:371 → 391
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:507 → 529
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:328 → 350
      zf-H2C2_2; Zinc-finger double domain
      cl02581
      Location:213 → 271
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

    13. XM_008771726.3 → XP_008769948.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

      See identical proteins and their annotated locations for XP_008769948.1

      UniProtKB/TrEMBL
      A6KN76, F7DP88, Q5FVP7
      Conserved Domains (6) summary
      smart00431
      Location:47 → 159
      SCAN; leucine rich region
      COG5048
      Location:367 → 514
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:371 → 391
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:507 → 529
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:328 → 350
      zf-H2C2_2; Zinc-finger double domain
      cl02581
      Location:213 → 271
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

    14. XM_039095718.2 → XP_038951646.1  zinc finger protein with KRAB and SCAN domains 3 isoform X3

      Conserved Domains (1) summary
      smart00431
      Location:47 → 159
      SCAN; leucine rich region

    15. XM_039095715.2 → XP_038951643.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

      UniProtKB/TrEMBL
      A6KN76, F7DP88, Q5FVP7
      Conserved Domains (6) summary
      smart00431
      Location:47 → 159
      SCAN; leucine rich region
      COG5048
      Location:367 → 514
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:371 → 391
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:507 → 529
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:328 → 350
      zf-H2C2_2; Zinc-finger double domain
      cl02581
      Location:213 → 271
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

    16. XM_063276450.1 → XP_063132520.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

      UniProtKB/TrEMBL
      A6KN76, F7DP88, Q5FVP7
      Related
      ENSRNOP00000069061.1, ENSRNOT00000081063.3

    17. XM_039095717.2 → XP_038951645.1  zinc finger protein with KRAB and SCAN domains 3 isoform X2

      Conserved Domains (4) summary
      COG5048
      Location:113 → 260
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:117 → 137
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:253 → 275
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:74 → 96
      zf-H2C2_2; Zinc-finger double domain
    Nucleotide Protein Strain
    Heading Accession and Version

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