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

Gene ID: 306977, updated on 2-Nov-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, Nov 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

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

    UniProtKB/TrEMBL
    A6KN76, F7DP88

  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

  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

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

    UniProtKB/TrEMBL
    A6KN76, F7DP88

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

    UniProtKB/TrEMBL
    A6KN76, F7DP88

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

    UniProtKB/TrEMBL
    A6KN76, F7DP88

  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
    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
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