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prdm1b PR domain containing 1b, with ZNF domain [ Danio rerio (zebrafish) ]

Gene ID: 110437762, updated on 28-Oct-2024

Summary

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Official Symbol
prdm1bprovided by ZNC
Official Full Name
PR domain containing 1b, with ZNF domainprovided by ZNC
Primary source
ZFIN:ZDB-GENE-080618-2
See related
Ensembl:ENSDARG00000098925 AllianceGenome:ZFIN:ZDB-GENE-080618-2
Gene type
protein coding
RefSeq status
MODEL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Summary
Predicted to enable DNA-binding transcription factor activity and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in cell fate commitment and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within cellular developmental process and methylation. Predicted to be active in cytoplasm and nucleus. Is expressed in retina and somite. Human ortholog(s) of this gene implicated in hepatocellular carcinoma and lung adenocarcinoma. Orthologous to human PRDM1 (PR/SET domain 1). [provided by Alliance of Genome Resources, Oct 2024]
Annotation information
Annotation category: partial on reference assembly
Orthologs
all
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Genomic context

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See prdm1b in Genome Data Viewer
Location:
chromosome: 19
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 19 NC_007130.7 (48160385..48186103)

Chromosome 19 - NC_007130.7Genomic Context describing neighboring genes Neighboring gene NME/NM23 nucleoside diphosphate kinase 2b, tandem duplicate 1 Neighboring gene bloodthirsty-related gene family, member 30 Neighboring gene crystallin beta-gamma domain containing 2 Neighboring gene si:ch73-359m17.11 Neighboring gene annexin A14

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_007130.7 Chromosome 19 Reference GRCz11 Primary Assembly

Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. Loss of prdm1a accelerates melanoma onset and progression. Iwanaga R, et al. Mol Carcinog, 2020 Sep. PMID 32562448, Free PMC Article
  2. Expression of patched, prdm1 and engrailed in the lamprey somite reveals conserved responses to Hedgehog signaling. Hammond KL, et al. Evol Dev, 2009 Jan-Feb. PMID 19196331
  3. Genome-wide survey and developmental expression mapping of zebrafish SET domain-containing genes. Sun XJ, et al. PLoS One, 2008 Jan 30. PMID 18231586, Free PMC Article
  4. Gene-expression analysis of hair cell regeneration in the zebrafish lateral line. Jiang L, et al. Proc Natl Acad Sci U S A, 2014 Apr 8. PMID 24706903, Free PMC Article
  5. A network of epigenetic regulators guides developmental haematopoiesis in vivo. Huang HT, et al. Nat Cell Biol, 2013 Dec. PMID 24240475, Free PMC Article

See all (8) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II cis-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
  
enables methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables transferase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cell fate commitment IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within cellular developmental process IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within methylation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of transcription by RNA polymerase II 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 cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
PR domain zinc finger protein 1
Names
PR domain zinc finger protein 1-like

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007130.7 Reference GRCz11 Primary Assembly

    Range
    48160385..48186103
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021468195.2 → XP_021323870.1  PR domain zinc finger protein 1 isoform X1

    UniProtKB/TrEMBL
    A0A8M9PS04
    Related
    ENSDARP00000148592.1, ENSDART00000186574.1
    Conserved Domains (5) summary
    smart00317
    Location:52 → 165
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5048
    Location:203 → 524
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:437 → 457
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:477 → 502
    zf-H2C2_2; Zinc-finger double domain
    cl21478
    Location:581 → 637
    ATP-synt_B; ATP synthase B/B' CF(0)

  2. XM_021468196.2 → XP_021323871.1  PR domain zinc finger protein 1 isoform X2

    UniProtKB/TrEMBL
    A0A8M9PNQ5
    Related
    ENSDARP00000137428.2, ENSDART00000164963.2
    Conserved Domains (5) summary
    smart00317
    Location:12 → 71
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5048
    Location:109 → 430
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:343 → 363
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:383 → 408
    zf-H2C2_2; Zinc-finger double domain
    cl21478
    Location:487 → 543
    ATP-synt_B; ATP synthase B/B' CF(0)
Nucleotide Protein Strain
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