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prdm4.L PR domain 4 L homeolog [ Xenopus laevis (African clawed frog) ]

Gene ID: 379872, updated on 4-Nov-2024

Summary

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Official Symbol
prdm4.L
Official Full Name
PR domain 4 L homeolog
Primary source
Xenbase:XB-GENE-958487
Locus tag
XELAEV_18002489mg
See related
EnsemblRapid:ENSXLAG00005005808 AllianceGenome:Xenbase:XB-GENE-958487
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Xenopus laevis
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Xenopus
Also known as
pfm1; prdm4
Summary
Predicted to enable several functions, including DNA-binding transcription factor activity; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and histone methyltransferase binding activity. Predicted to act upstream of or within methylation; regulation of transcription by RNA polymerase II; and transcription by RNA polymerase II. Predicted to be located in nucleus. Is expressed in musculoskeletal system; nervous system; pharyngeal arch; and visual system. Orthologous to human PRDM4 (PR/SET domain 4). [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See prdm4.L in Genome Data Viewer
Location:
chromosome: 3L
Exon count:
14
Annotation release Status Assembly Chr Location
101 current Xenopus_laevis_v10.1 (GCF_017654675.1) 3L NC_054375.1 (6612859..6632893)
100 previous assembly Xenopus_laevis_v2 (GCF_001663975.1) Unplaced Scaffold NW_016694822.1 (1682517..1700439)

Chromosome 3L - NC_054375.1Genomic Context describing neighboring genes Neighboring gene RNA 2',3'-cyclic phosphate and 5'-OH ligase L homeolog Neighboring gene achaete-scute homolog 4 Neighboring gene aldo-keto reductase family 1, member B1 (aldose reductase) L homeolog Neighboring gene provisional ortholog of carbonyl reductase 1 L homeolog

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Genetic and genomic tools for Xenopus research: The NIH Xenopus initiative. Klein SL, et al. Dev Dyn, 2002 Dec. PMID 12454917
  2. 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

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Clone Names

  • MGC53711, MGC132367

Gene Ontology Provided by Xenbase

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables histone methyltransferase binding IEA
Inferred from Electronic Annotation
more info
  
enables methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within methylation IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
PR domain 4 L homeolog
Names
PR domain containing 4 L homeolog

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_001086711.1 → NP_001080180.1  PR domain 4 L homeolog

    See identical proteins and their annotated locations for NP_001080180.1

    Status: PROVISIONAL

    Source sequence(s)
    BC108880
    UniProtKB/TrEMBL
    Q32N18, Q7ZYB2
    Conserved Domains (5) summary
    smart00317
    Location:386 → 493
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5048
    Location:570 → 707
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:577 → 597
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:575 → 597
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:589 → 614
    zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: Xenopus laevis Annotation Release 101 details...Open this link in a new tab

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

Reference Xenopus_laevis_v10.1 Primary Assembly

Genomic

  1. NC_054375.1 Reference Xenopus_laevis_v10.1 Primary Assembly

    Range
    6612859..6632893
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_041584945.1 → XP_041440879.1  PR domain 4 L homeolog isoform X1

    UniProtKB/TrEMBL
    A0A8J1MGN7, Q7ZYB2
    Related
    ENSXLAP00005017297.1, ENSXLAT00005017593.1
    Conserved Domains (4) summary
    COG5048
    Location:570 → 694
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:577 → 597
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18445
    Location:325 → 362
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:365 → 497
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins

  2. XM_041584946.1 → XP_041440880.1  PR domain 4 L homeolog isoform X2

    UniProtKB/TrEMBL
    A0A8J1MIJ2, Q7ZYB2
    Related
    ENSXLAP00005017304.1, ENSXLAT00005017600.1
    Conserved Domains (4) summary
    COG5048
    Location:566 → 690
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:573 → 593
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18445
    Location:321 → 358
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:361 → 493
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins

  3. XM_041584947.1 → XP_041440881.1  PR domain 4 L homeolog isoform X3

    UniProtKB/TrEMBL
    A0A8J1MHL8, Q7ZYB2
    Related
    ENSXLAP00005017284.1, ENSXLAT00005017580.1
    Conserved Domains (4) summary
    COG5048
    Location:500 → 624
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:507 → 527
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18445
    Location:255 → 292
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:295 → 427
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins
Nucleotide Protein Strain
Heading Accession and Version

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