prdm1a PR domain containing 1a, with ZNF domain [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: prdm1aprovided by ZNC
Official Full Name: PR domain containing 1a, with ZNF domainprovided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-2193
See related: Ensembl:ENSDARG00000002445 AllianceGenome:ZFIN:ZDB-GENE-030131-2193
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: nrd; ubo; prdm1; Blimp1; Blimp-1; zgc:91885; wu:fb99c12
Summary: Enables DNA-binding transcription factor activity. Acts upstream of or within several processes, including negative regulation of macromolecule metabolic process; positive regulation of cell differentiation; and skeletal system morphogenesis. Predicted to be active in cytoplasm and nucleus. Is expressed in several structures, including ectoderm; fin bud; gut; head; and mesoderm. Orthologous to human PRDM1 (PR/SET domain 1). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 16

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	16	NC_007127.7 (7430998..7443372, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	16	NC_007127.6 (7513652..7590613, complement)

Chromosome 16 - NC_007127.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Human split hand/foot variants are not as functional as wildtype human PRDM1 in the rescue of craniofacial defects.
Title: Human split hand/foot variants are not as functional as wildtype human PRDM1 in the rescue of craniofacial defects.
PRDM1 DNA-binding zinc finger domain is required for normal limb development and is disrupted in split hand/foot malformation.
Title: PRDM1 DNA-binding zinc finger domain is required for normal limb development and is disrupted in split hand/foot malformation.
Remodeling of the tumor microenvironment via disrupting Blimp1(+) effector Treg activity augments response to anti-PD-1 blockade.
Title: Remodeling of the tumor microenvironment via disrupting Blimp1(+) effector Treg activity augments response to anti-PD-1 blockade.
Expression of the M- and N-cadherins, previously implicated in driving adaxial cell migration, is largely unaffected by loss of Prdm1a function, suggesting that differential cadherin expression is not sufficient for adaxial cell migration
Title: Adaxial cell migration in the zebrafish embryo is an active cell autonomous property that requires the Prdm1a transcription factor.
Prdm1a functions as both a transcriptional activator and repressor during neural crest development.
Title: Prdm1a directly activates foxd3 and tfap2a during zebrafish neural crest specification.
identify sox6 cis-regulatory sequences that drive fast-twitch-specific expression in a Prdm1a-dependent manner
Title: Prdm1a and miR-499 act sequentially to restrict Sox6 activity to the fast-twitch muscle lineage in the zebrafish embryo.
prdm1a expression is upregulated in the absence of Notch function, and inhibiting Notch signaling fails to rescue prdm1a mutants
Title: prdm1a and olig4 act downstream of Notch signaling to regulate cell fate at the neural plate border.
prdm1a Regulates sox10 and islet1 in the development of neural crest and Rohon-Beard sensory neurons.
Title: prdm1a Regulates sox10 and islet1 in the development of neural crest and Rohon-Beard sensory neurons.
These results indicate an essential role for prdm1a in the development of the zebrafish craniofacial skeleton.
Title: Prdm1a is necessary for posterior pharyngeal arch development in zebrafish.
Blimp1 programs myoblasts to adopt the slow-twitch fiber fate and can repress the expression of fast muscle-specific myosin light chain, mylz2.
Title: Specification of vertebrate slow-twitch muscle fiber fate by the transcriptional regulator Blimp1.

Submit: New GeneRIF Correction See all GeneRIFs (19)

General gene information

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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 factor activity	IDA Inferred from Direct Assay more info	PubMed
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
acts_upstream_of_or_within cartilage development involved in endochondral bone morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
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 developmental pigmentation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic axis specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic cranial skeleton morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic neurocranium morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic pectoral fin morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic viscerocranium morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic viscerocranium morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within fin development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within methylation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within muscle cell fate determination	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within neural crest cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural crest cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pectoral fin morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pharyngeal system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of striated muscle cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
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 1a

Names: B lymphocyte-induced maturation protein 1; PR domain containing 1, with ZNF domain; PR domain-containing 1; U boot; narrowminded; u-boot

NP_955809.2

EC 2.1.1.-

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)

NM_199515.2 → NP_955809.2 PR domain zinc finger protein 1a

See identical proteins and their annotated locations for NP_955809.2

Status: PROVISIONAL

Source sequence(s)

BC080259

UniProtKB/TrEMBL

A0A8M1PFD2, Q68EH4

Related

ENSDARP00000004889.5, ENSDART00000017445.7

Conserved Domains (6) summary

smart00317
Location:95 → 200

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

COG5048
Location:517 → 634

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:524 → 544

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:522 → 544

zf-C2H2; Zinc finger, C2H2 type

pfam02354
Location:236 → 344

Latrophilin; Latrophilin Cytoplasmic C-terminal region

pfam13465
Location:564 → 589

zf-H2C2_2; Zinc-finger double domain