nkd1 NKD inhibitor of WNT signaling pathway 1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: nkd1provided by ZNC
Official Full Name: NKD inhibitor of WNT signaling pathway 1provided by ZNC
Primary source: ZFIN:ZDB-GENE-061108-3
See related: Ensembl:ENSDARG00000020053 AllianceGenome:ZFIN:ZDB-GENE-061108-3
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
Summary: Predicted to enable calcium ion binding activity. Acts upstream of or within several processes, including Kupffer's vesicle development; embryonic heart tube development; and negative regulation of canonical Wnt signaling pathway. Located in cytoplasm and plasma membrane. Is expressed in several structures, including forerunner cell group; hindbrain neural rod; mesoderm; neural tube; and tail bud. Orthologous to human NKD1 (NKD inhibitor of WNT signaling pathway 1). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 7

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	7	NC_007118.7 (37584785..37622298, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	7	NC_007118.6 (37311026..37351112, complement)

Chromosome 7 - NC_007118.7 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 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?

Nkd1 functions downstream of Axin2 to attenuate Wnt signaling.
Title: Nkd1 functions downstream of Axin2 to attenuate Wnt signaling.
This work reveals that the zebrafish Nkd1 EF-hand is essential to balance Wnt signaling inputs and modulate the appropriate outputs, while the Drosophila-like EF-Hand primarily functions in beta-catenin signaling.
Title: The Nkd EF-hand domain modulates divergent wnt signaling outputs in zebrafish.
Nkd1 activity is specifically dependent on Wnt ligand activation of the receptor. Nkd1 is recruited to the Wnt signalosome with Dvl2, where it becomes activated to move into the cytoplasm to interact with beta-catenin, inhibiting its nuclear accumulation.
Title: Wnt ligand-dependent activation of the negative feedback regulator Nkd1.
Nkd1 functions as a passive antagonist of Wnt signaling, functioning only when homeostatic levels of Wnt signaling have been breached or when Wnt signaling becomes destabilized.
Title: Nkd1 functions as a passive antagonist of Wnt signaling.
Data demonstrate that Nkd1 binds to beta-catenin and prevents its nuclear accumulation. Nkd1 function is dependent on its interaction with the cell membrane.
Title: Naked1 antagonizes Wnt signaling by preventing nuclear accumulation of β-catenin.
Nkd1 knockdown in the dorsal forerunner cells causes beta-catenin nuclear localization/transcriptional activation & changes in DFC migration, Kupffer's vesicle formation, ciliogenesis, left-right patterning, & asymmetric charon expression.
Title: Zebrafish Nkd1 promotes Dvl degradation and is required for left-right patterning.
data indicate that zebrafish Nkd1 and Nkd2 function to limit both canonical and non-canonical Wnt signaling
Title: Zebrafish Naked1 and Naked2 antagonize both canonical and non-canonical Wnt signaling.

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General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within Kupffer's vesicle development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within Spemann organizer formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within Wnt signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within Wnt signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic heart tube left/right pattern formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart jogging	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within left/right pattern formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of Wnt signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of canonical Wnt signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of canonical Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of protein import into nucleus	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within neural plate morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: protein naked cuticle homolog 1

Names: NKD1, WNT signaling pathway inhibitor; naked 1; naked cuticle homolog 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_001043333.1 → NP_001036798.1 protein naked cuticle homolog 1

See identical proteins and their annotated locations for NP_001036798.1

Status: PROVISIONAL

Source sequence(s)

AY863053

UniProtKB/Swiss-Prot

Q2TJA6

UniProtKB/TrEMBL

B0S7E2

Related

ENSDARP00000142757.1, ENSDART00000173523.2

Conserved Domains (1) summary

pfam05518
Location:268 → 370

Totivirus_coat; Totivirus coat protein

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

NC_007118.7 Reference GRCz11 Primary Assembly

Range

37584785..37622298 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005169004.5 → XP_005169061.1 protein naked cuticle homolog 1 isoform X1

UniProtKB/TrEMBL

A0A1I7Q3W8, A0A8M2BGA4

Related

ENSDARP00000052378.6, ENSDART00000052379.7

Conserved Domains (1) summary

pfam05518
Location:270 → 369

Totivirus_coat; Totivirus coat protein