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Nkd1 naked cuticle 1 [ Mus musculus (house mouse) ]

Gene ID: 93960, updated on 8-Feb-2024

Summary

Official Symbol
Nkd1provided by MGI
Official Full Name
naked cuticle 1provided by MGI
Primary source
MGI:MGI:2135954
See related
Ensembl:ENSMUSG00000031661 AllianceGenome:MGI:2135954
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Nkd; 2810434J10Rik; 9030215G15Rik
Summary
Enables PDZ domain binding activity. Involved in negative regulation of convergent extension involved in axis elongation and regulation of Wnt signaling pathway. Predicted to be located in plasma membrane. Predicted to be part of protein phosphatase type 2A complex. Predicted to be active in cytoplasm. Is expressed in several structures, including brain; genitourinary system; gut; retina; and unsegmented mesenchyme. Orthologous to human NKD1 (NKD inhibitor of WNT signaling pathway 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in lung adult (RPKM 30.7), bladder adult (RPKM 15.6) and 21 other tissues See more
Orthologs
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Genomic context

See Nkd1 in Genome Data Viewer
Location:
8 C3; 8 43.36 cM
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (89247961..89321515)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (88521342..88594887)

Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 35076 Neighboring gene predicted gene, 35162 Neighboring gene STARR-positive B cell enhancer ABC_E10516 Neighboring gene STARR-seq mESC enhancer starr_22236 Neighboring gene STARR-seq mESC enhancer starr_22237 Neighboring gene sorting nexin 20 Neighboring gene STARR-positive B cell enhancer ABC_E2869 Neighboring gene STARR-positive B cell enhancer ABC_E3791 Neighboring gene nucleotide-binding oligomerization domain containing 2 Neighboring gene STARR-positive B cell enhancer ABC_E6672

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (2)  1 citation
  • Endonuclease-mediated (1) 

Pathways from PubChem

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables PDZ domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in axis elongation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in convergent extension IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of Wnt signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in negative regulation of Wnt signaling pathway IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in negative regulation of canonical Wnt signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of canonical Wnt signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of MAPK cascade IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of Wnt signaling pathway, planar cell polarity pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of non-canonical Wnt signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of protein catabolic process ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within spermatogenesis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in membrane IEA
Inferred from Electronic Annotation
more info
 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
 
part_of protein phosphatase type 2A complex ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
protein naked cuticle homolog 1
Names
mNkd
mNkd1
naked cuticle 1 homolog
naked-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)

  1. NM_001163660.1NP_001157132.1  protein naked cuticle homolog 1 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AC126054, DV662736
    Consensus CDS
    CCDS52631.1
    UniProtKB/TrEMBL
    E9Q5K6
    Related
    ENSMUSP00000125935.2, ENSMUST00000169179.3
    Conserved Domains (1) summary
    pfam13499
    Location:3366
    EF-hand_7; EF-hand domain pair
  2. NM_027280.3NP_081556.3  protein naked cuticle homolog 1 isoform 1

    See identical proteins and their annotated locations for NP_081556.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC126054, AK166564, BC034838
    Consensus CDS
    CCDS22511.1
    UniProtKB/Swiss-Prot
    Q3TLD6, Q8K200, Q91Y46, Q99MH6
    Related
    ENSMUSP00000034086.6, ENSMUST00000034086.13

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000074.7 Reference GRCm39 C57BL/6J

    Range
    89247961..89321515
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030243873.2XP_030099733.1  protein naked cuticle homolog 1 isoform X1

    UniProtKB/TrEMBL
    E9Q5K6
    Related
    ENSMUSP00000147347.2, ENSMUST00000211113.2
    Conserved Domains (1) summary
    pfam13499
    Location:3366
    EF-hand_7; EF-hand domain pair