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Unc5d unc-5 netrin receptor D [ Mus musculus (house mouse) ]

Gene ID: 210801, updated on 11-Apr-2024

Summary

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Official Symbol
Unc5dprovided by MGI
Official Full Name
unc-5 netrin receptor Dprovided by MGI
Primary source
MGI:MGI:2389364
See related
Ensembl:ENSMUSG00000063626 AllianceGenome:MGI:2389364
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
Unc5h4; mKIAA1777; D930029E11Rik
Summary
Predicted to enable netrin receptor activity. Acts upstream of or within axon guidance; pyramidal neuron differentiation; and regulation of neuron migration. Located in cell surface. Is expressed in several structures, including brain; integumental system; jaw; limb; and sensory organ. Orthologous to human UNC5D (unc-5 netrin receptor D). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in CNS E18 (RPKM 4.0), cortex adult (RPKM 3.1) and 6 other tissues See more
Orthologs
human all
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Genomic context

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Location:
8 A2- A3; 8 16.47 cM
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (29136745..29709698, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (28646717..29219671, complement)

Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_21056 Neighboring gene testis expressed gene 24 pseudogene Neighboring gene STARR-seq mESC enhancer starr_21057 Neighboring gene STARR-seq mESC enhancer starr_21058 Neighboring gene STARR-seq mESC enhancer starr_21059 Neighboring gene predicted gene, 26795 Neighboring gene predicted gene, 32505 Neighboring gene STARR-seq mESC enhancer starr_21060 Neighboring gene STARR-seq mESC enhancer starr_21061 Neighboring gene STARR-seq mESC enhancer starr_21062 Neighboring gene STARR-seq mESC enhancer starr_21063 Neighboring gene STARR-seq mESC enhancer starr_21064 Neighboring gene STARR-seq mESC enhancer starr_21065 Neighboring gene predicted gene, 32567 Neighboring gene nuclear distribution gene C homolog (Aspergillus), pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Drebrin-like (Dbnl) Controls Neuronal Migration via Regulating N-Cadherin Expression in the Developing Cerebral Cortex. Inoue S, et al. J Neurosci, 2019 Jan 23. PMID 30504273, Free PMC Article
  2. A Prdm8 target gene Ebf3 regulates multipolar-to-bipolar transition in migrating neocortical cells. Iwai R, et al. Biochem Biophys Res Commun, 2018 Jan 1. PMID 29113800
  3. Dependence receptor UNC5D mediates nerve growth factor depletion-induced neuroblastoma regression. Zhu Y, et al. J Clin Invest, 2013 Jul. PMID 23778138, Free PMC Article
  4. Unc5B interacts with FLRT3 and Rnd1 to modulate cell adhesion in Xenopus embryos. Karaulanov E, et al. PLoS One, 2009 May 29. PMID 19492039, Free PMC Article
  5. Super-complexes of adhesion GPCRs and neural guidance receptors. Jackson VA, et al. Nat Commun, 2016 Apr 19. PMID 27091502, Free PMC Article

See all (61) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Data show that Unc5 cell guidance receptor Unc5D controls Latrophilin3 (LPHN3)-FLRT protein FLRT2-mediated cell adhesion.
    Title: Super-complexes of adhesion GPCRs and neural guidance receptors.
  2. Unc5d is primarily expressed by layer 4 cells in the primary sensory areas of the developing neocortex and may mediate the effect of netrin-4 on cortical cell survival in a lamina-specific manner.
    Title: Laminar and areal expression of unc5d and its role in cortical cell survival.
  3. UNC5D protein and nuclear RNA is localized in the multipolar cells of the subventricular zone throughout cortical development.
    Title: The cortical subventricular zone-specific molecule Svet1 is part of the nuclear RNA coded by the putative netrin receptor gene Unc5d and is expressed in multipolar migrating cells.
  4. Unc5h4 was cloned; its expression is in the developing limb and mammary gland in developing mouse
    Title: Cloning of three mouse Unc5 genes and their expression patterns at mid-gestation.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1777

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables netrin receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within apoptotic process IEA
Inferred from Electronic Annotation
more info
  
involved_in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within axon guidance IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in cell-cell adhesion via plasma-membrane adhesion molecules ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
  
involved_in netrin-activated signaling pathway IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within pyramidal neuron differentiation IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within regulation of neuron migration IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in signal transduction IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cell surface IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
netrin receptor UNC5D
Names
protein unc-5 homolog 4
protein unc-5 homolog D
unc5 homolog 4

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_001347498.1 → NP_001334427.1  netrin receptor UNC5D isoform 2 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks three in-frame exons in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC127329, AC132947, AC163090
    Consensus CDS
    CCDS85521.1
    UniProtKB/TrEMBL
    A6H5Z5, B7ZMT3
    Related
    ENSMUSP00000147306.2, ENSMUST00000211448.2

  2. NM_001347499.1 → NP_001334428.1  netrin receptor UNC5D isoform 3 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks one in-frame exon and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AC127329, AC132947, AC163090
    Consensus CDS
    CCDS85524.1
    UniProtKB/TrEMBL
    B7ZMT3, C5IAW8
    Related
    ENSMUSP00000147721.2, ENSMUST00000210785.2

  3. NM_001347500.1 → NP_001334429.1  netrin receptor UNC5D isoform 4 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks two in-frame exons and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AC127329, AC132947, AC163090
    Consensus CDS
    CCDS85523.1
    UniProtKB/TrEMBL
    A0A1B0GSR6, B7ZMT3
    Related
    ENSMUSP00000148043.2, ENSMUST00000209401.2

  4. NM_001347501.1 → NP_001334430.1  netrin receptor UNC5D isoform 5 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks two in-frame exons in the 5' coding region and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (5) is shorter than isoform 1.
    Source sequence(s)
    AC127329, AC132947, AC163090
    Consensus CDS
    CCDS85522.1
    UniProtKB/TrEMBL
    B7ZMT2, B7ZMT3
    Related
    ENSMUSP00000148236.2, ENSMUST00000210298.2

  5. NM_153135.3 → NP_694775.1  netrin receptor UNC5D isoform 1 precursor

    See identical proteins and their annotated locations for NP_694775.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC127329, AC163090, AJ487854
    Consensus CDS
    CCDS40314.1
    UniProtKB/Swiss-Prot
    B9EHC0, Q8K1S2
    UniProtKB/TrEMBL
    B7ZMT3
    Related
    ENSMUSP00000128521.3, ENSMUST00000168630.4
    Conserved Domains (5) summary
    cd08801
    Location:856 → 953
    Death_UNC5D; Death domain found in Uncoordinated-5D
    smart00209
    Location:253 → 304
    TSP1; Thrombospondin type 1 repeats
    pfam07679
    Location:159 → 247
    I-set; Immunoglobulin I-set domain
    pfam00791
    Location:545 → 640
    ZU5; ZU5 domain
    cl11960
    Location:161 → 247
    Ig; Immunoglobulin domain

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
    29136745..29709698 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006509054.5 → XP_006509117.1  netrin receptor UNC5D isoform X5

    UniProtKB/TrEMBL
    B7ZMT3
    Conserved Domains (5) summary
    cd08801
    Location:836 → 933
    Death_UNC5D; Death domain found in Uncoordinated-5D
    smart00209
    Location:253 → 304
    TSP1; Thrombospondin type 1 repeats
    pfam00791
    Location:546 → 642
    ZU5; ZU5 domain
    pfam17217
    Location:690 → 809
    UPA; UPA domain
    cl11960
    Location:161 → 247
    Ig; Immunoglobulin domain

  2. XM_006509051.5 → XP_006509114.1  netrin receptor UNC5D isoform X3

    UniProtKB/TrEMBL
    B7ZMT3
    Conserved Domains (5) summary
    cd08801
    Location:843 → 940
    Death_UNC5D; Death domain found in Uncoordinated-5D
    smart00209
    Location:253 → 304
    TSP1; Thrombospondin type 1 repeats
    pfam00791
    Location:533 → 629
    ZU5; ZU5 domain
    pfam17217
    Location:677 → 816
    UPA; UPA domain
    cl11960
    Location:161 → 247
    Ig; Immunoglobulin domain

  3. XM_006509055.5 → XP_006509118.1  netrin receptor UNC5D isoform X6

    UniProtKB/TrEMBL
    B7ZMT3
    Conserved Domains (5) summary
    cd08801
    Location:800 → 897
    Death_UNC5D; Death domain found in Uncoordinated-5D
    smart00209
    Location:253 → 301
    TSP1; Thrombospondin type 1 repeats
    pfam00791
    Location:490 → 586
    ZU5; ZU5 domain
    pfam17217
    Location:634 → 773
    UPA; UPA domain
    cl11960
    Location:161 → 247
    Ig; Immunoglobulin domain

  4. XM_006509052.5 → XP_006509115.1  netrin receptor UNC5D isoform X4

    UniProtKB/TrEMBL
    B7ZMT3
    Conserved Domains (5) summary
    cd08801
    Location:840 → 937
    Death_UNC5D; Death domain found in Uncoordinated-5D
    smart00209
    Location:253 → 304
    TSP1; Thrombospondin type 1 repeats
    pfam00791
    Location:530 → 626
    ZU5; ZU5 domain
    pfam17217
    Location:674 → 813
    UPA; UPA domain
    cl11960
    Location:161 → 247
    Ig; Immunoglobulin domain

  5. XM_006509050.5 → XP_006509113.1  netrin receptor UNC5D isoform X2

    UniProtKB/TrEMBL
    B7ZMT3
    Conserved Domains (5) summary
    cd08801
    Location:845 → 942
    Death_UNC5D; Death domain found in Uncoordinated-5D
    smart00209
    Location:253 → 304
    TSP1; Thrombospondin type 1 repeats
    pfam00791
    Location:535 → 631
    ZU5; ZU5 domain
    pfam17217
    Location:679 → 818
    UPA; UPA domain
    cl11960
    Location:161 → 247
    Ig; Immunoglobulin domain

  6. XM_006509049.5 → XP_006509112.1  netrin receptor UNC5D isoform X1

    UniProtKB/TrEMBL
    B7ZMT3
    Conserved Domains (5) summary
    cd08801
    Location:851 → 948
    Death_UNC5D; Death domain found in Uncoordinated-5D
    smart00209
    Location:253 → 304
    TSP1; Thrombospondin type 1 repeats
    pfam00791
    Location:541 → 637
    ZU5; ZU5 domain
    pfam17217
    Location:685 → 824
    UPA; UPA domain
    cl11960
    Location:161 → 247
    Ig; Immunoglobulin domain

  7. XM_036153853.1 → XP_036009746.1  netrin receptor UNC5D isoform X7

    UniProtKB/TrEMBL
    B7ZMT3
    Conserved Domains (6) summary
    cd08801
    Location:795 → 892
    Death_UNC5D; Death domain found in Uncoordinated-5D
    smart00209
    Location:253 → 301
    TSP1; Thrombospondin type 1 repeats
    pfam00791
    Location:485 → 581
    ZU5; ZU5 domain
    pfam17217
    Location:629 → 768
    UPA; UPA domain
    cd00096
    Location:165 → 169
    Ig; Ig strand A' [structural motif]
    cl11960
    Location:161 → 247
    Ig; Immunoglobulin domain
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8K1S2.1 GenPept UniProtKB/Swiss-Prot:Q8K1S2

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