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Dlk1 delta like non-canonical Notch ligand 1 [ Mus musculus (house mouse) ]

Gene ID: 13386, updated on 18-Apr-2024

Summary

Official Symbol
Dlk1provided by MGI
Official Full Name
delta like non-canonical Notch ligand 1provided by MGI
Primary source
MGI:MGI:94900
See related
Ensembl:ENSMUSG00000040856 AllianceGenome:MGI:94900
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
FA1; ZOG; pG2; DlkI; Peg9; SCP1; DLK-1; Ly107; pref-1
Summary
Predicted to enable calcium ion binding activity. Involved in negative regulation of fat cell differentiation and negative regulation of vascular endothelial cell proliferation. Acts upstream of or within several processes, including bone mineralization; negative regulation of Notch signaling pathway; and positive regulation of bone resorption. Located in external side of plasma membrane. Is expressed in several structures, including alimentary system; branchial arch; embryo mesenchyme; genitourinary system; and nervous system. Orthologous to human DLK1 (delta like non-canonical Notch ligand 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in limb E14.5 (RPKM 294.1), liver E14.5 (RPKM 215.8) and 7 other tissues See more
Orthologs
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Genomic context

Location:
12 F1; 12 60.17 cM
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (109418411..109429262)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (109452485..109463336)

Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene CapStarr-seq enhancer MGSCv37_chr12:110295982-110296239 Neighboring gene STARR-positive B cell enhancer mm9_chr12:110312387-110312688 Neighboring gene STARR-positive B cell enhancer mm9_chr12:110313106-110313407 Neighboring gene predicted gene, 52002 Neighboring gene brain-enriched guanylate kinase-associated Neighboring gene macrophage migration inhibitory factor, pseudogene 7 Neighboring gene STARR-seq mESC enhancer starr_33259 Neighboring gene STARR-seq mESC enhancer starr_33260 Neighboring gene CapStarr-seq enhancer MGSCv37_chr12:110676232-110676385 Neighboring gene VISTA enhancer mm799 Neighboring gene predicted gene, 34081 Neighboring gene predicted gene, 34017 Neighboring gene microRNA 1906-1 Neighboring gene maternally expressed 3

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)

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables calcium 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 bone mineralization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cell differentiation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within embryo development IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within embryonic skeletal system development IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within multicellular organism growth IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of Notch signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within negative regulation of Notch signaling pathway IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in negative regulation of Notch signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of fat cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of ossification ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of osteoblast differentiation ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of vascular endothelial cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within ossification IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within osteoblast differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of bone resorption IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of bone resorption ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of cytokine production IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of osteoclast differentiation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within post-embryonic development IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of bone remodeling ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in external side of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in extracellular space ISO
Inferred from Sequence Orthology
more info
 
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
protein delta homolog 1
Names
adipocyte differentiation inhibitor protein
delta-like 1 homolog
fetal antigen 1
preadipocyte factor 1
stromal cell derived protein 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_001190703.2NP_001177632.1  protein delta homolog 1 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001177632.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AC165954
    Consensus CDS
    CCDS49173.1
    UniProtKB/TrEMBL
    E9PVN3, Q9DAU5
    Related
    ENSMUSP00000105469.2, ENSMUST00000109843.8
    Conserved Domains (1) summary
    cd00054
    Location:88125
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
  2. NM_001190704.2NP_001177633.1  protein delta homolog 1 isoform 3 precursor

    See identical proteins and their annotated locations for NP_001177633.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 3), compared to isoform 1.
    Source sequence(s)
    AC165954
    Consensus CDS
    CCDS56863.1
    UniProtKB/TrEMBL
    B4YB46, E9PVN2, E9PVN3
    Related
    ENSMUSP00000105468.3, ENSMUST00000109842.9
    Conserved Domains (1) summary
    cd00054
    Location:177207
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
  3. NM_001190705.2NP_001177634.1  protein delta homolog 1 isoform 4 precursor

    See identical proteins and their annotated locations for NP_001177634.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 4), compared to isoform 1.
    Source sequence(s)
    AC165954
    Consensus CDS
    CCDS49174.1
    UniProtKB/TrEMBL
    B4YB48, E9PVN3
    Related
    ENSMUSP00000105472.5, ENSMUST00000109846.11
    Conserved Domains (1) summary
    cd00054
    Location:88125
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
  4. NM_001421736.1NP_001408665.1  protein delta homolog 1 isoform 5 precursor

    Status: VALIDATED

    Source sequence(s)
    AC165954
    UniProtKB/TrEMBL
    G3UWU8
  5. NM_010052.6NP_034182.2  protein delta homolog 1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_034182.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC165954
    Consensus CDS
    CCDS26168.1
    UniProtKB/Swiss-Prot
    Q07645, Q09163, Q62208
    UniProtKB/TrEMBL
    Q925U3
    Related
    ENSMUSP00000105470.5, ENSMUST00000109844.11
    Conserved Domains (1) summary
    cd00054
    Location:88125
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

RNA

  1. NR_033813.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains an alternate 5' exon and uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC165954, AK133664, CV562715

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_000078.7 Reference GRCm39 C57BL/6J

    Range
    109418411..109429262
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030246536.1XP_030102396.1  protein delta homolog 1 isoform X2

    UniProtKB/TrEMBL
    E9PVN3, G3UWU8
    Conserved Domains (1) summary
    cd00054
    Location:177207
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
  2. XM_011243992.4XP_011242294.1  protein delta homolog 1 isoform X1

    See identical proteins and their annotated locations for XP_011242294.1

    UniProtKB/Swiss-Prot
    Q07645, Q09163, Q62208
    Conserved Domains (1) summary
    cd00054
    Location:88125
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...