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Aliases for STARD3NL Gene

Aliases for STARD3NL Gene

  • STARD3 N-Terminal Like 2 3 5
  • MLN64 N-Terminal Domain Homolog 3 4
  • MENTHO 3 4
  • STARD3 N-Terminal-Like Protein 3

External Ids for STARD3NL Gene

Previous GeneCards Identifiers for STARD3NL Gene

  • GC07P037865
  • GC07P037958
  • GC07P037991
  • GC07P038184

Summaries for STARD3NL Gene

Entrez Gene Summary for STARD3NL Gene

  • This gene encodes a late-endosomal protein that contains a conserved MENTAL (MLN64 N-terminal) domain. The encoded protein binds cholesterol molecules and may play a role in endosomal cholesterol transport through interactions with metastatic lymph node protein 64 (MLN64). [provided by RefSeq, Sep 2011]

GeneCards Summary for STARD3NL Gene

STARD3NL (STARD3 N-Terminal Like) is a Protein Coding gene. Among its related pathways are Cholesterol and Sphingolipids transport / Distribution to the intracellular membrane compartments (normal and CF) and Metabolism. An important paralog of this gene is STARD3.

UniProtKB/Swiss-Prot for STARD3NL Gene

  • Tethering protein that creates contact site between the endoplasmic reticulum and late endosomes: localizes to late endosome membranes and contacts the endoplasmic reticulum via interaction with VAPA and VAPB (PubMed:24105263).

Gene Wiki entry for STARD3NL Gene

Additional gene information for STARD3NL Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for STARD3NL Gene

Genomics for STARD3NL Gene

GeneHancer (GH) Regulatory Elements for STARD3NL Gene

Promoters and enhancers for STARD3NL Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07I038177 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 599.3 +1.1 1147 4.3 PKNOX1 SMAD1 ZFP64 ARID4B SIN3A DMAP1 POLR2B ZNF143 FOS SP3 STARD3NL TRGC2
GH07I038215 Enhancer 1.2 Ensembl ENCODE dbSUPER 25.4 +41.1 41111 8.2 ELF3 PKNOX1 FOXA2 RB1 ARNT ZSCAN4 BATF IRF4 RAD21 ARID2 STARD3NL TRGC2 SFRP4
GH07I038185 Enhancer 0.5 ENCODE 48.3 +8.2 8237 2.1 FOSL1 PKNOX1 ATF7 EBF1 PRDM10 KLF5 SPI1 STARD3NL TRGC1 TRGC2
GH07I038329 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 13.1 +152.9 152870 2.6 HDAC1 ZNF335 ZNF143 ATF7 CAVIN1 ELF1 HDAC8 ZNF592 MEF2D NFIC ENSG00000272908 TRGV8 STARD3NL TRGV5P TARP GC07P038328 TRGV7 TRG
GH07I038334 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 11.3 +158.1 158135 3.7 HDGF PKNOX1 ARNT SIN3A ZNF2 POLR2B E2F8 ZNF143 ZNF263 SP3 TRGV7 ENSG00000272908 TRGV5 TRGV5P STARD3NL AMPH TRGV6 TRG
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around STARD3NL on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the STARD3NL gene promoter:

Genomic Locations for STARD3NL Gene

Genomic Locations for STARD3NL Gene
chr7:38,178,206-38,230,671
(GRCh38/hg38)
Size:
52,466 bases
Orientation:
Plus strand
chr7:38,217,824-38,270,272
(GRCh37/hg19)

Genomic View for STARD3NL Gene

Genes around STARD3NL on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
STARD3NL Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for STARD3NL Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for STARD3NL Gene

Proteins for STARD3NL Gene

  • Protein details for STARD3NL Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95772-STR3N_HUMAN
    Recommended name:
    STARD3 N-terminal-like protein
    Protein Accession:
    O95772
    Secondary Accessions:
    • A4D1X0

    Protein attributes for STARD3NL Gene

    Size:
    234 amino acids
    Molecular mass:
    26655 Da
    Quaternary structure:
    • Homodimer (PubMed:16709157). Interacts (via the MENTAL domain) with STARD3NL (PubMed:16709157). Interacts (via FFAT motif) with VAPA. Interacts (via FFAT motif) with VAPB (PubMed:24105263).

    Alternative splice isoforms for STARD3NL Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for STARD3NL Gene

Post-translational modifications for STARD3NL Gene

No Post-translational modifications

No data available for DME Specific Peptides for STARD3NL Gene

Domains & Families for STARD3NL Gene

Gene Families for STARD3NL Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for STARD3NL Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for STARD3NL Gene

Graphical View of Domain Structure for InterPro Entry

O95772

UniProtKB/Swiss-Prot:

STR3N_HUMAN :
  • The FFAT motif mediates interaction with VAPA and VAPB.
  • Belongs to the STARD3 family.
Domain:
  • The FFAT motif mediates interaction with VAPA and VAPB.
  • The MENTAL domain anchors the protein in endosome membranes and exposes the START domain in the cytosol (By similarity). It binds cholesterol and mediates homotypic as well as heterotypic interactions between STARD3 and STARD3NL (PubMed:15718238, PubMed:16709157).
Family:
  • Belongs to the STARD3 family.
genes like me logo Genes that share domains with STARD3NL: view

Function for STARD3NL Gene

Molecular function for STARD3NL Gene

UniProtKB/Swiss-Prot Function:
Tethering protein that creates contact site between the endoplasmic reticulum and late endosomes: localizes to late endosome membranes and contacts the endoplasmic reticulum via interaction with VAPA and VAPB (PubMed:24105263).

Phenotypes From GWAS Catalog for STARD3NL Gene

Gene Ontology (GO) - Molecular Function for STARD3NL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15718238
GO:0015485 cholesterol binding IBA,IDA 15718238
GO:0042803 protein homodimerization activity IDA 15718238
genes like me logo Genes that share ontologies with STARD3NL: view
genes like me logo Genes that share phenotypes with STARD3NL: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for STARD3NL Gene

Localization for STARD3NL Gene

Subcellular locations from UniProtKB/Swiss-Prot for STARD3NL Gene

Late endosome membrane; Multi-pass membrane protein. Note=Localizes to contact sites between the endoplasmic reticulum and late endosomes: associates with the endoplasmic reticulum membrane via interaction with VAPA and VAPB. {ECO:0000269 PubMed:24105263}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for STARD3NL gene
Compartment Confidence
cytosol 5
lysosome 5
endosome 5
plasma membrane 3
peroxisome 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for STARD3NL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005765 lysosomal membrane HDA,IDA 17897319
GO:0005768 endosome IEA --
GO:0005789 colocalizes_with endoplasmic reticulum membrane IDA 24105263
GO:0005829 cytosol TAS --
GO:0016020 membrane HDA,IEA 19946888
genes like me logo Genes that share ontologies with STARD3NL: view

Pathways & Interactions for STARD3NL Gene

genes like me logo Genes that share pathways with STARD3NL: view

Interacting Proteins for STARD3NL Gene

Gene Ontology (GO) - Biological Process for STARD3NL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006700 C21-steroid hormone biosynthetic process TAS --
GO:0099044 vesicle tethering to endoplasmic reticulum IDA 24105263
genes like me logo Genes that share ontologies with STARD3NL: view

No data available for SIGNOR curated interactions for STARD3NL Gene

Drugs & Compounds for STARD3NL Gene

No Compound Related Data Available

Transcripts for STARD3NL Gene

Unigene Clusters for STARD3NL Gene

STARD3 N-terminal like:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for STARD3NL Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b · 11c ^ 12a · 12b · 12c ^ 13 ^ 14
SP1: - - - - - - - -
SP2: - - - - - - -
SP3: - - - - - - -
SP4: - - - - - - -
SP5: - - - -
SP6: - - - - - - - - -
SP7: - - -
SP8: - - - - - -
SP9: - - - -
SP10: - -
SP11:

Relevant External Links for STARD3NL Gene

GeneLoc Exon Structure for
STARD3NL
ECgene alternative splicing isoforms for
STARD3NL

Expression for STARD3NL Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for STARD3NL Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for STARD3NL Gene

This gene is overexpressed in Breast (20.4), Bone (13.8), Pancreas (12.1), and Fetal Brain (11.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for STARD3NL Gene



Protein tissue co-expression partners for STARD3NL Gene

NURSA nuclear receptor signaling pathways regulating expression of STARD3NL Gene:

STARD3NL

SOURCE GeneReport for Unigene cluster for STARD3NL Gene:

Hs.744885

Evidence on tissue expression from TISSUES for STARD3NL Gene

  • Nervous system(4.7)
  • Kidney(4.3)
  • Intestine(4.2)
  • Liver(4.2)
  • Blood(4.1)
genes like me logo Genes that share expression patterns with STARD3NL: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for STARD3NL Gene

Orthologs for STARD3NL Gene

This gene was present in the common ancestor of animals.

Orthologs for STARD3NL Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia STARD3NL 33 34
  • 99.57 (n)
cow
(Bos Taurus)
Mammalia STARD3NL 33 34
  • 92.88 (n)
dog
(Canis familiaris)
Mammalia STARD3NL 33 34
  • 92.45 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia STARD3NL 34
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Stard3nl 33 16 34
  • 89.03 (n)
rat
(Rattus norvegicus)
Mammalia Stard3nl 33
  • 88.75 (n)
oppossum
(Monodelphis domestica)
Mammalia STARD3NL 34
  • 78 (a)
OneToOne
chicken
(Gallus gallus)
Aves STARD3NL 33 34
  • 80.6 (n)
lizard
(Anolis carolinensis)
Reptilia STARD3NL 34
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia stard3nl 33
  • 69.92 (n)
zebrafish
(Danio rerio)
Actinopterygii stard3nl 33 34
  • 66.81 (n)
wufa01c03 33
fruit fly
(Drosophila melanogaster)
Insecta Start1 34
  • 13 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea tag-340 34
  • 11 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 1 (a)
OneToMany
Species where no ortholog for STARD3NL was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for STARD3NL Gene

ENSEMBL:
Gene Tree for STARD3NL (if available)
TreeFam:
Gene Tree for STARD3NL (if available)

Paralogs for STARD3NL Gene

Paralogs for STARD3NL Gene

(1) SIMAP similar genes for STARD3NL Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with STARD3NL: view

Variants for STARD3NL Gene

Sequence variations from dbSNP and Humsavar for STARD3NL Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
rs1000159862 -- 38,231,061(+) T/C downstream_transcript_variant
rs1000225633 -- 38,212,773(+) G/A intron_variant
rs1000232655 -- 38,187,849(+) A/C/G genic_upstream_transcript_variant, intron_variant
rs1000356124 -- 38,216,173(+) C/T intron_variant
rs1000437193 -- 38,226,794(+) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for STARD3NL Gene

Variant ID Type Subtype PubMed ID
nsv1128311 CNV deletion 24896259
esv3571746 CNV loss 25503493
esv32671 CNV loss 17666407
esv29985 CNV loss 17803354
esv2762664 CNV loss 21179565
esv2759524 CNV loss 17122850
esv2734274 CNV deletion 23290073
esv1010248 CNV deletion 20482838
dgv89n68 CNV gain 17160897

Variation tolerance for STARD3NL Gene

Residual Variation Intolerance Score: 22.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.29; 6.52% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for STARD3NL Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
STARD3NL

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for STARD3NL Gene

Disorders for STARD3NL Gene

Additional Disease Information for STARD3NL

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for STARD3NL Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for STARD3NL Gene

Publications for STARD3NL Gene

  1. MENTHO, a MLN64 homologue devoid of the START domain. (PMID: 12393907) Alpy F … Tomasetto C (The Journal of biological chemistry 2002) 2 3 4 22 58
  2. STARD3 or STARD3NL and VAP form a novel molecular tether between late endosomes and the ER. (PMID: 24105263) Alpy F … Tomasetto C (Journal of cell science 2013) 2 3 4 58
  3. MLN64 and MENTHO, two mediators of endosomal cholesterol transport. (PMID: 16709157) Alpy F … Tomasetto C (Biochemical Society transactions 2006) 3 4 22 58
  4. Functional characterization of the MENTAL domain. (PMID: 15718238) Alpy F … Tomasetto C (The Journal of biological chemistry 2005) 3 4 22 58
  5. Touché! STARD3 and STARD3NL tether the ER to endosomes. (PMID: 27068960) Wilhelm LP … Alpy F (Biochemical Society transactions 2016) 2 3 58

Products for STARD3NL Gene

Sources for STARD3NL Gene

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