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STARD3NL Gene

protein-coding   GIFtS: 48
GCID: GC07P038218

STARD3 N-Terminal Like

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
STARD3 N-Terminal Like1 2
MENTHO2 3 5
STARD3 N-Terminal-Like Protein2 3
MLN64 N-Terminal Domain Homolog2

External Ids:    HGNC: 191691   Entrez Gene: 839302   Ensembl: ENSG000000102707   OMIM: 6117595   UniProtKB: O957723   

Export aliases for STARD3NL gene to outside databases

Previous GC identifers: GC07P037865 GC07P037958 GC07P037991 GC07P038184


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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. An important paralog of this gene is STARD3.

Gene Wiki entry for STARD3NL Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the STARD3NL gene promoter:
         HFH-3   AML1a   Bach2   IRF-1   FOXI1   RORalpha1   POU2F1   FOXJ2 (long isoform)   POU2F1a   FOXJ2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): STARD3NL promoter sequence
   Search Chromatin IP Primers for STARD3NL

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat STARD3NL


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 7p14-p13   Ensembl cytogenetic band:  7p14.1   HGNC cytogenetic band: 7p14-p13

STARD3NL Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
STARD3NL gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07P038218:  view genomic region     (about GC identifiers)

Start:
38,217,824 bp from pter      End:
38,270,272 bp from pter
Size:
52,449 bases      Orientation:
plus strand

1 alternative location:
Chr7+,CRA_TCAG 38,255,611-38,307,950     

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: MENTO_HUMAN, O95772 (See protein sequence)
Recommended Name: MLN64 N-terminal domain homolog  
Size: 234 amino acids; 26655 Da
Subunit: Can form homodimers. Interacts with STARD3
Alternative initiation: 2 isoforms:  O95772-1   O95772-2   

Explore the universe of human proteins at neXtProt for STARD3NL: NX_O95772

Explore proteomics data for STARD3NL at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See STARD3NL Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_114405.1  
    ENSEMBL proteins: 
     ENSP00000009041   ENSP00000394000   ENSP00000379334   ENSP00000411933   ENSP00000395455  
     ENSP00000402028   ENSP00000439436  

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    Cloud-Clone Corp. Proteins for STARD3NL

     
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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR019498 MENTAL

    Graphical View of Domain Structure for InterPro Entry O95772

    ProtoNet protein and cluster: O95772

    UniProtKB/Swiss-Prot: MENTO_HUMAN, O95772
    Similarity: Contains 1 MENTAL domain


    Find genes that share domains with STARD3NL           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Phenotypes:
         1 GenomeRNAi human phenotype for STARD3NL:
     Decreased p24 protein expressi 

         1 MGI phenotypic allele for Stard3nl (no phenotypes)

    Find genes that share phenotypes with STARD3NL           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Stard3nltm1Lex for STARD3NL

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for STARD3NL
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    miRNA
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    Block miRNA regulation of human, mouse, rat STARD3NL using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate STARD3NL (see all 20):
    hsa-miR-3200-5p hsa-miR-520d-5p hsa-let-7d hsa-miR-202 hsa-let-7c hsa-let-7g hsa-miR-1276 hsa-let-7a
    SwitchGear 3'UTR luciferase reporter plasmidSTARD3NL 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat STARD3NL

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    MENTO_HUMAN, O95772: Late endosome membrane; Multi-pass membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endosome5
    plasma membrane3
    cytosol1
    endoplasmic reticulum1
    peroxisome1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005765lysosomal membrane IDA17897319
    GO:0016021integral component of membrane IEA--
    GO:0031902late endosome membrane IEA--

    Find genes that share ontologies with STARD3NL           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for STARD3NL About    
    See pathways by source

    SuperPathContained pathways About
    1Cholesterol and Sphingolipids transport Distribution to the intracellular membrane compartments normal and CF
    Cholesterol and Sphingolipids transport Distribution to the intracellular membrane compartments normal and CF

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 GeneGo (Thomson Reuters) Pathway for STARD3NL
        Cholesterol and Sphingolipids transport / Distribution to the intracellular membrane compartments (normal and CF)



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    Interactions:

        Search GeneGlobe Interaction Network for STARD3NL

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    3 Interacting proteins for STARD3NL (ENSP000000090414) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBCENSP000003448184STRING: ENSP00000344818
    ELAVL1ENSP000003852694STRING: ENSP00000385269
    ELK1ENSP000002471614STRING: ENSP00000247161
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for STARD3NL (MENTO)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for STARD3NL gene: 
    NM_032016.3  

    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000009041(uc003tfr.3) ENST00000434197 ENST00000471550 ENST00000396013
    ENST00000440144 ENST00000453225 ENST00000429075 ENST00000544203
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate STARD3NL (see all 20):
    hsa-miR-3200-5p hsa-miR-520d-5p hsa-let-7d hsa-miR-202 hsa-let-7c hsa-let-7g hsa-miR-1276 hsa-let-7a
    SwitchGear 3'UTR luciferase reporter plasmidSTARD3NL 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat STARD3NL
      QuantiFast Probe-based Assays in human, mouse, rat STARD3NL

    Selected AceView cDNA sequences (see all 297):

    BQ184158 CR624249 AA515676 BC003074 AA318911 AW292803 AA845306 BQ716734 
    BM457597 AI380140 AL044003 BQ185842 R12855 AI571128 BM128381 CR613249 
    CR610017 BF111213 AI333293 BX345822 BV177712 BX461576 CR600146 CR622332 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for STARD3NL (see all 11)    About this scheme

    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:                                                        -     -                       -     -                                                         


    ECgene alternative splicing isoforms for STARD3NL

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    STARD3NL expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    STARD3NL Expression
    About this image


    STARD3NL expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 3) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 6 entries
             Zeugopod Long Bone
     
     Limb (Muscoskeletal System)    fully expand to see all 2 entries
             Pelvic Girdle
     
     Cartilage (Muscoskeletal System)    fully expand to see all 2 entries
             Meckel's Cartilage
    STARD3NL Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    STARD3NL Protein Expression
        Custom PCR Arrays for STARD3NL
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    In Situ
    Assay Products:
     

     
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for STARD3NL gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Stard3nl1 , 5 STARD3 N-terminal like1, 5 89.03(n)1
    94.44(a)1
      13 (6.89 cM)5
    762051  NM_024270.21  NP_077232.21 
     193576775 
    chicken
    (Gallus gallus)
    Aves STARD3NL1 STARD3 N-terminal like 80.6(n)
    83.19(a)
      420730  XM_418829.4  XP_418829.1 
    lizard
    (Anolis carolinensis)
    Reptilia STARD3NL6
    STARD3 N-terminal like
    85(a)
    1 ↔ 1
    6(47875665-47904779)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia stard3nl1 STARD3 N-terminal like 69.92(n)
    72.09(a)
      100170475  NM_001130258.1  NP_001123730.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufa01c032 wufa01c03 73.62(n)   334718  BI429021.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Start16
    Start1
    13(a)
    1 → many
    2R(20462079-20465199)
    worm
    (Caenorhabditis elegans)
    Secernentea tag-3406
    Protein TAG-340 (tag-340) mRNA, complete cds
    11(a)
    1 → many
    III(4900073-4903179) WBGene00017826


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for STARD3NL gene
    STARD32  STAR2  
    1 SIMAP similar gene for STARD3NL using alignment to 6 protein entries:     MENTO_HUMAN (see all proteins):
    STARD3

    Find genes that share paralogs with STARD3NL           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for STARD3NL (see all 1087)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 7 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs560943021,2
    C--38141461(+) AAGAAA/TAGAAA 1 -- int10--------
    rs762381761,2
    C,F--38141466(+) AAGAAT/AAGAAT 1 -- int13Minor allele frequency- A:0.50WA CSA 6
    rs1134713671,2
    C--38146748(+) TGCTC-/ATT   
      T
    /TTTA
    TTTGT
    1 -- int11CSA 2
    rs759013381,2
    F--38188229(+) AAGTGT/CTGGCA 1 -- us2k11Minor allele frequency- C:0.04WA 118
    rs755698521,2
    C,F--38188232(+) TGTTGG/ACAAAG 1 -- us2k11Minor allele frequency- A:0.09WA 118
    rs1408151941,2
    C--38188411(+) ATAAG-/AACAGG 1 -- us2k10--------
    rs1496844451,2
    --38188526(+) AAAATA/GAAAAT 1 -- us2k10--------
    rs1890441491,2
    --38188577(+) ATAGTA/GTTAAG 1 -- us2k10--------
    rs78004891,2
    C,F--38188606(+) agtgcG/Atatta 1 -- us2k1 tfbs31Minor allele frequency- A:0.09WA 118
    rs757725251,2
    C,F--38188672(+) TCAGAA/GTTGTG 1 -- us2k11Minor allele frequency- G:0.03EA 120

    HapMap Linkage Disequilibrium report for STARD3NL (38217824 - 38270272 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for STARD3NL:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv1010248CNV Deletion20482838
    esv2734274CNV Deletion23290073
    esv29985CNV Loss17803354
    esv32671CNV Loss17666407
    dgv89n68CNV Gain17160897
    dgv2076e1CNV Complex17122850

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing STARD3NL
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 611759    OMIM disorders: --


    Find genes that share disorders with STARD3NL           About GenesLikeMe

    Genetic Association Database (GAD): STARD3NL
    Human Genome Epidemiology (HuGE) Navigator: STARD3NL (8 documents)

    Export disorders for STARD3NL gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for STARD3NL gene, integrated from 10 sources (see all 31):
    (articles sorted by number of sources associating them with STARD3NL)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. MENTHO, a MLN64 homologue devoid of the START domain. (PubMed id 12393907)1, 2, 3, 9 Alpy F.... Tomasetto C. (J. Biol. Chem. 2002)
    2. MLN64 and MENTHO, two mediators of endosomal cholesterol transport. (PubMed id 16709157)1, 2, 9 Alpy F. and Tomasetto C. (Biochem. Soc. Trans. 2006)
    3. Beyond single-marker analyses: mining whole genome scans for insights into treatment responses in severe sepsis. (PubMed id 22310353)1, 4 Man M....Garcia J.G. (Pharmacogenomics J. 2013)
    4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    5. Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies. (PubMed id 19801982)1, 4 Rivadeneira F....Uitterlinden A.G. (Nat. Genet. 2009)
    6. Polymorphisms in the estrogen receptor 1 and vitamin C and matrix metalloproteinase gene families are associated with susceptibility to lymphoma. (PubMed id 18636124)1, 4 Skibola C.F....Smith M.T. (PLoS ONE 2008)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    8. The DNA sequence of human chromosome 7. (PubMed id 12853948)1, 2 Hillier L.W.... Wilson R.K. (Nature 2003)
    9. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (Genome Res. 2003)
    10. Functional characterization of the MENTAL domain. (PubMed id 15718238)1, 9 Alpy F....Tomasetto C. (J. Biol. Chem. 2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 83930 HGNC: 19169 AceView: STARD3NL Ensembl:ENSG00000010270 euGenes: HUgn83930
    ECgene: STARD3NL H-InvDB: STARD3NL

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for STARD3NL Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for STARD3NL gene:
    Search GeneIP for patents involving STARD3NL

    GeneCards and IP:
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