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Aliases for MIR4709 Gene

Subcategory (RNA class) for MIR4709 Gene

miRNA

Quality Score for this RNA gene is

3

Aliases for MIR4709 Gene

  • MicroRNA 4709 2 3
  • NPC2 4 5
  • NPC Intracellular Cholesterol Transporter 2 5
  • Niemann-Pick Disease Type C2 Protein 4
  • Human Epididymis-Specific Protein 1 4
  • Hsa-Mir-4709 3
  • Mir-4709 3
  • HE1 4

External Ids for MIR4709 Gene

Previous GeneCards Identifiers for MIR4709 Gene

  • GC14U901277
  • GC14M074949

Summaries for MIR4709 Gene

Entrez Gene Summary for MIR4709 Gene

  • microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

GeneCards Summary for MIR4709 Gene

MIR4709 (MicroRNA 4709) is an RNA Gene, and is affiliated with the miRNA class. Diseases associated with MIR4709 include Niemann-Pick Disease, Type C2 and Niemann-Pick Disease. Among its related pathways are Metabolism and Immune System.

UniProtKB/Swiss-Prot for MIR4709 Gene

  • Intracellular cholesterol transporter which acts in concert with NPC1 and plays an important role in the egress of cholesterol from the endosomal/lysosomal compartment. Both NPC1 and NPC2 function as the cellular tag team duo (TTD) to catalyze the mobilization of cholesterol within the multivesicular environment of the late endosome (LE) to effect egress through the limiting bilayer of the LE. NPC2 binds unesterified cholesterol that has been released from LDLs in the lumen of the late endosomes/lysosomes and transfers it to the cholesterol-binding pocket of the N-terminal domain of NPC1. Cholesterol binds to NPC1 with the hydroxyl group buried in the binding pocket and is exported from the limiting membrane of late endosomes/ lysosomes to the ER and plasma membrane by an unknown mechanism. The secreted form of NCP2 regulates biliary cholesterol secretion via stimulation of ABCG5/ABCG8-mediated cholesterol transport.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MIR4709 Gene

Genomics for MIR4709 Gene

Regulatory Elements for MIR4709 Gene

Enhancers for MIR4709 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH14F074500 0.2 ENCODE 0.4 -6.9 -6875 1.3 ZNF263 CTCF ZNF654 NFIA L3MBTL2 ZIC2 RAD21 ZFHX2 POLR2A SMC3 SYNDIG1L MIR4709 NPC2 GC14M074212
GH14F074502 0.6 ENCODE 0.4 -8.2 -8156 0.2 CTCF ZNF680 ZNF143 SMC3 RAD21 LTBP2 SYNDIG1L MIR4709 NPC2 GC14M074212
GH14F074508 0.4 ENCODE 0.4 -14.4 -14396 0.2 CTCF POLR2A ZBTB33 RAD21 LTBP2 SYNDIG1L GC14M074212 MIR4709 NPC2
GH14F074506 0.2 ENCODE 0.4 -12.2 -12248 0.0 LTBP2 SYNDIG1L GC14M074212 MIR4709 NPC2
GH14F074509 0.9 Ensembl ENCODE 0.3 -16.8 -16819 3.1 TFAP4 ZMYM3 ZIC2 HIC1 GATA3 ZFHX2 PATZ1 FOSL2 FOS EGR2 SYNDIG1L ISCA2 GC14M074212 NPC2 MIR4709
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around MIR4709 on UCSC Golden Path with GeneCards custom track

Promoters for MIR4709 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001623848 1077 3001 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZNF48 YY1 ZNF121 GLIS2 ZNF143

Genomic Location for MIR4709 Gene

Chromosome:
14
Start:
74,476,192 bp from pter
End:
74,494,177 bp from pter
Size:
17,986 bases
Orientation:
Minus strand

Genomic View for MIR4709 Gene

Genes around MIR4709 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MIR4709 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MIR4709 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MIR4709 Gene

Proteins for MIR4709 Gene

  • Protein details for MIR4709 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P61916-NPC2_HUMAN
    Recommended name:
    Epididymal secretory protein E1
    Protein Accession:
    P61916
    Secondary Accessions:
    • B4DQV7
    • Q15668
    • Q29413

    Protein attributes for MIR4709 Gene

    Size:
    151 amino acids
    Molecular mass:
    16570 Da
    Quaternary structure:
    • Interacts with NUS1/NgBR, the interaction stabilizes NCP2 and regulates cholesterol trafficking. Interacts with DHDDS. Interacts with NPC1 (via the second lumenal domain) in a cholestrol-dependent manner (By similarity). Interacts with NEDD4L (via C2 domain) (By similarity). Interacts with NPC1L1.
    • Interacts with NUS1/NgBR, the interaction stabilizes NCP2 and regulates cholesterol trafficking. Interacts with DHDDS. Interacts with NPC1 (via the second lumenal domain) in a cholestrol-dependent manner (By similarity). Interacts with NEDD4L (via C2 domain) (By similarity). Interacts with NPC1L1.

    Three dimensional structures from OCA and Proteopedia for MIR4709 Gene

    Alternative splice isoforms for MIR4709 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for MIR4709 Gene

Post-translational modifications for MIR4709 Gene

  • Glycosylation at Asn 58 and Asn 135
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for MIR4709 Gene

Domains & Families for MIR4709 Gene

Gene Families for MIR4709 Gene

Protein Domains for MIR4709 Gene

Graphical View of Domain Structure for InterPro Entry

P61916

UniProtKB/Swiss-Prot:

NPC2_HUMAN :
  • Belongs to the NPC2 family.
Family:
  • Belongs to the NPC2 family.
genes like me logo Genes that share domains with MIR4709: view

No data available for Suggested Antigen Peptide Sequences for MIR4709 Gene

Function for MIR4709 Gene

Molecular function for MIR4709 Gene

UniProtKB/Swiss-Prot Function:
Intracellular cholesterol transporter which acts in concert with NPC1 and plays an important role in the egress of cholesterol from the endosomal/lysosomal compartment. Both NPC1 and NPC2 function as the cellular tag team duo (TTD) to catalyze the mobilization of cholesterol within the multivesicular environment of the late endosome (LE) to effect egress through the limiting bilayer of the LE. NPC2 binds unesterified cholesterol that has been released from LDLs in the lumen of the late endosomes/lysosomes and transfers it to the cholesterol-binding pocket of the N-terminal domain of NPC1. Cholesterol binds to NPC1 with the hydroxyl group buried in the binding pocket and is exported from the limiting membrane of late endosomes/ lysosomes to the ER and plasma membrane by an unknown mechanism. The secreted form of NCP2 regulates biliary cholesterol secretion via stimulation of ABCG5/ABCG8-mediated cholesterol transport.
UniProtKB/Swiss-Prot Induction:
Down-regulated in response to enterovirus 71 (EV71) infection.

Gene Ontology (GO) - Molecular Function for MIR4709 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015485 cholesterol binding IDA --
GO:0019899 enzyme binding IPI --
genes like me logo Genes that share ontologies with MIR4709: view

Animal Model Products

miRNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for MIR4709 Gene

Localization for MIR4709 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MIR4709 Gene

Secreted. Endoplasmic reticulum. Lysosome.

Gene Ontology (GO) - Cellular Components for MIR4709 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005622 intracellular IEA --
GO:0005764 lysosome IDA --
GO:0005783 endoplasmic reticulum IEA --
GO:0070062 extracellular exosome IDA --
genes like me logo Genes that share ontologies with MIR4709: view

No data available for Subcellular locations from COMPARTMENTS for MIR4709 Gene

Pathways & Interactions for MIR4709 Gene

genes like me logo Genes that share pathways with MIR4709: view

Gene Ontology (GO) - Biological Process for MIR4709 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0008202 steroid metabolic process IEA --
GO:0008203 cholesterol metabolic process IEA --
GO:0009615 response to virus IEP --
GO:0015914 phospholipid transport TAS --
genes like me logo Genes that share ontologies with MIR4709: view

No data available for SIGNOR curated interactions for MIR4709 Gene

Transcripts for MIR4709 Gene

mRNA/cDNA for MIR4709 Gene

(10) Ensembl transcripts including schematic representations, and UCSC links where relevant :

miRNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for MIR4709 Gene

No ASD Table

Relevant External Links for MIR4709 Gene

GeneLoc Exon Structure for
MIR4709
ECgene alternative splicing isoforms for
MIR4709

Expression for MIR4709 Gene

mRNA expression in normal human tissues for MIR4709 Gene

NURSA nuclear receptor signaling pathways regulating expression of MIR4709 Gene:

MIR4709

mRNA Expression by UniProt/SwissProt for MIR4709 Gene:

P61916-NPC2_HUMAN
Tissue specificity: Epididymis.
genes like me logo Genes that share expression patterns with MIR4709: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for MIR4709 Gene

Orthologs for MIR4709 Gene

This gene was present in the common ancestor of animals.

Orthologs for MIR4709 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NPC2 35
  • 100 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Npc2 35
  • 81 (a)
OneToOne
cow
(Bos Taurus)
Mammalia NPC2 35
  • 77 (a)
OneToOne
dog
(Canis familiaris)
Mammalia NPC2 35
  • 77 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NPC2 35
  • 66 (a)
OneToOne
chicken
(Gallus gallus)
Aves NPC2 35
  • 69 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NPC2 35
  • 66 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii npc2 35
  • 58 (a)
OneToMany
NPC2 (2 of 2) 35
  • 57 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Npc2a 35
  • 35 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 45 (a)
OneToMany
-- 35
  • 45 (a)
OneToMany
Species where no ortholog for MIR4709 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for MIR4709 Gene

ENSEMBL:
Gene Tree for MIR4709 (if available)
TreeFam:
Gene Tree for MIR4709 (if available)

Paralogs for MIR4709 Gene

No data available for Paralogs for MIR4709 Gene

Variants for MIR4709 Gene

Sequence variations from dbSNP and Humsavar for MIR4709 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type
rs104894457 Pathogenic 74,480,707(-) CAGTA(C/T)AGATC upstream-variant-2KB, reference, stop-gained
rs140130028 Pathogenic 74,480,701(+) ACTTA(C/T)GATCT upstream-variant-2KB, reference, missense, splice-donor-variant
rs114950106 Benign 74,480,292(+) ACCTG(C/G/T)GGATG intron-variant, upstream-variant-2KB, utr-variant-3-prime
rs10140782 -- 74,480,780(+) TTTAT(C/G)TGGAG upstream-variant-2KB, splice-acceptor-variant
rs10220503 -- 74,480,389(+) AGCAA(A/C)CTCCT intron-variant, upstream-variant-2KB, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for MIR4709 Gene

Variant ID Type Subtype PubMed ID
esv3634943 CNV gain 21293372
nsv832829 CNV loss 17160897

Relevant External Links for MIR4709 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
MIR4709

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for MIR4709 Gene

Disorders for MIR4709 Gene

MalaCards: The human disease database

(3) MalaCards diseases for MIR4709 Gene - From: GeneCards

Disorder Aliases PubMed IDs
niemann-pick disease, type c2
  • niemann-pick disease type c2
niemann-pick disease
  • lipoid histiocytosis
pick disease
  • pick's disease
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

NPC2_HUMAN
  • Niemann-Pick disease C2 (NPC2) [MIM:607625]: A lysosomal storage disorder that affects the viscera and the central nervous system. It is due to defective intracellular processing and transport of low-density lipoprotein derived cholesterol. It causes accumulation of cholesterol in lysosomes, with delayed induction of cholesterol homeostatic reactions. Niemann-Pick disease type C2 has a highly variable clinical phenotype. Clinical features include variable hepatosplenomegaly and severe progressive neurological dysfunction such as ataxia, dystonia and dementia. The age of onset can vary from infancy to late adulthood. {ECO:0000269 PubMed:11125141, ECO:0000269 PubMed:11567215, ECO:0000269 PubMed:12447927, ECO:0000269 PubMed:12955717, ECO:0000269 PubMed:15937921, ECO:0000269 PubMed:16126423}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for MIR4709

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
MIR4709
genes like me logo Genes that share disorders with MIR4709: view

No data available for Genatlas for MIR4709 Gene

Publications for MIR4709 Gene

  1. N-terminome analysis of the human mitochondrial proteome. (PMID: 25944712) Vaca Jacome A.S. … Carapito C. (Proteomics 2015) 4 64
  2. An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome. (PMID: 24275569) Bian Y. … Zou H. (J. Proteomics 2014) 4 64
  3. Novel function of Niemann-Pick C1-like 1 as a negative regulator of Niemann-Pick C2 protein. (PMID: 22095670) Yamanashi Y. … Suzuki H. (Hepatology 2012) 4 64
  4. miRBase: integrating microRNA annotation and deep-sequencing data. (PMID: 21037258) Kozomara A. … Griffiths-Jones S. (Nucleic Acids Res. 2011) 3 64
  5. Identification of new microRNAs in paired normal and tumor breast tissue suggests a dual role for the ERBB2/Her2 gene. (PMID: 21199797) Persson H. … Rovira C. (Cancer Res. 2011) 3 64

Products for MIR4709 Gene

Sources for MIR4709 Gene

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