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Aliases for MIR3656 Gene

Subcategory (RNA class) for MIR3656 Gene

miRNA

Quality Score for this RNA gene is

3

Aliases for MIR3656 Gene

  • MicroRNA 3656 2 3
  • TRAPPC4 4 5
  • Hematopoietic Stem/Progenitor Cell Protein 172 4
  • Trafficking Protein Particle Complex 4 5
  • TRS23 Homolog 4
  • Hsa-Mir-3656 3
  • Synbindin 4
  • Mir-3656 3
  • SBDN 4

External Ids for MIR3656 Gene

Previous GeneCards Identifiers for MIR3656 Gene

  • GC11U901768
  • GC11P118896
  • GC11P119020
  • GC11P119024
  • GC11P119027
  • GC11P119031

Summaries for MIR3656 Gene

Entrez Gene Summary for MIR3656 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 MIR3656 Gene

MIR3656 (MicroRNA 3656) is an RNA Gene, and is affiliated with the miRNA class. Among its related pathways are Transport to the Golgi and subsequent modification and Vesicle-mediated transport.

UniProtKB/Swiss-Prot for MIR3656 Gene

  • May play a role in vesicular transport from endoplasmic reticulum to Golgi.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MIR3656 Gene

Genomics for MIR3656 Gene

Regulatory Elements for MIR3656 Gene

Enhancers for MIR3656 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
GH11F119062 0.9 Ensembl ENCODE 12.3 +44.6 44569 0.4 BCOR HDAC1 GTF3C2 ZNF316 ADNP NFE2 RCOR1 MAFK NFE2L2 SMARCE1 ENSG00000254909 VPS11 ENSG00000254428 RPL23AP64 UBE4A HMBS H2AFX C2CD2L DPAGT1 SLC37A4
GH11F119065 0.6 ENCODE 12.3 +47.2 47173 0.2 BCOR CTCF HDAC1 WRNIP1 JUN ZMYM3 ZNF48 RAD21 GATA3 GATA2 H2AFX C2CD2L DPAGT1 SLC37A4 MIR3656 RPS25 TRAPPC4 HINFP NLRX1 FOXR1
GH11F119066 0.5 ENCODE 12.3 +49.1 49133 2.0 HDGF PKNOX1 MLX ZFP64 ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207 VPS11 HMBS H2AFX C2CD2L DPAGT1 SLC37A4 MIR3656 RPS25 TRAPPC4 HINFP
GH11F119076 0.4 ENCODE 12 +59.5 59498 2.5 ZNF316 ZNF146 KDM1A EMSY MAFK VPS11 HMBS C2CD2L DPAGT1 HYOU1 ENSG00000255114 SLC37A4 RPS25 TRAPPC4 MIR3656
GH11F119015 0.7 ENCODE 0.8 -0.4 -372 4.6 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 YY1 TRAPPC4 BCL9L ARCN1 ENSG00000254909 UBE4A RPS25 RPL23AP64 ENSG00000254428 ENSG00000222529 FOXR1
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around MIR3656 on UCSC Golden Path with GeneCards custom track

Promoters for MIR3656 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000112326 68 3001 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 YY1

Genomic Location for MIR3656 Gene

Chromosome:
11
Start:
119,018,432 bp from pter
End:
119,025,454 bp from pter
Size:
7,023 bases
Orientation:
Plus strand

Genomic View for MIR3656 Gene

Genes around MIR3656 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MIR3656 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MIR3656 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MIR3656 Gene

Proteins for MIR3656 Gene

  • Protein details for MIR3656 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y296-TPPC4_HUMAN
    Recommended name:
    Trafficking protein particle complex subunit 4
    Protein Accession:
    Q9Y296
    Secondary Accessions:
    • A8K3A5
    • B4DME1

    Protein attributes for MIR3656 Gene

    Size:
    219 amino acids
    Molecular mass:
    24340 Da
    Quaternary structure:
    • Component of the multisubunit TRAPP (transport protein particle) complex, which includes at least TRAPPC2, TRAPPC2L, TRAPPC3, TRAPPC3L, TRAPPC4, TRAPPC5, TRAPPC8, TRAPPC9, TRAPPC10, TRAPPC11 and TRAPPC12. Interacts with SDC2 (By similarity).
    • Component of the multisubunit TRAPP (transport protein particle) complex, which includes at least TRAPPC2, TRAPPC2L, TRAPPC3, TRAPPC3L, TRAPPC4, TRAPPC5, TRAPPC8, TRAPPC9, TRAPPC10, TRAPPC11 and TRAPPC12. Interacts with SDC2 (By similarity).

    Three dimensional structures from OCA and Proteopedia for MIR3656 Gene

    Alternative splice isoforms for MIR3656 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for MIR3656 Gene

Post-translational modifications for MIR3656 Gene

  • Ubiquitination at Lys 41
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for MIR3656 Gene

Domains & Families for MIR3656 Gene

Gene Families for MIR3656 Gene

Protein Domains for MIR3656 Gene

Graphical View of Domain Structure for InterPro Entry

Q9Y296

UniProtKB/Swiss-Prot:

TPPC4_HUMAN :
  • Belongs to the TRAPP small subunits family. TRAPPC4 subfamily.
Family:
  • Belongs to the TRAPP small subunits family. TRAPPC4 subfamily.
genes like me logo Genes that share domains with MIR3656: view

No data available for Suggested Antigen Peptide Sequences for MIR3656 Gene

Function for MIR3656 Gene

Molecular function for MIR3656 Gene

UniProtKB/Swiss-Prot Function:
May play a role in vesicular transport from endoplasmic reticulum to Golgi.

Gene Ontology (GO) - Molecular Function for MIR3656 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0017112 Rab guanyl-nucleotide exchange factor activity IBA --
genes like me logo Genes that share ontologies with MIR3656: 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 MIR3656 Gene

Localization for MIR3656 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MIR3656 Gene

Golgi apparatus, cis-Golgi network. Endoplasmic reticulum.

Gene Ontology (GO) - Cellular Components for MIR3656 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005794 Golgi apparatus IEA --
GO:0005795 Golgi stack ISS --
GO:0005829 cytosol TAS --
GO:0008021 synaptic vesicle ISS --
genes like me logo Genes that share ontologies with MIR3656: view

No data available for Subcellular locations from COMPARTMENTS for MIR3656 Gene

Pathways & Interactions for MIR3656 Gene

genes like me logo Genes that share pathways with MIR3656: view

Gene Ontology (GO) - Biological Process for MIR3656 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006888 ER to Golgi vesicle-mediated transport IBA --
GO:0016192 vesicle-mediated transport IEA --
GO:0016358 dendrite development ISS --
GO:0043547 positive regulation of GTPase activity IEA --
genes like me logo Genes that share ontologies with MIR3656: view

No data available for SIGNOR curated interactions for MIR3656 Gene

Transcripts for MIR3656 Gene

mRNA/cDNA for MIR3656 Gene

(15) 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 MIR3656 Gene

No ASD Table

Relevant External Links for MIR3656 Gene

GeneLoc Exon Structure for
MIR3656
ECgene alternative splicing isoforms for
MIR3656

Expression for MIR3656 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for MIR3656 Gene

NURSA nuclear receptor signaling pathways regulating expression of MIR3656 Gene:

MIR3656
genes like me logo Genes that share expression patterns with MIR3656: 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 , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for MIR3656 Gene

Orthologs for MIR3656 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for MIR3656 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TRAPPC4 35
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia TRAPPC4 35
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia TRAPPC4 35
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Trappc4 35
  • 98 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TRAPPC4 35
  • 96 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TRAPPC4 35
  • 92 (a)
OneToOne
chicken
(Gallus gallus)
Aves TRAPPC4 35
  • 89 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TRAPPC4 35
  • 88 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii trappc4 35
  • 87 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Trs23 35
  • 58 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea trpp-4 35
  • 47 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TRS23 35 37
  • 31 (a)
OneToOne
Species where no ortholog for MIR3656 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)
  • 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)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)

Evolution for MIR3656 Gene

ENSEMBL:
Gene Tree for MIR3656 (if available)
TreeFam:
Gene Tree for MIR3656 (if available)

Paralogs for MIR3656 Gene

No data available for Paralogs for MIR3656 Gene

Variants for MIR3656 Gene

Sequence variations from dbSNP and Humsavar for MIR3656 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs10892321 -- 119,018,404(+) GGCAA(A/G)AGGCG upstream-variant-2KB
rs111611823 -- 119,018,344(+) AAAAG(A/C/G)AAGCG upstream-variant-2KB, utr-variant-5-prime
rs112148456 -- 119,018,306(+) TAGCA(A/G)CAGAC upstream-variant-2KB, utr-variant-5-prime
rs11217123 -- 119,017,235(+) ATTAC(G/T)AACAG intron-variant, upstream-variant-2KB
rs11217124 -- 119,018,422(-) ACTTC(C/T)TCTGC upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for MIR3656 Gene

Variant ID Type Subtype PubMed ID
nsv826101 CNV gain 20364138

Relevant External Links for MIR3656 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
MIR3656

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for MIR3656 Gene

Disorders for MIR3656 Gene

Relevant External Links for MIR3656

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
MIR3656

No disorders were found for MIR3656 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for MIR3656 Gene

Publications for MIR3656 Gene

  1. miRBase: integrating microRNA annotation and deep-sequencing data. (PMID: 21037258) Kozomara A. … Griffiths-Jones S. (Nucleic Acids Res. 2011) 3 64
  2. Initial characterization of the human central proteome. (PMID: 21269460) Burkard T.R. … Colinge J. (BMC Syst. Biol. 2011) 4 64
  3. C4orf41 and TTC-15 are mammalian TRAPP components with a role at an early stage in ER-to-Golgi trafficking. (PMID: 21525244) Scrivens P.J. … Sacher M. (Mol. Biol. Cell 2011) 4 64
  4. Discovery of microRNAs and other small RNAs in solid tumors. (PMID: 20483914) Meiri E. … Sitbon E. (Nucleic Acids Res. 2010) 3 64
  5. TRAPPC2L is a novel, highly conserved TRAPP-interacting protein. (PMID: 19416478) Scrivens P.J. … Sacher M. (Traffic 2009) 4 64

Products for MIR3656 Gene

Sources for MIR3656 Gene

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