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Aliases for MIR5004 Gene

Subcategory (RNA class) for MIR5004 Gene

miRNA

Quality Score for this RNA gene is

3

Aliases for MIR5004 Gene

  • MicroRNA 5004 2 3
  • SYNGAP1 4 5
  • Synaptic Ras GTPase-Activating Protein 1 4
  • Synaptic Ras GTPase Activating Protein 1 5
  • Synaptic Ras-GAP 1 4
  • Neuronal RasGAP 4
  • Hsa-Mir-5004 3
  • Mir-5004 3
  • KIAA1938 4

External Ids for MIR5004 Gene

Previous GeneCards Identifiers for MIR5004 Gene

  • GC06U902261

Summaries for MIR5004 Gene

Entrez Gene Summary for MIR5004 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 MIR5004 Gene

MIR5004 (MicroRNA 5004) is an RNA Gene, and is affiliated with the miRNA class. Among its related pathways are RET signaling and Immune System. An important paralog of this gene is RASAL2.

UniProtKB/Swiss-Prot for MIR5004 Gene

  • Major constituent of the PSD essential for postsynaptic signaling. Inhibitory regulator of the Ras-cAMP pathway. Member of the NMDAR signaling complex in excitatory synapses, it may play a role in NMDAR-dependent control of AMPAR potentiation, AMPAR membrane trafficking and synaptic plasticity. Regulates AMPAR-mediated miniature excitatory postsynaptic currents. Exhibits dual GTPase-activating specificity for Ras and Rap. May be involved in certain forms of brain injury, leading to long-term learning and memory deficits (By similarity).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MIR5004 Gene

Genomics for MIR5004 Gene

Regulatory Elements for MIR5004 Gene

Enhancers for MIR5004 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
GH06F032965 1.2 ENCODE 20.8 -449.0 -448993 10.4 CREB3L1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 SP3 NFYC BRD2 VPS52 ATF6B LEMD2 RING1 RXRB DAXX MIR6873 HCG25 PPT2
GH06F033203 0.2 ENCODE 20 -213.3 -213258 5.8 HDGF PKNOX1 CREB3L1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 BRD2 RING1 VPS52 RXRB LEMD2 MIR6873 DAXX HCG25 RGL2 MIR5004
GH06F033270 1.1 ENCODE 19.9 -144.5 -144533 8.4 CREB3L1 MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC TBX21 DAXX RPS18 BRD2 VPS52 MIR6873 RGL2 LEMD2 RXRB ITPR3 MIR5004
GH06F033812 0.4 ENCODE 16.4 +393.2 393208 0.2 ZFP64 ARID4B SIN3A DMAP1 ZNF48 SLC30A9 ZNF143 MXD4 MIER2 REST MIR5004 IP6K3 GC06M033805 LOC105375025
GH06F034132 1.1 ENCODE 16.3 +713.1 713068 0.2 ELF3 ARID4B SIN3A ZNF48 ZSCAN9 DNMT3B RARA CHAMP1 SLC30A9 ZNF143 MIR5004 GRM4 IP6K3 LEMD2 MLN PIR53321
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around MIR5004 on UCSC Golden Path with GeneCards custom track

Promoters for MIR5004 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001703179 839 1401 PKNOX1 ARNT GLI4 CBX5 GATA2 ZNF263 NCOA1 REST ZNF518A MBD2
ENSR00001188811 -1961 1801 HDGF PKNOX1 ARNT CREB3L1 MLX WRNIP1 ZFP64 ARID4B SIN3A FEZF1

Genomic Location for MIR5004 Gene

Chromosome:
6
Start:
33,419,661 bp from pter
End:
33,457,541 bp from pter
Size:
37,881 bases
Orientation:
Plus strand

Genomic View for MIR5004 Gene

Genes around MIR5004 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MIR5004 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MIR5004 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MIR5004 Gene

Proteins for MIR5004 Gene

  • Protein details for MIR5004 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96PV0-SYGP1_HUMAN
    Recommended name:
    Ras/Rap GTPase-activating protein SynGAP
    Protein Accession:
    Q96PV0
    Secondary Accessions:
    • A2AB17
    • A2BEL6
    • A2BEL7
    • A8MQC4
    • Q8TCS2
    • Q9UGE2

    Protein attributes for MIR5004 Gene

    Size:
    1343 amino acids
    Molecular mass:
    148284 Da
    Quaternary structure:
    • Interacts KLHL17, CAMK2A and CAMK2B (By similarity). Interacts with MPDZ.
    • Interacts KLHL17, CAMK2A and CAMK2B (By similarity). Interacts with MPDZ.
    SequenceCaution:
    • Sequence=BAB67831.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for MIR5004 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for MIR5004 Gene

Post-translational modifications for MIR5004 Gene

  • Phosphorylated by CaM-kinase II. Dephosphorylated upon NMDA receptor activation or SYNGAP1/MPDZ complex disruption. Phosphorylation by PLK2 promotes its activity (By similarity).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for MIR5004 Gene

Domains & Families for MIR5004 Gene

Graphical View of Domain Structure for InterPro Entry

Q96PV0

UniProtKB/Swiss-Prot:

SYGP1_HUMAN :
  • The C2 domain is required for RapGAP activity.
Domain:
  • The C2 domain is required for RapGAP activity.
  • Contains 1 C2 domain.
  • Contains 1 PH domain.
  • Contains 1 Ras-GAP domain.
genes like me logo Genes that share domains with MIR5004: view

No data available for Gene Families and Suggested Antigen Peptide Sequences for MIR5004 Gene

Function for MIR5004 Gene

Molecular function for MIR5004 Gene

UniProtKB/Swiss-Prot Function:
Major constituent of the PSD essential for postsynaptic signaling. Inhibitory regulator of the Ras-cAMP pathway. Member of the NMDAR signaling complex in excitatory synapses, it may play a role in NMDAR-dependent control of AMPAR potentiation, AMPAR membrane trafficking and synaptic plasticity. Regulates AMPAR-mediated miniature excitatory postsynaptic currents. Exhibits dual GTPase-activating specificity for Ras and Rap. May be involved in certain forms of brain injury, leading to long-term learning and memory deficits (By similarity).

Gene Ontology (GO) - Molecular Function for MIR5004 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 GTPase activator activity IEA --
GO:0017124 SH3 domain binding IEA --
genes like me logo Genes that share ontologies with MIR5004: 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 MIR5004 Gene

Localization for MIR5004 Gene

Gene Ontology (GO) - Cellular Components for MIR5004 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA --
GO:0005829 cytosol TAS --
GO:0014069 postsynaptic density IEA --
GO:0016020 membrane IEA --
GO:0031235 intrinsic component of the cytoplasmic side of the plasma membrane IBA --
genes like me logo Genes that share ontologies with MIR5004: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from COMPARTMENTS for MIR5004 Gene

Pathways & Interactions for MIR5004 Gene

SuperPathways for MIR5004 Gene

SuperPathway Contained pathways
1 RET signaling
2 Developmental Biology
3 Cytokine Signaling in Immune system
4 HIV Life Cycle
.45
5 Immune System
genes like me logo Genes that share pathways with MIR5004: view

Pathways by source for MIR5004 Gene

Gene Ontology (GO) - Biological Process for MIR5004 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction IEA --
GO:0007265 Ras protein signal transduction IEA --
GO:0007389 pattern specification process IEA --
GO:0008542 visual learning IEA --
GO:0016358 dendrite development IEA --
genes like me logo Genes that share ontologies with MIR5004: view

No data available for SIGNOR curated interactions for MIR5004 Gene

Transcripts for MIR5004 Gene

mRNA/cDNA for MIR5004 Gene

(29) 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 MIR5004 Gene

No ASD Table

Relevant External Links for MIR5004 Gene

GeneLoc Exon Structure for
MIR5004
ECgene alternative splicing isoforms for
MIR5004

Expression for MIR5004 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for MIR5004 Gene

NURSA nuclear receptor signaling pathways regulating expression of MIR5004 Gene:

MIR5004
genes like me logo Genes that share expression patterns with MIR5004: 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 MIR5004 Gene

Orthologs for MIR5004 Gene

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

Orthologs for MIR5004 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SYNGAP1 35
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SYNGAP1 35
  • 99 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Syngap1 35
  • 99 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SYNGAP1 35
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SYNGAP1 35
  • 92 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SYNGAP1 35
  • 77 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii SYNGAP1 (2 of 2) 35
  • 65 (a)
OneToMany
SYNGAP1 (1 of 2) 35
  • 63 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG42684 35
  • 19 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea gap-2 35
  • 24 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BUD2 35
  • 15 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6146 35
  • 33 (a)
OneToMany
Species where no ortholog for MIR5004 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)
  • chicken (Gallus gallus)
  • 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)

Evolution for MIR5004 Gene

ENSEMBL:
Gene Tree for MIR5004 (if available)
TreeFam:
Gene Tree for MIR5004 (if available)

Paralogs for MIR5004 Gene

Paralogs for MIR5004 Gene

genes like me logo Genes that share paralogs with MIR5004: view

Variants for MIR5004 Gene

Sequence variations from dbSNP and Humsavar for MIR5004 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs797046028 Pathogenic 33,438,819(+) GCGAG(-/G)TAGAC downstream-variant-500B, reference, frameshift-variant
rs863224930 Pathogenic 33,437,801(+) GCCCC(-/G)CTCTG upstream-variant-2KB, reference, frameshift-variant
rs7759963 Likely benign 33,438,779(+) GGAGA(A/G)TTCAT downstream-variant-500B, reference, synonymous-codon
rs201107225 Uncertain significance 33,438,487(+) TTCCG(C/T)GAGAA downstream-variant-500B, reference, synonymous-codon
rs797046027 Uncertain significance 33,438,205(+) GTGCA(A/G)TCTTG upstream-variant-2KB, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for MIR5004 Gene

Variant ID Type Subtype PubMed ID
nsv1019212 CNV gain 25217958
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1119076 CNV deletion 24896259
nsv602832 CNV loss 21841781
nsv830635 CNV loss 17160897
nsv830637 CNV loss 17160897

Relevant External Links for MIR5004 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
MIR5004

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for MIR5004 Gene

Disorders for MIR5004 Gene

UniProtKB/Swiss-Prot

SYGP1_HUMAN
  • Mental retardation, autosomal dominant 5 (MRD5) [MIM:612621]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD5 patients show global developmental delay with delayed motor development, hypotonia, moderate-to-severe mental retardation, and severe language impairment. Epilepsy and autism can be present in some patients. {ECO:0000269 PubMed:19196676, ECO:0000269 PubMed:21076407, ECO:0000269 PubMed:21237447, ECO:0000269 PubMed:23161826}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for MIR5004

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
MIR5004

No disorders were found for MIR5004 Gene.

No data available for MalaCards and Genatlas for MIR5004 Gene

Publications for MIR5004 Gene

  1. Mutations in SYNGAP1 cause intellectual disability, autism, and a specific form of epilepsy by inducing haploinsufficiency. (PMID: 23161826) Berryer M.H. … Di Cristo G. (Hum. Mutat. 2013) 4 64
  2. miRBase: integrating microRNA annotation and deep-sequencing data. (PMID: 21037258) Kozomara A. … Griffiths-Jones S. (Nucleic Acids Res. 2011) 3 64
  3. Enhancing miRNA annotation confidence in miRBase by continuous cross dataset analysis. (PMID: 21558790) Hansen T.B. … Bramsen J.B. (RNA Biol 2011) 3 64
  4. De novo SYNGAP1 mutations in nonsyndromic intellectual disability and autism. (PMID: 21237447) Hamdan F.F. … Michaud J.L. (Biol. Psychiatry 2011) 4 64
  5. A de novo paradigm for mental retardation. (PMID: 21076407) Vissers L.E. … Veltman J.A. (Nat. Genet. 2010) 4 64

Products for MIR5004 Gene

Sources for MIR5004 Gene

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