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 ... See more...

Aliases for MIR5004 Gene

Data sources for MIR5004 Gene:

RNA type for MIR5004 Gene

miRNA

Aliases for MIR5004 Gene

External Ids for MIR5004 Gene

Previous GeneCards Identifiers for MIR5004 Gene

  • GC06U902261
  • GC06P033410

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. Diseases associated with MIR5004 include Autosomal Dominant Non-Syndromic Intellectual Disability 5. Among its related pathways are RET signaling and Signaling by GPCR.

Additional gene information for MIR5004 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for MIR5004 Gene

Genomics for MIR5004 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for MIR5004 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
GH06J033423 Promoter/Enhancer 2.3 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 0.4 -11.3 -11335 6 SP1 ZNF654 NCOR1 IKZF1 ZNF600 MYC ZNF592 NFIC POLR2A ZIC2 lnc-CUTA-2 DAXX LEMD2 BRD2 WDR46 RXRB VPS52 RGL2 KIFC1 SYNGAP1
GH06J033430 Promoter/Enhancer 1.8 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 0.4 -5.9 -5911 4.5 SP1 IKZF1 ZNF600 CEBPA POLR2A ZBTB10 SIN3A ETS1 ZNF341 MNT RING1 HCG25 DAXX ZBTB9 PHF1 RXRB BRD2 LEMD2 ENSG00000272217 VPS52
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around MIR5004 on the GeneHancer Hub at the UCSC Golden Path

Genomic Locations for MIR5004 Gene

Latest Assembly
chr6:33,438,331-33,438,437
(GRCh38/hg38)
Size:
107 bases
Orientation:
Plus strand

Previous Assembly
chr6:33,406,108-33,406,214
(GRCh37/hg19 by Entrez Gene)
Size:
107 bases
Orientation:
Plus strand

Alternative Locations (GRCh38/hg38)

  • chr6(ALT_REF_LOCI_7):4,887,056-4,887,162 (+)

Genomic View for MIR5004 Gene

Genes around MIR5004 on UCSC Golden Path with GeneCards custom track
MIR5004 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

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

Post-translational modifications for MIR5004 Gene

No Post-translational modifications

No data available for DME Specific Peptides for MIR5004 Gene

Domains & Families for MIR5004 Gene

Gene Families for MIR5004 Gene

HGNC:
genes like me logo Genes that share domains with MIR5004: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for MIR5004 Gene

Function for MIR5004 Gene

Phenotypes From GWAS Catalog for MIR5004 Gene

CRISPR products for research

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for MIR5004 Gene

Localization for MIR5004 Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for MIR5004 Gene

Pathways & Interactions for MIR5004 Gene

PathCards logo

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 Innate 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

None

No data available for Interacting Proteins and SIGNOR curated interactions for MIR5004 Gene

Drugs & Compounds for MIR5004 Gene

No Compound Related Data Available

Transcripts for MIR5004 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for MIR5004 Gene

RNAcentral Transcript ID RNA Type Length (nts) # of Sources Source Identifiers and Annotations
URS000075DBA5_9606 pre_miRNA 107 4

RefSeq: NR_049800,

Ensembl: ENST00000579078 (view in UCSC) ,

miRBase: MI0017870,

ENA: LM611500.1:1..107:precursor_RNA,

URS000054A671_9606 miRNA 22 3

RefSeq: NR_049800,

miRBase: MIMAT0021027,

ENA: LM382881.1:1..22:ncRNA, LM611500.1:21..42:ncRNA,

URS000075DCE2_9606 miRNA 22 3

RefSeq: NR_049800,

miRBase: MIMAT0021028,

ENA: LM611500.1:67..88:ncRNA,

MIR5004 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for MIR5004 Gene

1 NCBI additional mRNA sequence :

Alternative Splicing Database (ASD) splice patterns (SP) for MIR5004 Gene

No ASD Table

Relevant External Links for MIR5004 Gene

GeneLoc Exon Structure for
MIR5004

Expression for MIR5004 Gene

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

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

Primer products for research

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 , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for MIR5004 Gene

Orthologs for MIR5004 Gene

Evolution for MIR5004 Gene

ENSEMBL:
Gene Tree for MIR5004 (if available)
TreeFam:
Gene Tree for MIR5004 (if available)
Alliance of Genome Resources:
Additional Orthologs for MIR5004

No data available for Orthologs for MIR5004 Gene

Paralogs for MIR5004 Gene

No data available for Paralogs for MIR5004 Gene

Variants for MIR5004 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for MIR5004 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
1012769 Uncertain Significance: not provided 33,438,425(+) C/G
NM_006772.3(SYNGAP1):c.1393C>G (p.Leu465Val)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT
864681 Uncertain Significance: Mental retardation, autosomal dominant 5 33,438,411(+) G/A
NM_006772.3(SYNGAP1):c.1387-8G>A
NON_CODING_TRANSCRIPT_VARIANT,INTRON
982619 Uncertain Significance: Mental retardation, autosomal dominant 5 33,438,435(+) T/C
NM_006772.3(SYNGAP1):c.1403T>C (p.Met468Thr)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT
987236 Likely Pathogenic: not provided 33,438,416(+) CA/C
NM_006772.3(SYNGAP1):c.1387-2del
SPLICE_ACCEPTOR_VARIANT,NON_CODING_TRANSCRIPT
rs1057518183 Pathogenic: not provided 33,438,423(+) TC/T
NM_006772.3(SYNGAP1):c.1393del (p.Leu465fs)
FRAMESHIFT_VARIANT,NON_CODING_TRANSCRIPT

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for MIR5004 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Additional Variant Information for MIR5004 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
MIR5004
Leiden Open Variation Database (LOVD)
MIR5004

SNP Genotyping and Copy Number Assays for research

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

Disorders for MIR5004 Gene

MalaCards: The human disease database

(1) MalaCards diseases for MIR5004 Gene - From: CVR

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for MIR5004

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

No data available for UniProtKB/Swiss-Prot and Genatlas for MIR5004 Gene

Publications for MIR5004 Gene

  1. miRBase: integrating microRNA annotation and deep-sequencing data. (PMID: 21037258) Kozomara A … Griffiths-Jones S (Nucleic acids research 2011) 3
  2. Enhancing miRNA annotation confidence in miRBase by continuous cross dataset analysis. (PMID: 21558790) Hansen TB … Bramsen JB (RNA biology 2011) 3
  3. miRBase: microRNA sequences, targets and gene nomenclature. (PMID: 16381832) Griffiths-Jones S … Enright AJ (Nucleic acids research 2006) 3

Products for MIR5004 Gene

Sources for MIR5004 Gene