MIR5000 (microRNA 5000) - Rat Genome Database

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Gene: MIR5000 (microRNA 5000) Homo sapiens
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Symbol: MIR5000
Name: microRNA 5000
RGD ID: 6483865
HGNC Page HGNC:43464
Description: 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]
Type: ncrna (Ensembl: miRNA)
RefSeq Status: PROVISIONAL
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38275,090,812 - 75,090,914 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl275,090,812 - 75,090,914 (+)EnsemblGRCh38hg38GRCh38
GRCh37275,317,939 - 75,318,041 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map2p12NCBI
HuRef275,055,365 - 75,055,467 (+)NCBIHuRef
CHM1_1275,247,229 - 75,247,331 (+)NCBICHM1_1
T2T-CHM13v2.0275,099,650 - 75,099,752 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:16381832   PMID:21558790   PMID:21606961   PMID:24898979   PMID:32094308  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2p16.1-11.2(chr2:58279519-83586962)x3 copy number gain See cases [RCV000136053] Chr2:58279519..83586962 [GRCh38]
Chr2:58506654..83814086 [GRCh37]
Chr2:58360158..83667597 [NCBI36]
Chr2:2p16.1-11.2		 pathogenic
GRCh38/hg38 2p13.1-12(chr2:74432069-75181627)x3 copy number gain See cases [RCV000136651] Chr2:74432069..75181627 [GRCh38]
Chr2:74659196..75408753 [GRCh37]
Chr2:74512704..75262261 [NCBI36]
Chr2:2p13.1-12		 likely benign|uncertain significance
GRCh38/hg38 2p16.3-11.2(chr2:47620388-86702722)x3 copy number gain See cases [RCV000137586] Chr2:47620388..86702722 [GRCh38]
Chr2:47847527..86929845 [GRCh37]
Chr2:47701031..86783356 [NCBI36]
Chr2:2p16.3-11.2		 uncertain significance
GRCh38/hg38 2p25.1-11.2(chr2:7495123-87705899)x3 copy number gain See cases [RCV000141494] Chr2:7495123..87705899 [GRCh38]
Chr2:7635254..88005418 [GRCh37]
Chr2:7552705..87786533 [NCBI36]
Chr2:2p25.1-11.2		 benign
GRCh38/hg38 2p13.1-12(chr2:74375779-75517520)x1 copy number loss See cases [RCV000143456] Chr2:74375779..75517520 [GRCh38]
Chr2:74602906..75744646 [GRCh37]
Chr2:74456414..75598154 [NCBI36]
Chr2:2p13.1-12		 likely pathogenic
miRNA Target Status

Predicted Targets
Summary Value
Count of predictions:36013
Count of gene targets:12147
Count of transcripts:25677
Interacting mature miRNAs:hsa-miR-5000-3p, hsa-miR-5000-5p
Prediction methods:Microtar, Miranda, Pita, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component
High
Medium 1
Low 32 14 31 15 101 17 54 20 47 41 80 50 9 21 1
Below cutoff 49 20 26 5 38 4 68 32 57 19 26 36 3 28 30

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000577717
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl275,090,812 - 75,090,914 (+)Ensembl
RefSeq Acc Id: NR_049796
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38275,090,812 - 75,090,914 (+)NCBI
GRCh37275,317,939 - 75,318,041 (+)NCBI
HuRef275,055,365 - 75,055,467 (+)NCBI
CHM1_1275,247,229 - 75,247,331 (+)NCBI
T2T-CHM13v2.0275,099,650 - 75,099,752 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC MIR5000 COSMIC
Ensembl Genes ENSG00000263909 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000577717 ENTREZGENE
GTEx ENSG00000263909 GTEx
HGNC ID HGNC:43464 ENTREZGENE
Human Proteome Map MIR5000 Human Proteome Map
miRBase MI0017866 ENTREZGENE
NCBI Gene MIR5000 ENTREZGENE
RNAcentral URS000075A2CA RNACentral
  URS000075BECA RNACentral
  URS000075C735 RNACentral