MIR4643 (microRNA 4643) - Rat Genome Database

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Gene: MIR4643 (microRNA 4643) Homo sapiens
Analyze
Symbol: MIR4643
Name: microRNA 4643
RGD ID: 5134173
HGNC Page HGNC:41814
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
GRCh38691,521,660 - 91,521,737 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl691,521,660 - 91,521,737 (+)EnsemblGRCh38hg38GRCh38
GRCh37692,231,378 - 92,231,455 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map6q15NCBI
HuRef689,450,514 - 89,450,591 (+)NCBIHuRef
CHM1_1692,328,771 - 92,328,848 (+)NCBICHM1_1
T2T-CHM13v2.0692,733,415 - 92,733,492 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:16381832   PMID:21199797  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 6q15(chr6:89931798-91707636)x3 copy number gain See cases [RCV000134297] Chr6:89931798..91707636 [GRCh38]
Chr6:90641517..92417354 [GRCh37]
Chr6:90698238..92474075 [NCBI36]
Chr6:6q15
uncertain significance
GRCh38/hg38 6q15(chr6:91481909-91795455)x3 copy number gain See cases [RCV000134651] Chr6:91481909..91795455 [GRCh38]
Chr6:92191627..92505173 [GRCh37]
Chr6:92248348..92561894 [NCBI36]
Chr6:6q15
benign
GRCh38/hg38 6q14.2-16.1(chr6:83838303-98822313)x1 copy number loss See cases [RCV000135773] Chr6:83838303..98822313 [GRCh38]
Chr6:84548022..99270189 [GRCh37]
Chr6:84604741..99376910 [NCBI36]
Chr6:6q14.2-16.1
pathogenic
GRCh38/hg38 6q14.3-16.1(chr6:85804273-93189258)x1 copy number loss See cases [RCV000135450] Chr6:85804273..93189258 [GRCh38]
Chr6:86513991..93898976 [GRCh37]
Chr6:86570710..93955697 [NCBI36]
Chr6:6q14.3-16.1
pathogenic
GRCh38/hg38 6q15-16.1(chr6:90888950-93582834)x1 copy number loss See cases [RCV000136984] Chr6:90888950..93582834 [GRCh38]
Chr6:91598668..94292552 [GRCh37]
Chr6:91655389..94349273 [NCBI36]
Chr6:6q15-16.1
uncertain significance
GRCh38/hg38 6q15-16.1(chr6:90687494-93806515)x1 copy number loss See cases [RCV000140304] Chr6:90687494..93806515 [GRCh38]
Chr6:91397213..94516233 [GRCh37]
Chr6:91453934..94572954 [NCBI36]
Chr6:6q15-16.1
pathogenic
GRCh38/hg38 6q13-24.1(chr6:74382807-142040500)x3 copy number gain See cases [RCV000139729] Chr6:74382807..142040500 [GRCh38]
Chr6:75092523..142361637 [GRCh37]
Chr6:75149243..142403330 [NCBI36]
Chr6:6q13-24.1
pathogenic
GRCh38/hg38 6q15(chr6:89339079-92096042)x3 copy number gain See cases [RCV000142031] Chr6:89339079..92096042 [GRCh38]
Chr6:90048798..92805760 [GRCh37]
Chr6:90105517..92862481 [NCBI36]
Chr6:6q15
uncertain significance
GRCh38/hg38 6q14.1-16.1(chr6:75926199-92710793)x1 copy number loss See cases [RCV000143505] Chr6:75926199..92710793 [GRCh38]
Chr6:76635916..93420511 [GRCh37]
Chr6:76692636..93477232 [NCBI36]
Chr6:6q14.1-16.1
pathogenic
GRCh38/hg38 6q14.1-16.1(chr6:82569098-93753476)x1 copy number loss See cases [RCV000052192] Chr6:82569098..93753476 [GRCh38]
Chr6:83278815..94463194 [GRCh37]
Chr6:83335534..94519915 [NCBI36]
Chr6:6q14.1-16.1
pathogenic
miRNA Target Status

Predicted Targets
Summary Value
Count of predictions:13817
Count of gene targets:6062
Count of transcripts:11171
Interacting mature miRNAs:hsa-miR-4643
Prediction methods:Microtar, Miranda, Pita, Pita,Targetscan, 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 endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system entire extraembryonic component
High
Medium 1
Low 2 7 2 12 2 1 4 2 10 2 9
Below cutoff 4 1 6 3 2 5 2 1 4 1

Sequence


RefSeq Acc Id: ENST00000577473
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl691,521,660 - 91,521,737 (+)Ensembl
RefSeq Acc Id: NR_039786
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38691,521,660 - 91,521,737 (+)NCBI
GRCh37692,231,378 - 92,231,455 (+)ENTREZGENE
HuRef689,450,514 - 89,450,591 (+)ENTREZGENE
CHM1_1692,328,771 - 92,328,848 (+)NCBI
T2T-CHM13v2.0692,733,415 - 92,733,492 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC MIR4643 COSMIC
Ensembl Genes ENSG00000263734 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000577473 ENTREZGENE
GTEx ENSG00000263734 GTEx
HGNC ID HGNC:41814 ENTREZGENE
Human Proteome Map MIR4643 Human Proteome Map
miRBase MI0017270 ENTREZGENE
NCBI Gene 100616174 ENTREZGENE
RNAcentral URS00002FBE0C RNACentral
  URS000075B78A RNACentral