MIR5689 (microRNA 5689) - Rat Genome Database

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Gene: MIR5689 (microRNA 5689) Homo sapiens
Analyze
Symbol: MIR5689
Name: microRNA 5689
RGD ID: 6483943
HGNC Page HGNC:43479
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
GRCh38610,439,717 - 10,439,794 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl610,439,717 - 10,439,794 (+)EnsemblGRCh38hg38GRCh38
GRCh37610,439,950 - 10,440,027 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map6p24.3NCBI
CHM1_1610,442,196 - 10,442,273 (+)NCBICHM1_1
T2T-CHM13v2.0610,307,449 - 10,307,526 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:16381832   PMID:21980368  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 6p25.3-24.1(chr6:164360-13339881)x3 copy number gain See cases [RCV000134022] Chr6:164360..13339881 [GRCh38]
Chr6:164360..13340113 [GRCh37]
Chr6:109360..13448092 [NCBI36]
Chr6:6p25.3-24.1		 pathogenic
GRCh38/hg38 6p25.2-24.1(chr6:4068792-13267799)x1 copy number loss See cases [RCV000136132] Chr6:4068792..13267799 [GRCh38]
Chr6:4069026..13268031 [GRCh37]
Chr6:4014025..13376010 [NCBI36]
Chr6:6p25.2-24.1		 pathogenic
GRCh38/hg38 6p25.3-22.3(chr6:152634-15732163)x3 copy number gain See cases [RCV000138121] Chr6:152634..15732163 [GRCh38]
Chr6:152634..15732394 [GRCh37]
Chr6:97634..15840373 [NCBI36]
Chr6:6p25.3-22.3		 likely benign
GRCh38/hg38 6p25.2-21.33(chr6:3224310-30657190)x3 copy number gain See cases [RCV000138956] Chr6:3224310..30657190 [GRCh38]
Chr6:3224544..30624967 [GRCh37]
Chr6:3169543..30732946 [NCBI36]
Chr6:6p25.2-21.33		 pathogenic
GRCh38/hg38 6p25.3-22.3(chr6:155807-17058414)x3 copy number gain See cases [RCV000140307] Chr6:155807..17058414 [GRCh38]
Chr6:155807..17058645 [GRCh37]
Chr6:100807..17166624 [NCBI36]
Chr6:6p25.3-22.3		 pathogenic
GRCh38/hg38 6p25.3-24.2(chr6:156974-11550817)x3 copy number gain See cases [RCV000142295] Chr6:156974..11550817 [GRCh38]
Chr6:156974..11551050 [GRCh37]
Chr6:101974..11659036 [NCBI36]
Chr6:6p25.3-24.2		 likely pathogenic
GRCh38/hg38 6p25.2-22.3(chr6:2862640-16697788)x1 copy number loss See cases [RCV000142435] Chr6:2862640..16697788 [GRCh38]
Chr6:2862874..16698019 [GRCh37]
Chr6:2807873..16805998 [NCBI36]
Chr6:6p25.2-22.3		 pathogenic
GRCh38/hg38 6p25.3-23(chr6:152634-14417003)x3 copy number gain See cases [RCV000143334] Chr6:152634..14417003 [GRCh38]
Chr6:152634..14417234 [GRCh37]
Chr6:97634..14525213 [NCBI36]
Chr6:6p25.3-23		 pathogenic
GRCh38/hg38 6p25.3-24.1(chr6:156974-13081201)x3 copy number gain See cases [RCV000143698] Chr6:156974..13081201 [GRCh38]
Chr6:156974..13081433 [GRCh37]
Chr6:101974..13189419 [NCBI36]
Chr6:6p25.3-24.1		 likely pathogenic
GRCh38/hg38 6p25.3-23(chr6:156974-13855925)x1 copy number loss See cases [RCV000143782] Chr6:156974..13855925 [GRCh38]
Chr6:156974..13856156 [GRCh37]
Chr6:101974..13964135 [NCBI36]
Chr6:6p25.3-23		 pathogenic
GRCh38/hg38 6p25.3-12.3(chr6:156974-46789291)x3 copy number gain See cases [RCV000143497] Chr6:156974..46789291 [GRCh38]
Chr6:156974..46757028 [GRCh37]
Chr6:101974..46864987 [NCBI36]
Chr6:6p25.3-12.3		 pathogenic
GRCh38/hg38 6p25.3-22.3(chr6:106431-18360595)x3 copy number gain See cases [RCV000051869] Chr6:106431..18360595 [GRCh38]
Chr6:106431..18360826 [GRCh37]
Chr6:51431..18468805 [NCBI36]
Chr6:6p25.3-22.3		 pathogenic
GRCh38/hg38 6p25.3-23(chr6:389423-13474956)x3 copy number gain See cases [RCV000051896] Chr6:389423..13474956 [GRCh38]
Chr6:389423..13475188 [GRCh37]
Chr6:334423..13583167 [NCBI36]
Chr6:6p25.3-23		 pathogenic
miRNA Target Status

Predicted Targets
Summary Value
Count of predictions:11307
Count of gene targets:5302
Count of transcripts:9480
Interacting mature miRNAs:hsa-miR-5689
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 appendage
High
Medium
Low 3 1 2 1 6 1 2 2 1 1 2 3 1
Below cutoff 2 1 1 3 5 1 3 5 3 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000581998
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl610,439,717 - 10,439,794 (+)Ensembl
RefSeq Acc Id: NR_049872
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38610,439,717 - 10,439,794 (+)NCBI
GRCh37610,439,950 - 10,440,027 (+)NCBI
CHM1_1610,442,196 - 10,442,273 (+)NCBI
T2T-CHM13v2.0610,307,449 - 10,307,526 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC MIR5689 COSMIC
Ensembl Genes ENSG00000263705 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000581998 ENTREZGENE
GTEx ENSG00000263705 GTEx
HGNC ID HGNC:43479 ENTREZGENE
Human Proteome Map MIR5689 Human Proteome Map
miRBase MI0019294 ENTREZGENE
NCBI Gene MIR5689 ENTREZGENE
RNAcentral URS000075B8DC RNACentral
  URS000075DECF RNACentral