MIR4688 (microRNA 4688) - Rat Genome Database

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Gene: MIR4688 (microRNA 4688) Homo sapiens
Analyze
Symbol: MIR4688
Name: microRNA 4688
RGD ID: 5134078
HGNC Page HGNC:41897
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
Previously known as: mir-4688
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381146,376,402 - 46,376,484 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1146,376,402 - 46,376,484 (+)EnsemblGRCh38hg38GRCh38
GRCh371146,397,952 - 46,398,034 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map11p11.2NCBI
HuRef1146,104,910 - 46,104,992 (+)NCBIHuRef
CHM1_11146,396,388 - 46,396,470 (+)NCBICHM1_1
T2T-CHM13v2.01146,532,478 - 46,532,560 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16381832   PMID:21037258   PMID:21199797   PMID:31137016  


Genomics

Variants

.
Variants in MIR4688
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_001105540.1(DGKZ):c.1647C>T (p.Ile549=) single nucleotide variant Malignant melanoma [RCV000069367] Chr11:46372782 [GRCh38]
Chr11:46394332 [GRCh37]
Chr11:46350908 [NCBI36]
Chr11:11p11.2		 not provided
NM_001105540.1(DGKZ):c.2218C>T (p.Pro740Ser) single nucleotide variant Malignant melanoma [RCV000069368] Chr11:46374989 [GRCh38]
Chr11:46396539 [GRCh37]
Chr11:46353115 [NCBI36]
Chr11:11p11.2		 not provided
GRCh38/hg38 11p12-11.2(chr11:41118322-48643003)x1 copy number loss See cases [RCV000135405] Chr11:41118322..48643003 [GRCh38]
Chr11:41139872..48664555 [GRCh37]
Chr11:41096448..48621131 [NCBI36]
Chr11:11p12-11.2		 pathogenic
GRCh38/hg38 11p12-11.12(chr11:39179252-49135735)x1 copy number loss See cases [RCV000137391] Chr11:39179252..49135735 [GRCh38]
Chr11:39200802..49157287 [GRCh37]
Chr11:39157378..49113863 [NCBI36]
Chr11:11p12-11.12		 pathogenic
GRCh38/hg38 11p12-11.12(chr11:42727555-49135735)x3 copy number gain See cases [RCV000139422] Chr11:42727555..49135735 [GRCh38]
Chr11:42749105..49157287 [GRCh37]
Chr11:42705681..49113863 [NCBI36]
Chr11:11p12-11.12		 likely pathogenic
GRCh38/hg38 11p13-11.2(chr11:35663578-46959820)x1 copy number loss See cases [RCV000052679] Chr11:35663578..46959820 [GRCh38]
Chr11:35685126..46981371 [GRCh37]
Chr11:35641702..46937947 [NCBI36]
Chr11:11p13-11.2		 pathogenic
GRCh38/hg38 11p12-11.2(chr11:36508280-48643003)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052680]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052680]|See cases [RCV000052680] Chr11:36508280..48643003 [GRCh38]
Chr11:36529830..48664555 [GRCh37]
Chr11:36486406..48621131 [NCBI36]
Chr11:11p12-11.2		 pathogenic
NM_001199267.2(DGKZ):c.2158+18G>A single nucleotide variant not provided [RCV002121959] Chr11:46376415 [GRCh38]
Chr11:46397965 [GRCh37]
Chr11:11p11.2		 likely benign
miRNA Target Status

Predicted Targets
Summary Value
Count of predictions:67694
Count of gene targets:21296
Count of transcripts:55829
Interacting mature miRNAs:hsa-miR-4688
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
Low 265 385 279 37 280 19 597 254 526 27 224 335 18 200 387
Below cutoff 232 374 164 51 191 32 376 342 473 31 95 103 20 127 253 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000577966
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1146,376,402 - 46,376,484 (+)Ensembl
RefSeq Acc Id: NR_039837
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381146,376,402 - 46,376,484 (+)NCBI
GRCh371146,397,952 - 46,398,034 (+)ENTREZGENE
HuRef1146,104,910 - 46,104,992 (+)ENTREZGENE
CHM1_11146,396,388 - 46,396,470 (+)NCBI
T2T-CHM13v2.01146,532,478 - 46,532,560 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC MIR4688 COSMIC
Ensembl Genes ENSG00000264102 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000577966 ENTREZGENE
GTEx ENSG00000264102 GTEx
HGNC ID HGNC:41897 ENTREZGENE
Human Proteome Map MIR4688 Human Proteome Map
miRBase MI0017321 ENTREZGENE
NCBI Gene 100616368 ENTREZGENE
RNAcentral URS000032D69B RNACentral
  URS000075E114 RNACentral