MIR3909 (microRNA 3909) - Rat Genome Database

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Gene: MIR3909 (microRNA 3909) Homo sapiens
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Symbol: MIR3909
Name: microRNA 3909
RGD ID: 4888839
HGNC Page HGNC
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
RefSeq Status: PROVISIONAL
Also known as: mir-3909
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2235,335,640 - 35,335,758 (+)EnsemblGRCh38hg38GRCh38
GRCh382235,335,640 - 35,335,758 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372235,731,633 - 35,731,751 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map22q12.3NCBI
HuRef2218,692,718 - 18,692,836 (+)NCBIHuRef
CHM1_12235,689,817 - 35,689,935 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:16381832   PMID:20224791   PMID:20498841   PMID:21037258   PMID:29548280  


Genomics

miRNA Target Status

Confirmed Targets
Gene TargetMature miRNAMethod NameResult TypeData TypeSupport TypePMID
CARHSP1hsa-miR-3909Mirtarbaseexternal_infoCLASHFunctional MTI (Weak)23622248

Predicted Targets
Summary Value
Count of predictions:26508
Count of gene targets:11572
Count of transcripts:23050
Interacting mature miRNAs:hsa-miR-3909
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 2 45 2 2
Low 124 430 133 87 547 70 606 62 105 63 162 276 22 60 299 3
Below cutoff 247 409 198 75 287 37 692 245 209 43 161 235 38 176 413

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000579518
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2235,335,640 - 35,335,758 (+)Ensembl
RefSeq Acc Id: NR_037471
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382235,335,640 - 35,335,758 (+)NCBI
GRCh372235,731,633 - 35,731,751 (+)ENTREZGENE
HuRef2218,692,718 - 18,692,836 (+)ENTREZGENE
CHM1_12235,689,817 - 35,689,935 (+)NCBI
Sequence:

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 22q11.1-13.33(chr22:16916608-50739836)x3 copy number gain See cases [RCV000133646] Chr22:16916608..50739836 [GRCh38]
Chr22:17397498..51178264 [GRCh37]
Chr22:15777498..49525130 [NCBI36]
Chr22:22q11.1-13.33
pathogenic
GRCh38/hg38 22q11.1-13.33(chr22:16916743-50739785)x3 copy number gain See cases [RCV000134730] Chr22:16916743..50739785 [GRCh38]
Chr22:17397633..51178213 [GRCh37]
Chr22:15777633..49525079 [NCBI36]
Chr22:22q11.1-13.33
pathogenic
GRCh38/hg38 22q11.23-12.3(chr22:23279231-36247369)x3 copy number gain See cases [RCV000138172] Chr22:23279231..36247369 [GRCh38]
Chr22:23621418..36643415 [GRCh37]
Chr22:21951418..34973361 [NCBI36]
Chr22:22q11.23-12.3
pathogenic
GRCh38/hg38 22q11.21-12.3(chr22:20907226-37187347)x3 copy number gain See cases [RCV000137926] Chr22:20907226..37187347 [GRCh38]
Chr22:21261514..37583387 [GRCh37]
Chr22:19591514..35913333 [NCBI36]
Chr22:22q11.21-12.3
pathogenic
GRCh38/hg38 22q12.3-13.33(chr22:33768441-50739977)x3 copy number gain See cases [RCV000051682] Chr22:33768441..50739977 [GRCh38]
Chr22:34164428..51178405 [GRCh37]
Chr22:32494428..49525271 [NCBI36]
Chr22:22q12.3-13.33
pathogenic
GRCh38/hg38 22q12.3-13.1(chr22:35333993-38900177)x1 copy number loss See cases [RCV000051364] Chr22:35333993..38900177 [GRCh38]
Chr22:35729986..39296182 [GRCh37]
Chr22:34059986..37626128 [NCBI36]
Chr22:22q12.3-13.1
pathogenic

Additional Information

Database Acc Id Source(s)
COSMIC MIR3909 COSMIC
Ensembl Genes ENSG00000266320 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000579518 ENTREZGENE
GTEx ENSG00000266320 GTEx
HGNC ID HGNC:38987 ENTREZGENE
Human Proteome Map MIR3909 Human Proteome Map
miRBase MI0016413 ENTREZGENE
NCBI Gene 100500826 ENTREZGENE
RNAcentral URS000022B729 RNACentral
  URS000075C219 RNACentral