MIR548A3 (microRNA 548a-3) - Rat Genome Database

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Gene: MIR548A3 (microRNA 548a-3) Homo sapiens
Analyze
Symbol: MIR548A3
Name: microRNA 548a-3
RGD ID: 1603129
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: MIRN548A3
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
NCBI Annotation Information: Note: MIR548A3 (GeneID 693127) was annotated incorrectly on NCBI's Build 37.2. Its correct location is chr8: 105496597-105496693 (-). [17 Jun 2014]
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl8104,484,369 - 104,484,465 (-)EnsemblGRCh38hg38GRCh38
GRCh388104,484,369 - 104,484,465 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh378105,496,597 - 105,496,693 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 368105,565,772 - 105,565,868 (-)NCBINCBI36hg18NCBI36
Celera1458,927,825 - 58,962,785 (-)NCBI
Cytogenetic Map8q22.3NCBI
HuRef1459,055,544 - 59,090,504 (-)NCBIHuRef
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
silver atom  (EXP)
silver(0)  (EXP)

References

References - curated
1. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16381832   PMID:16505370   PMID:17604727   PMID:30556306  


Genomics

Position Markers
D14S95E  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371478,909,920 - 78,909,996UniSTSGRCh37
Build 361477,979,673 - 77,979,749RGDNCBI36
Celera1458,947,678 - 58,947,754RGD
Cytogenetic Map14q31UniSTS
HuRef1459,075,397 - 59,075,473UniSTS

miRNA Target Status

Confirmed Targets
Gene TargetMature miRNAMethod NameResult TypeData TypeSupport TypePMID
MTA2hsa-miR-548a-3pMirtarbaseexternal_infoCLASHFunctional MTI (Weak)23622248
LRP1Bhsa-miR-548a-5pOncomiRDBexternal_infoNANA21057533

Predicted Targets
Summary Value
Count of predictions:50591
Count of gene targets:12634
Count of transcripts:27795
Interacting mature miRNAs:hsa-miR-548a-3p, hsa-miR-548a-5p
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 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
High
Medium 2
Low 25 16 41 26 84 27 97 38 108 70 77 110 2 9
Below cutoff 48 23 17 9 23 9 45 40 146 17 43 32 3 11 29

Sequence

Nucleotide Sequences
RefSeq Transcripts NR_030330 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AP002847 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000385297
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8104,484,369 - 104,484,465 (-)Ensembl
RefSeq Acc Id: NR_030330
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh388104,484,369 - 104,484,465 (-)NCBI
GRCh378105,496,597 - 105,496,693 (-)NCBI
Celera758,927,825 - 58,962,785 (-)ENTREZGENE
HuRef759,055,545 - 59,090,505 (-)ENTREZGENE
Sequence:
Promoters
RGD ID:6806702
Promoter ID:HG_KWN:61889
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:K562
Transcripts:ENST00000385297
Position:
Human AssemblyChrPosition (strand)Source
Build 368105,565,966 - 105,566,667 (-)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 8q22.1-24.3(chr8:94682154-145068656)x3 copy number gain See cases [RCV000134353] Chr8:94682154..145068656 [GRCh38]
Chr8:95694382..146294042 [GRCh37]
Chr8:95763558..146264846 [NCBI36]
Chr8:8q22.1-24.3
pathogenic
GRCh38/hg38 8q22.3-23.1(chr8:101884819-107356143)x1 copy number loss See cases [RCV000134099] Chr8:101884819..107356143 [GRCh38]
Chr8:102897047..108368371 [GRCh37]
Chr8:102966223..108437547 [NCBI36]
Chr8:8q22.3-23.1
pathogenic
GRCh38/hg38 8q21.3-24.23(chr8:86300584-137022587)x3 copy number gain See cases [RCV000135621] Chr8:86300584..137022587 [GRCh38]
Chr8:87312813..138034830 [GRCh37]
Chr8:87381929..138104012 [NCBI36]
Chr8:8q21.3-24.23
pathogenic|likely pathogenic
GRCh38/hg38 8q22.3-23.1(chr8:101199826-105802098)x1 copy number loss See cases [RCV000136812] Chr8:101199826..105802098 [GRCh38]
Chr8:102212054..106814326 [GRCh37]
Chr8:102281230..106883502 [NCBI36]
Chr8:8q22.3-23.1
pathogenic
GRCh38/hg38 8q22.3-23.1(chr8:101171263-109127664)x1 copy number loss See cases [RCV000138134] Chr8:101171263..109127664 [GRCh38]
Chr8:102183491..110139893 [GRCh37]
Chr8:102252667..110209069 [NCBI36]
Chr8:8q22.3-23.1
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241605-145054781)x3 copy number gain See cases [RCV000138643] Chr8:241605..145054781 [GRCh38]
Chr8:191605..146280167 [GRCh37]
Chr8:181605..146250971 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q21.3-24.3(chr8:87931152-145068712)x3 copy number gain See cases [RCV000138551] Chr8:87931152..145068712 [GRCh38]
Chr8:88943380..146294098 [GRCh37]
Chr8:89012496..146264902 [NCBI36]
Chr8:8q21.3-24.3
pathogenic
GRCh38/hg38 8q21.13-24.3(chr8:77480050-145068712)x3 copy number gain See cases [RCV000139036] Chr8:77480050..145068712 [GRCh38]
Chr8:78392286..146294098 [GRCh37]
Chr8:78554841..146264902 [NCBI36]
Chr8:8q21.13-24.3
pathogenic
GRCh38/hg38 8q22.1-24.3(chr8:97382873-145070385)x3 copy number gain See cases [RCV000140447] Chr8:97382873..145070385 [GRCh38]
Chr8:98395101..146295771 [GRCh37]
Chr8:98464277..146266575 [NCBI36]
Chr8:8q22.1-24.3
pathogenic
GRCh38/hg38 8q11.1-24.3(chr8:46031340-139285494)x3 copy number gain See cases [RCV000139539] Chr8:46031340..139285494 [GRCh38]
Chr8:46942962..140297737 [GRCh37]
Chr8:47062127..140366919 [NCBI36]
Chr8:8q11.1-24.3
pathogenic
GRCh38/hg38 8q22.3-24.3(chr8:100867343-145070385)x3 copy number gain See cases [RCV000141694] Chr8:100867343..145070385 [GRCh38]
Chr8:101879571..146295771 [GRCh37]
Chr8:101948747..146266575 [NCBI36]
Chr8:8q22.3-24.3
pathogenic
GRCh38/hg38 8q22.2-23.1(chr8:100179408-106524667)x1 copy number loss See cases [RCV000141697] Chr8:100179408..106524667 [GRCh38]
Chr8:101191636..107536895 [GRCh37]
Chr8:101260812..107606071 [NCBI36]
Chr8:8q22.2-23.1
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:208048-145070385)x3 copy number gain See cases [RCV000141808] Chr8:208048..145070385 [GRCh38]
Chr8:158048..146295771 [GRCh37]
Chr8:148048..146266575 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8p21.3-q24.3(chr8:21291522-145070385)x3 copy number gain See cases [RCV000142021] Chr8:21291522..145070385 [GRCh38]
Chr8:21149033..146295771 [GRCh37]
Chr8:21193313..146266575 [NCBI36]
Chr8:8p21.3-q24.3
pathogenic
GRCh38/hg38 8q22.3-24.3(chr8:103306336-145068712)x3 copy number gain See cases [RCV000142810] Chr8:103306336..145068712 [GRCh38]
Chr8:104318564..146294098 [GRCh37]
Chr8:104387740..146264902 [NCBI36]
Chr8:8q22.3-24.3
pathogenic|likely pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:226452-145068712)x3 copy number gain See cases [RCV000142858] Chr8:226452..145068712 [GRCh38]
Chr8:176452..146294098 [GRCh37]
Chr8:166452..146264902 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q21.13-24.3(chr8:78614077-145054634)x3 copy number gain See cases [RCV000142597] Chr8:78614077..145054634 [GRCh38]
Chr8:79526312..146280020 [GRCh37]
Chr8:79688867..146250824 [NCBI36]
Chr8:8q21.13-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000148092] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q21.2-24.3(chr8:85765999-145070385)x3 copy number gain See cases [RCV000143659] Chr8:85765999..145070385 [GRCh38]
Chr8:86778228..146295771 [GRCh37]
Chr8:86863079..146266575 [NCBI36]
Chr8:8q21.2-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145049449)x3 copy number gain See cases [RCV000051206] Chr8:241530..145049449 [GRCh38]
Chr8:191530..146274835 [GRCh37]
Chr8:181530..146245639 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q22.1-24.3(chr8:95606052-145054775)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053677]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053677]|See cases [RCV000053677] Chr8:95606052..145054775 [GRCh38]
Chr8:96618280..146280161 [GRCh37]
Chr8:96687456..146250965 [NCBI36]
Chr8:8q22.1-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000053602] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:244417-145054775)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053604]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053604]|See cases [RCV000053604] Chr8:244417..145054775 [GRCh38]
Chr8:194417..146280161 [GRCh37]
Chr8:184417..146250965 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic

Additional Information

Database Acc Id Source(s)
COSMIC MIR548A3 COSMIC
Ensembl Genes ENSG00000208032 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000385297 ENTREZGENE
GTEx ENSG00000208032 GTEx
HGNC ID HGNC:32798 ENTREZGENE
Human Proteome Map MIR548A3 Human Proteome Map
miRBase MI0003612 ENTREZGENE
NCBI Gene 693127 ENTREZGENE
PharmGKB PA164722819 PharmGKB
RNAcentral URS000038037E RNACentral
  URS00005F5B1B RNACentral
  URS000075E95F RNACentral