Mir542 (microRNA 542) - Rat Genome Database

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Gene: Mir542 (microRNA 542) Rattus norvegicus
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Symbol: Mir542 (Ensembl: Mir542-2)
Name: microRNA 542 (Ensembl:microRNA mir-542-2)
RGD ID: 2325422
Description: Predicted to act upstream of or within cellular response to leukemia inhibitory factor; hematopoietic stem cell differentiation; and sensory perception of sound. Biomarker of renal fibrosis. Orthologous to human MIR542 (microRNA 542); INTERACTS WITH 2,5-hexanedione; atrazine; bis(2-ethylhexyl) phthalate.
Type: ncrna (Ensembl: miRNA)
RefSeq Status: PROVISIONAL
Previously known as: microRNA mir-542; microRNA mir-542-2; rno-mir-542; rno-mir-542-1
RGD Orthologs
Human
Mouse
Dog
Pig
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X137,722,176 - 137,722,254 (-)NCBIGRCr8
mRatBN7.2X132,802,623 - 132,802,701 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX132,802,623 - 132,802,701 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX134,962,672 - 134,962,750 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X138,545,520 - 138,545,598 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X136,111,232 - 136,111,310 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X158,152,146 - 158,152,224 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX158,152,146 - 158,152,224 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X152,777,453 - 152,777,531 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Cytogenetic MapXq36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. MicroRNA-542-3p Suppresses Tumor Cell Invasion via Targeting AKT Pathway in Human Astrocytoma. Cai J, etal., J Biol Chem. 2015 Oct 9;290(41):24678-88. doi: 10.1074/jbc.M115.649004. Epub 2015 Aug 18.
2. MiR-542-3p drives renal fibrosis by targeting AGO1 in vivo and in vitro. Li J, etal., Life Sci. 2020 Aug 15;255:117845. doi: 10.1016/j.lfs.2020.117845. Epub 2020 May 26.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16274478   PMID:16381832   PMID:17604727   PMID:20403161   PMID:20439489   PMID:20660734   PMID:23646144   PMID:31829291   PMID:35416722   PMID:37976699   PMID:38572673  


Genomics

Comparative Map Data
Mir542
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X137,722,176 - 137,722,254 (-)NCBIGRCr8
mRatBN7.2X132,802,623 - 132,802,701 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX132,802,623 - 132,802,701 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX134,962,672 - 134,962,750 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X138,545,520 - 138,545,598 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X136,111,232 - 136,111,310 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X158,152,146 - 158,152,224 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX158,152,146 - 158,152,224 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X152,777,453 - 152,777,531 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Cytogenetic MapXq36NCBI
MIR542
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X134,541,341 - 134,541,437 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX134,541,341 - 134,541,437 (-)EnsemblGRCh38hg38GRCh38
GRCh37X133,675,371 - 133,675,467 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X133,503,036 - 133,503,132 (-)NCBINCBI36Build 36hg18NCBI36
CeleraX134,062,199 - 134,062,295 (-)NCBICelera
Cytogenetic MapXq26.3NCBI
HuRefX123,074,367 - 123,074,463 (-)NCBIHuRef
CHM1_1X133,587,121 - 133,587,217 (-)NCBICHM1_1
T2T-CHM13v2.0X132,866,540 - 132,866,636 (-)NCBIT2T-CHM13v2.0
Mir542
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X52,138,280 - 52,138,364 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX52,138,280 - 52,138,364 (-)EnsemblGRCm39 Ensembl
GRCm38X53,049,403 - 53,049,487 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX53,049,403 - 53,049,487 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X50,402,580 - 50,402,664 (-)NCBIGRCm37MGSCv37mm9NCBIm37
CeleraX40,475,386 - 40,475,470 (-)NCBICelera
Cytogenetic MapXA5NCBI
cM MapX29.31NCBI
MIR542
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X105,178,359 - 105,178,417 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX105,178,347 - 105,178,430 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX91,289,030 - 91,289,088 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X107,038,111 - 107,038,169 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX107,038,099 - 107,038,182 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X104,451,564 - 104,451,622 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X106,317,541 - 106,317,599 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X106,109,007 - 106,109,065 (-)NCBIUU_Cfam_GSD_1.0
MIR542
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX110,382,597 - 110,382,676 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X110,382,597 - 110,382,676 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X93956491138956491Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X103312877148312877Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX112934952138400867Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat


Expression

RNA-SEQ Expression

ectoderm
endocrine system
endoderm
mesenchyme
mesoderm
reproductive system
respiratory system
1 1 1 1 1 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NR_032122 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAXUCZ010000021 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000073411
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX158,152,146 - 158,152,224 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000118651
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX132,802,623 - 132,802,701 (-)Ensembl
RefSeq Acc Id: NR_032122
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X137,722,176 - 137,722,254 (-)NCBI
mRatBN7.2X132,802,623 - 132,802,701 (-)NCBI
Rnor_6.0X158,152,146 - 158,152,224 (+)NCBI
Rnor_5.0X152,777,453 - 152,777,531 (+)NCBI
Sequence:
Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2325422 AgrOrtholog
BioCyc Gene G2FUF-995 BioCyc
Ensembl Genes ENSRNOG00000049278 Ensembl
  ENSRNOG00000070890 Ensembl
miRBase MI0003528 ENTREZGENE
NCBI Gene 100314199 ENTREZGENE
PhenoGen Mir542 PhenoGen
RatGTEx ENSRNOG00000049278 RatGTEx
  ENSRNOG00000070890 RatGTEx
RNAcentral URS00001AF64C RNACentral
  URS00004F859B RNACentral
  URS000075D753 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Mir542  microRNA 542  Mir542  microRNA mir-542-2  Data merged from RGD:149736101 737654 PROVISIONAL
2021-08-09 Mir542  microRNA mir-542-2      Symbol and Name status set to provisional 45752 PROVISIONAL
2013-08-14 Mir542  microRNA 542  Mir542  microRNA mir-542  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-06-02 Mir542  microRNA mir-542      Symbol and Name status set to provisional 70820 PROVISIONAL