Mir138-1 (microRNA 138-1) - Rat Genome Database

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Gene: Mir138-1 (microRNA 138-1) Rattus norvegicus
Analyze
Symbol: Mir138-1
Name: microRNA 138-1
RGD ID: 2325568
Description: Predicted to enable mRNA 3'-UTR binding activity and mRNA base-pairing translational repressor activity. Predicted to be involved in several processes, including negative regulation of adipose tissue development; negative regulation of cell differentiation; and negative regulation of protein metabolic process. Predicted to act upstream of or within several processes, including female sex differentiation; long-term synaptic potentiation; and myelination. Predicted to be located in cytoplasm. Orthologous to human MIR138-1 (microRNA 138-1); INTERACTS WITH quartz; valproic acid; 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (ortholog).
Type: ncrna (Ensembl: miRNA)
RefSeq Status: PROVISIONAL
Previously known as: microRNA mir-138-1; rno-mir-138-1
RGD Orthologs
Human
Mouse
Dog
Pig
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88131,178,434 - 131,178,532 (+)NCBIGRCr8
mRatBN7.28122,300,966 - 122,301,064 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8122,300,966 - 122,301,064 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8127,896,200 - 127,896,298 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08126,095,138 - 126,095,236 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08123,921,335 - 123,921,433 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08131,731,726 - 131,731,824 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8131,731,726 - 131,731,824 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08130,886,768 - 130,886,866 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera8121,418,831 - 121,418,929 (+)NCBICelera
Cytogenetic Map8q32NCBI
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

Cellular Component
cytoplasm  (ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14691248   PMID:15345052   PMID:16381832   PMID:17604727   PMID:17805466   PMID:20223197   PMID:20403161   PMID:20805985   PMID:23485012   PMID:23946534   PMID:24874717   PMID:25858512  
PMID:27648837   PMID:29614311   PMID:31599400   PMID:32114772   PMID:32240614   PMID:33649812   PMID:36252562   PMID:37096660  


Genomics

Comparative Map Data
Mir138-1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88131,178,434 - 131,178,532 (+)NCBIGRCr8
mRatBN7.28122,300,966 - 122,301,064 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8122,300,966 - 122,301,064 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8127,896,200 - 127,896,298 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08126,095,138 - 126,095,236 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08123,921,335 - 123,921,433 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08131,731,726 - 131,731,824 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8131,731,726 - 131,731,824 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08130,886,768 - 130,886,866 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera8121,418,831 - 121,418,929 (+)NCBICelera
Cytogenetic Map8q32NCBI
MIR138-1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38344,114,212 - 44,114,310 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl344,114,212 - 44,114,310 (+)EnsemblGRCh38hg38GRCh38
GRCh37344,155,704 - 44,155,802 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36344,130,707 - 44,130,805 (+)NCBINCBI36Build 36hg18NCBI36
Celera344,093,960 - 44,094,058 (+)NCBICelera
Cytogenetic Map3p21.32NCBI
CHM1_1344,105,818 - 44,105,916 (+)NCBICHM1_1
T2T-CHM13v2.0344,129,777 - 44,129,875 (+)NCBIT2T-CHM13v2.0
Mir138-1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399122,511,941 - 122,512,039 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9122,511,941 - 122,512,039 (+)EnsemblGRCm39 Ensembl
GRCm389122,682,876 - 122,682,974 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9122,682,876 - 122,682,974 (+)EnsemblGRCm38mm10GRCm38
MGSCv379122,591,994 - 122,592,092 (+)NCBIGRCm37MGSCv37mm9NCBIm37
Celera9123,136,295 - 123,136,393 (+)NCBICelera
Cytogenetic Map9F4NCBI
cM Map973.05NCBI
MIR138A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1232,223,136 - 2,223,197 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl232,223,128 - 2,223,205 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha232,260,635 - 2,260,696 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0232,472,862 - 2,472,923 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl232,472,854 - 2,472,931 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1232,312,565 - 2,312,626 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0232,443,379 - 2,443,440 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0232,405,402 - 2,405,463 (-)NCBIUU_Cfam_GSD_1.0
MIR138
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1327,450,130 - 27,450,214 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11327,450,130 - 27,450,214 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21330,329,402 - 30,329,486 (+)NCBISscrofa10.2Sscrofa10.2susScr3

miRNA Target Status

Predicted Targets
Summary Value
Count of predictions:3957
Count of gene targets:3078
Count of transcripts:3296
Interacting mature miRNAs:rno-miR-138-1-3p
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat

Markers in Region
AU046736  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28122,300,034 - 122,300,240 (+)MAPPERmRatBN7.2
Rnor_6.08131,730,795 - 131,731,000NCBIRnor6.0
Rnor_5.08130,885,837 - 130,886,042UniSTSRnor5.0
RGSC_v3.48127,389,347 - 127,389,552UniSTSRGSC3.4


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

endocrine system hemolymphoid system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium
Low 9 11 1 1 33 9 8 7 1
Below cutoff 2 1 1 1 4 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NR_031885 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAXUCZ010000008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000053764
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8122,300,966 - 122,301,064 (+)Ensembl
Rnor_6.0 Ensembl8131,731,726 - 131,731,824 (+)Ensembl
RefSeq Acc Id: NR_031885
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88131,178,434 - 131,178,532 (+)NCBI
mRatBN7.28122,300,966 - 122,301,064 (+)NCBI
Rnor_6.08131,731,726 - 131,731,824 (+)NCBI
Rnor_5.08130,886,768 - 130,886,866 (+)NCBI
Celera8121,418,831 - 121,418,929 (+)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:2325568 AgrOrtholog
BioCyc Gene G2FUF-28643 BioCyc
Ensembl Genes ENSRNOG00000035641 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000053764 ENTREZGENE
miRBase MI0000912 ENTREZGENE
NCBI Gene 100314033 ENTREZGENE
PhenoGen Mir138-1 PhenoGen
RatGTEx ENSRNOG00000035641 RatGTEx
RNAcentral URS00003980D0 RNACentral
  URS000040780F RNACentral
  URS000075A2CD RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-14 Mir138-1  microRNA 138-1  Mir138-1  microRNA mir-138-1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-06-02 Mir138-1  microRNA mir-138-1      Symbol and Name status set to provisional 70820 PROVISIONAL