MIR125A (microRNA 125a) - Rat Genome Database

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Gene: MIR125A (microRNA 125a) Homo sapiens
Analyze
Symbol: MIR125A
Name: microRNA 125a
RGD ID: 1353053
HGNC Page HGNC
Description: Predicted to act upstream of or within several processes, including cellular response to estrogen stimulus; cellular response to leukemia inhibitory factor; and long-term synaptic potentiation. Predicted to be located in synapse. Biomarker of hepatocellular carcinoma and stomach cancer.
Type: ncrna
RefSeq Status: PROVISIONAL
Also known as: mir-125a; MIRN125A; miRNA125A
RGD Orthologs
Mouse
Rat
Dog
Pig
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1951,693,254 - 51,693,339 (+)EnsemblGRCh38hg38GRCh38
GRCh381951,693,254 - 51,693,339 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371952,196,507 - 52,196,592 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361956,888,318 - 56,888,403 (+)NCBINCBI36hg18NCBI36
Celera1949,246,042 - 49,246,127 (+)NCBI
Cytogenetic Map19q13.41NCBI
HuRef1948,527,448 - 48,527,533 (+)NCBIHuRef
CHM1_11952,198,304 - 52,198,389 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
BMP signaling pathway  (ISO)
cell aging  (ISO)
cellular response to cortisone stimulus  (ISO)
cellular response to estrogen stimulus  (ISO)
cellular response to glucose stimulus  (ISO)
cellular response to interleukin-6  (ISO)
cellular response to leukemia inhibitory factor  (ISO)
cellular response to lipopolysaccharide  (ISO)
cellular response to platelet-derived growth factor stimulus  (ISO)
cellular response to transforming growth factor beta stimulus  (ISO)
gene silencing by miRNA  (ISO)
L-ascorbic acid metabolic process  (ISO)
long-term synaptic potentiation  (ISO)
miRNA mediated inhibition of translation  (ISO)
negative regulation of interleukin-17 production  (ISO)
negative regulation of interleukin-6 production  (ISO)
negative regulation of osteoblast differentiation  (ISO)
negative regulation of stem cell differentiation  (ISO)
negative regulation of transforming growth factor beta production  (ISO)
negative regulation of vascular associated smooth muscle cell migration  (ISO)
negative regulation of vascular associated smooth muscle cell proliferation  (ISO)
positive regulation of fat cell differentiation  (ISO)
positive regulation of neuron death  (ISO)
positive regulation of vascular associated smooth muscle cell apoptotic process  (ISO)
positive regulation of vascular associated smooth muscle cell migration  (ISO)
positive regulation of vascular associated smooth muscle cell proliferation  (ISO)
regulation of cytokine production involved in inflammatory response  (ISO)
regulation of erythrocyte differentiation  (ISO)
regulation of progesterone biosynthetic process  (ISO)

Cellular Component
synapse  (ISO)

References

Additional References at PubMed
PMID:12007417   PMID:16381832   PMID:17400653   PMID:17604727   PMID:17616659   PMID:18320040   PMID:19048628   PMID:19411564   PMID:19702827   PMID:19818772   PMID:19875930   PMID:19881956  
PMID:19950226   PMID:20190813   PMID:20569443   PMID:20665731   PMID:21037258   PMID:21220473   PMID:21317190   PMID:21777146   PMID:21788734   PMID:21931172   PMID:22357933   PMID:22550173  
PMID:22644326   PMID:22690848   PMID:22747700   PMID:22768249   PMID:23079745   PMID:23327190   PMID:23525486   PMID:23583196   PMID:23595744   PMID:23606749   PMID:23618359   PMID:23783428  
PMID:23843939   PMID:24044511   PMID:24139697   PMID:24334759   PMID:24360988   PMID:24402874   PMID:24484870   PMID:24675842   PMID:24690917   PMID:24737570   PMID:24759737   PMID:24819167  
PMID:24824183   PMID:24877885   PMID:24896104   PMID:24901105   PMID:24913817   PMID:24945821   PMID:24990808   PMID:25109760   PMID:25116893   PMID:25231560   PMID:25256711   PMID:25336585  
PMID:25370896   PMID:25406362   PMID:25479352   PMID:25504437   PMID:25542152   PMID:25560389   PMID:25598421   PMID:25673044   PMID:25755772   PMID:25772251   PMID:25800681   PMID:25815788  
PMID:25833836   PMID:25863684   PMID:25962054   PMID:25963922   PMID:25998575   PMID:26011312   PMID:26017674   PMID:26071398   PMID:26151241   PMID:26227218   PMID:26270249   PMID:26297542  
PMID:26389681   PMID:26398444   PMID:26424054   PMID:26531722   PMID:26563755   PMID:26646586   PMID:26646931   PMID:26693202   PMID:26713860   PMID:26731991   PMID:26758190   PMID:26766902  
PMID:26782438   PMID:26800505   PMID:26875774   PMID:26962687   PMID:27000524   PMID:27014994   PMID:27074047   PMID:27094723   PMID:27133073   PMID:27133078   PMID:27220320   PMID:27231954  
PMID:27252357   PMID:27424784   PMID:27522004   PMID:27693788   PMID:27698367   PMID:27814341   PMID:27836539   PMID:27888002   PMID:27903586   PMID:27982429   PMID:28140520   PMID:28402230  
PMID:28405612   PMID:28408353   PMID:28445974   PMID:28467514   PMID:28596599   PMID:28631574   PMID:28646161   PMID:28695772   PMID:28714018   PMID:28724745   PMID:28732738   PMID:28761107  
PMID:28771224   PMID:28798470   PMID:28800792   PMID:28859241   PMID:28939591   PMID:28950256   PMID:28982331   PMID:29076440   PMID:29106389   PMID:29121972   PMID:29133857   PMID:29179212  
PMID:29209130   PMID:29344850   PMID:29345059   PMID:29505034   PMID:29634399   PMID:29635126   PMID:29663500   PMID:29689270   PMID:29693153   PMID:29749475   PMID:29750426   PMID:29767234  
PMID:30076753   PMID:30089723   PMID:30132551   PMID:30149002   PMID:30153074   PMID:30187954   PMID:30203815   PMID:30225271   PMID:30226579   PMID:30237316   PMID:30242085   PMID:30245693  
PMID:30302847   PMID:30370524   PMID:30372804   PMID:30387833   PMID:30394225   PMID:30412716   PMID:30536969   PMID:30670152   PMID:30782086   PMID:30785086   PMID:30843663   PMID:30863948  
PMID:30868841   PMID:31014918   PMID:31042422   PMID:31112584   PMID:31114983   PMID:31115097   PMID:31141316   PMID:31254127   PMID:31301414   PMID:31325708   PMID:31349052   PMID:31452281  
PMID:31489990   PMID:31499051   PMID:31527306   PMID:31558421   PMID:31575334   PMID:31595566   PMID:31646555   PMID:31683458   PMID:31696556   PMID:31698596   PMID:31702027   PMID:31764100  
PMID:31820498   PMID:31821602   PMID:31894257   PMID:31967348   PMID:31991700   PMID:31992303   PMID:32077163   PMID:32122654   PMID:32232900   PMID:32266868   PMID:32281166   PMID:32309886  
PMID:32321346   PMID:32410140   PMID:32468257   PMID:32473637   PMID:32484698   PMID:32595646   PMID:32614237   PMID:32638950   PMID:32709089   PMID:32802182   PMID:33000203   PMID:33038923  
PMID:33040804   PMID:33130085   PMID:33283704   PMID:33370717   PMID:33524878   PMID:33528317   PMID:33760137  


Genomics

Comparative Map Data
MIR125A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1951,693,254 - 51,693,339 (+)EnsemblGRCh38hg38GRCh38
GRCh381951,693,254 - 51,693,339 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371952,196,507 - 52,196,592 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361956,888,318 - 56,888,403 (+)NCBINCBI36hg18NCBI36
Celera1949,246,042 - 49,246,127 (+)NCBI
Cytogenetic Map19q13.41NCBI
HuRef1948,527,448 - 48,527,533 (+)NCBIHuRef
CHM1_11952,198,304 - 52,198,389 (+)NCBICHM1_1
Mir125a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391718,051,074 - 18,051,141 (+)NCBIGRCm39mm39
GRCm39 Ensembl1718,051,074 - 18,051,141 (+)Ensembl
GRCm381717,830,812 - 17,830,879 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1717,830,812 - 17,830,879 (+)EnsemblGRCm38mm10GRCm38
MGSCv371717,967,776 - 17,967,843 (+)NCBIGRCm37mm9NCBIm37
Celera1718,771,463 - 18,771,530 (+)NCBICelera
Cytogenetic Map17A3.2NCBI
Mir125a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2158,677,626 - 58,677,710 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl159,704,827 - 59,704,911 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0159,704,827 - 59,704,911 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0160,624,485 - 60,624,569 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera154,858,584 - 54,858,668 (+)NCBICelera
Cytogenetic Map1q12NCBI
MIR125A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11105,400,273 - 105,400,332 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1105,400,270 - 105,400,337 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1104,973,786 - 104,973,845 (-)NCBI
ROS_Cfam_1.01105,910,190 - 105,910,249 (-)NCBI
UMICH_Zoey_3.11105,582,422 - 105,582,481 (-)NCBI
UNSW_CanFamBas_1.01105,223,538 - 105,223,597 (-)NCBI
UU_Cfam_GSD_1.01106,018,313 - 106,018,372 (-)NCBI
MIR125A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl658,331,566 - 58,331,645 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1658,331,566 - 58,331,645 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2651,858,852 - 51,858,931 (+)NCBISscrofa10.2Sscrofa10.2susScr3

miRNA Target Status

Confirmed Targets
Gene TargetMature miRNAMethod NameResult TypeData TypeSupport TypePMID
IP6K2hsa-miR-125a-3pMirtarbaseexternal_infoCLASHFunctional MTI (Weak)23622248
TNFAIP3hsa-miR-125a-5pMirtarbaseexternal_infoqRT-PCR//Western blotFunctional MTI22550173
CDKN1Ahsa-miR-125a-5pMirtarbaseexternal_infoqRT-PCR//Luciferase reporter assay//Western blotFunctional MTI20190813
LIN28Ahsa-miR-125a-5pMirtarbaseexternal_infoLuciferase reporter assayFunctional MTI16227573
NTRK3hsa-miR-125a-5pMirtarbaseexternal_infoLuciferase reporter assay//Western blotFunctional MTI17483472
NTRK3hsa-miR-125a-5pMirtarbaseexternal_infoLuciferase reporter assayFunctional MTI19179615
NTRK3hsa-miR-125a-5pMirtarbaseexternal_infoLuciferase reporter assayFunctional MTI18973228
CD34hsa-miR-125a-5pMirtarbaseexternal_infoLuciferase reporter assay//Microarray//Western bloFunctional MTI18308931
TP53hsa-miR-125a-5pMirtarbaseexternal_infoLuciferase reporter assay//Northern blot//qRT-PCR/Functional MTI19818772
LIFhsa-miR-125a-5pMirtarbaseexternal_infoELISANon-Functional MTI (Weak)19011087
MTUS1hsa-miR-125a-5pMirtarbaseexternal_infoMicroarray//Northern blotFunctional MTI (Weak)16331254
VEGFAhsa-miR-125a-5pMirtarbaseexternal_infoELISA//Luciferase reporter assayNon-Functional MTI18320040
ERBB3hsa-miR-125a-5pMirtarbaseexternal_infoLuciferase reporter assay//Northern blot//qRT-PCR/Functional MTI17110380
ERBB3hsa-miR-125a-5pMirtarbaseexternal_infoLuciferase reporter assay//Microarray//Western bloFunctional MTI20864407
ERBB2hsa-miR-125a-5pMirtarbaseexternal_infoLuciferase reporter assayFunctional MTI21220473
KLF13hsa-miR-125a-5pMirtarbaseexternal_infoELISA//Luciferase reporter assay//qRT-PCR//WesternFunctional MTI20589685
ARID3Bhsa-miR-125a-5pMirtarbaseexternal_infoImmunofluorescence//qRT-PCR//Western blotFunctional MTI19881956
BAK1hsa-miR-125a-5pMirtarbaseexternal_infoFlow//Luciferase reporter assay//qRT-PCR//Western Functional MTI20616003
ELAVL1hsa-miR-125a-5pMirtarbaseexternal_infoLuciferase reporter assay//Western blotFunctional MTI19875930
CCL5hsa-miR-125a-5pMirtarbaseexternal_infoELISAFunctional MTI (Weak)20589685
MMP11hsa-miR-125a-5pMirtarbaseexternal_infoImmunohistochemistry//Luciferase reporter assay//qFunctional MTI22768249
HK2hsa-miR-125a-5pMirtarbaseexternal_infoLuciferase reporter assayFunctional MTI22593586
ARPC5hsa-miR-125a-5pMirtarbaseexternal_infoSequencingFunctional MTI (Weak)20371350
YES1hsa-miR-125a-5pMirtarbaseexternal_infoCLASHFunctional MTI (Weak)23622248
ERBB3hsa-miR-125a-5pTarbaseexternal_infoNothernblot POSITIVE
CD34hsa-miR-125a-5pTarbaseexternal_infoReporter GenePOSITIVE
CD34hsa-miR-125a-5pTarbaseexternal_infoWesternblitPOSITIVE
ZFAND1hsa-miR-125a-5pTarbaseexternal_infoSequencingPOSITIVE
ERBB2hsa-miR-125a-5pMirecordsexternal_info{changed}NA17110380
LIN28Ahsa-miR-125a-5pMirecordsexternal_infoNANA16227573
ARID3Bhsa-miR-125a-5pMirecordsexternal_infoNANA19881956
ELAVL1hsa-miR-125a-5pMirecordsexternal_info{unchanged}NA19875930
SIRT7hsa-miR-125a-5pOncomiRDBexternal_infoNANA23079745
MMP11hsa-miR-125a-5pOncomiRDBexternal_infoNANA22768249
TNFAIP3hsa-miR-125a-5pOncomiRDBexternal_infoNANA22550173
ERBB2hsa-miR-125a-5pOncomiRDBexternal_infoNANA21220473
PDPNhsa-miR-125a-5pOncomiRDBexternal_infoNANA20665731
NTRK3hsa-miR-125a-5pOncomiRDBexternal_infoNANA18973228
NTRK3hsa-miR-125a-5pOncomiRDBexternal_infoNANA17483472
ERBB2hsa-miR-125a-5pOncomiRDBexternal_infoNANA17110380
LIN28AP1hsa-miR-125a-5pTarbaseexternal_infoOtherPOSITIVE

Predicted Targets
Summary Value
Count of predictions:43169
Count of gene targets:14215
Count of transcripts:30662
Interacting mature miRNAs:hsa-miR-125a-3p, hsa-miR-125a-5p
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 entire extraembryonic component
High
Medium 1
Low 4 1 6 1 9 3 8 14 16 11 12 18 1
Below cutoff 4 1 4 2 9 3 12 18 15 6 9 13

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000385273
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1951,693,254 - 51,693,339 (+)Ensembl
RefSeq Acc Id: NR_029693
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381951,693,254 - 51,693,339 (+)NCBI
GRCh371952,196,507 - 52,196,592 (+)RGD
Celera1949,246,042 - 49,246,127 (+)RGD
HuRef1948,527,448 - 48,527,533 (+)ENTREZGENE
CHM1_11952,198,304 - 52,198,389 (+)NCBI
Sequence:

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 19q13.33-13.43(chr19:50191219-58535818)x3 copy number gain See cases [RCV000050883] Chr19:50191219..58535818 [GRCh38]
Chr19:50694476..59047185 [GRCh37]
Chr19:55386288..63738997 [NCBI36]
Chr19:19q13.33-13.43
pathogenic
GRCh38/hg38 19q13.33-13.43(chr19:47929575-58572206)x3 copy number gain See cases [RCV000052915] Chr19:47929575..58572206 [GRCh38]
Chr19:48432832..59083573 [GRCh37]
Chr19:53124644..63775385 [NCBI36]
Chr19:19q13.33-13.43
pathogenic
GRCh38/hg38 19q13.33-13.43(chr19:49907832-58557889)x3 copy number gain See cases [RCV000052925] Chr19:49907832..58557889 [GRCh38]
Chr19:50411089..59069256 [GRCh37]
Chr19:55102901..63761068 [NCBI36]
Chr19:19q13.33-13.43
pathogenic
GRCh38/hg38 19q13.41-13.43(chr19:51141518-58539965)x3 copy number gain See cases [RCV000052926] Chr19:51141518..58539965 [GRCh38]
Chr19:51644775..59051332 [GRCh37]
Chr19:56336587..63743144 [NCBI36]
Chr19:19q13.41-13.43
pathogenic
GRCh38/hg38 19q13.33-13.43(chr19:47908540-58539965)x3 copy number gain See cases [RCV000052914] Chr19:47908540..58539965 [GRCh38]
Chr19:48411797..59051332 [GRCh37]
Chr19:53103609..63743144 [NCBI36]
Chr19:19q13.33-13.43
pathogenic
GRCh38/hg38 19q13.33-13.43(chr19:50152520-58581203)x3 copy number gain See cases [RCV000135843] Chr19:50152520..58581203 [GRCh38]
Chr19:50655777..59092570 [GRCh37]
Chr19:55347589..63784382 [NCBI36]
Chr19:19q13.33-13.43
pathogenic
GRCh38/hg38 19q13.41(chr19:51681235-51936423)x3 copy number gain See cases [RCV000138486] Chr19:51681235..51936423 [GRCh38]
Chr19:52184488..52439676 [GRCh37]
Chr19:56876300..57131488 [NCBI36]
Chr19:19q13.41
likely benign
GRCh38/hg38 19q13.41(chr19:51202361-51993020)x3 copy number gain See cases [RCV000143450] Chr19:51202361..51993020 [GRCh38]
Chr19:51705617..52496273 [GRCh37]
Chr19:56397429..57188085 [NCBI36]
Chr19:19q13.41
uncertain significance
GRCh37/hg19 19q13.33-13.43(chr19:50489390-59095359)x3 copy number gain See cases [RCV000445925] Chr19:50489390..59095359 [GRCh37]
Chr19:19q13.33-13.43
pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:260912-58956888) copy number gain See cases [RCV000512296] Chr19:260912..58956888 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:260912-58956888)x3 copy number gain See cases [RCV000511289] Chr19:260912..58956888 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic|uncertain significance
GRCh37/hg19 19q13.41(chr19:52152017-52299885)x3 copy number gain not provided [RCV000752746] Chr19:52152017..52299885 [GRCh37]
Chr19:19q13.41
benign
GRCh37/hg19 19p13.3-q13.43(chr19:68029-59110290)x3 copy number gain not provided [RCV000752439] Chr19:68029..59110290 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:260912-59097160)x3 copy number gain not provided [RCV000752444] Chr19:260912..59097160 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic
GRCh37/hg19 19q13.33-13.43(chr19:50740074-59097160)x3 copy number gain not provided [RCV000740208] Chr19:50740074..59097160 [GRCh37]
Chr19:19q13.33-13.43
pathogenic
GRCh37/hg19 19q13.31-13.42(chr19:44738088-53621561)x3 copy number gain not provided [RCV001007050] Chr19:44738088..53621561 [GRCh37]
Chr19:19q13.31-13.42
pathogenic
GRCh37/hg19 19q13.32-13.42(chr19:47939842-54626871) copy number gain not provided [RCV001249294] Chr19:47939842..54626871 [GRCh37]
Chr19:19q13.32-13.42
not provided
GRCh37/hg19 19q13.33-13.43(chr19:48463931-57095254)x3 copy number gain not provided [RCV001259944] Chr19:48463931..57095254 [GRCh37]
Chr19:19q13.33-13.43
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:31505 AgrOrtholog
COSMIC MIR125A COSMIC
Ensembl Genes ENSG00000208008 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000385273 ENTREZGENE
GTEx ENSG00000208008 GTEx
HGNC ID HGNC:31505 ENTREZGENE
Human Proteome Map MIR125A Human Proteome Map
miRBase MI0000469 ENTREZGENE
NCBI Gene 406910 ENTREZGENE
OMIM 611191 OMIM
PharmGKB PA164722401 PharmGKB
RNAcentral URS00001F0C23 RNACentral
  URS00005A4DCF RNACentral
  URS000075D168 RNACentral