MIR196A2 (microRNA 196a-2) - Rat Genome Database

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Gene: MIR196A2 (microRNA 196a-2) Homo sapiens
Analyze
Symbol: MIR196A2
Name: microRNA 196a-2
RGD ID: 1353191
HGNC Page HGNC:31568
Description: Enables mRNA base-pairing post-transcriptional repressor activity. Involved in several processes, including miRNA-mediated gene silencing; negative regulation of cell migration involved in sprouting angiogenesis; and negative regulation of lamellipodium assembly. Predicted to be part of RISC complex. Implicated in hepatocellular carcinoma.
Type: ncrna
RefSeq Status: PROVISIONAL
Previously known as: mir-196a-2; MIRN196-2; MIRN196A2
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
GRCh381253,991,738 - 53,991,847 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1253,991,738 - 53,991,847 (+)EnsemblGRCh38hg38GRCh38
GRCh371254,385,522 - 54,385,631 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361252,671,788 - 52,671,897 (+)NCBINCBI36hg18NCBI36
Celera1254,035,139 - 54,035,248 (+)NCBI
Cytogenetic Map12q13.13NCBI
HuRef1251,423,233 - 51,423,342 (+)NCBIHuRef
CHM1_11254,352,227 - 54,352,336 (+)NCBICHM1_1
T2T-CHM13v2.01253,957,244 - 53,957,353 (+)NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. A functional polymorphism in pre-microRNA-196a-2 contributes to the susceptibility of hepatocellular carcinoma in a Turkish population: a case-control study. Akkız H, etal., J Viral Hepat. 2011 Jul;18(7):e399-407. doi: 10.1111/j.1365-2893.2010.01414.x. Epub 2010 Dec 23.
2. MicroRNA-196A-2 polymorphisms and hepatocellular carcinoma in patients with chronic hepatitis B. Kim HY, etal., J Med Virol. 2014 Mar;86(3):446-53. doi: 10.1002/jmv.23848. Epub 2013 Nov 19.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12554859   PMID:12624257   PMID:15105502   PMID:16381832   PMID:17604727   PMID:17616659   PMID:19138993   PMID:19293314   PMID:19514064   PMID:19567675   PMID:19834808   PMID:19847796  
PMID:19851984   PMID:19881472   PMID:20188135   PMID:20229273   PMID:20466450   PMID:20480203   PMID:20488170   PMID:20501619   PMID:20549817   PMID:20585341   PMID:20640596   PMID:20732906  
PMID:20842445   PMID:20848167   PMID:21037258   PMID:21073609   PMID:21080878   PMID:21241442   PMID:21345130   PMID:21483822   PMID:21565628   PMID:21604580   PMID:21617338   PMID:21624236  
PMID:21625865   PMID:21637771   PMID:21815818   PMID:21902575   PMID:21907588   PMID:21962133   PMID:22001830   PMID:22159951   PMID:22161766   PMID:22222140   PMID:22291993   PMID:22358059  
PMID:22426473   PMID:22545021   PMID:22659075   PMID:22692992   PMID:22719192   PMID:22768213   PMID:22773844   PMID:22832484   PMID:22872486   PMID:22876840   PMID:22882355   PMID:22952151  
PMID:23138850   PMID:23143626   PMID:23160898   PMID:23202363   PMID:23228090   PMID:23250869   PMID:23423813   PMID:23433405   PMID:23516510   PMID:23593385   PMID:23719600   PMID:23792053  
PMID:23928854   PMID:24039706   PMID:24107909   PMID:24178064   PMID:24291415   PMID:24320161   PMID:24328526   PMID:24377545   PMID:24399071   PMID:24463357   PMID:24595083   PMID:24622064  
PMID:24633889   PMID:24681820   PMID:24716941   PMID:24727796   PMID:24816919   PMID:24860819   PMID:24952884   PMID:24972764   PMID:24978643   PMID:25077922   PMID:25107948   PMID:25176041  
PMID:25474430   PMID:25483824   PMID:25501512   PMID:25546664   PMID:25555557   PMID:25557604   PMID:25658319   PMID:25860510   PMID:25896941   PMID:26008204   PMID:26045752   PMID:26052033  
PMID:26054667   PMID:26062455   PMID:26097603   PMID:26112096   PMID:26125831   PMID:26208586   PMID:26235181   PMID:26261539   PMID:26345764   PMID:26345790   PMID:26365437   PMID:26406571  
PMID:26458899   PMID:26464719   PMID:26518769   PMID:26529280   PMID:26554236   PMID:26608782   PMID:26625766   PMID:26710106   PMID:26805933   PMID:26823863   PMID:26866381   PMID:26886638  
PMID:27043015   PMID:27156151   PMID:27173281   PMID:27323019   PMID:27379568   PMID:27462775   PMID:27487239   PMID:27525669   PMID:27591936   PMID:27636879   PMID:27706635   PMID:27706712  
PMID:27718165   PMID:27741504   PMID:27796868   PMID:27813602   PMID:27816459   PMID:27880723   PMID:27993883   PMID:28164681   PMID:28440445   PMID:28527151   PMID:28649807   PMID:28741852  
PMID:28791406   PMID:28841705   PMID:29091952   PMID:29186852   PMID:29521182   PMID:29594807   PMID:29771422   PMID:29802998   PMID:29965793   PMID:29986379   PMID:30072171   PMID:30278502  
PMID:30387842   PMID:30485833   PMID:30521014   PMID:30560371   PMID:30621631   PMID:30633243   PMID:30637557   PMID:30863967   PMID:30872409   PMID:30988277   PMID:31053729   PMID:31099134  
PMID:31099778   PMID:31123171   PMID:31131489   PMID:31151930   PMID:31352088   PMID:31472066   PMID:31692368   PMID:31713780   PMID:31913716   PMID:32279913   PMID:32320336   PMID:32626994  
PMID:32651705   PMID:32675397   PMID:32686997   PMID:32711415   PMID:32727776   PMID:32928012   PMID:33034957   PMID:33130965   PMID:33228759   PMID:33287939   PMID:33416178   PMID:33463131  
PMID:33469841   PMID:33554246   PMID:33636314   PMID:33660021   PMID:33678493   PMID:33925232   PMID:34158819   PMID:34191854   PMID:34196150   PMID:34435522   PMID:34951996   PMID:35317427  
PMID:35627132   PMID:35633562   PMID:35655924   PMID:35770306  


Genomics

Comparative Map Data
MIR196A2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381253,991,738 - 53,991,847 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1253,991,738 - 53,991,847 (+)EnsemblGRCh38hg38GRCh38
GRCh371254,385,522 - 54,385,631 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361252,671,788 - 52,671,897 (+)NCBINCBI36hg18NCBI36
Celera1254,035,139 - 54,035,248 (+)NCBI
Cytogenetic Map12q13.13NCBI
HuRef1251,423,233 - 51,423,342 (+)NCBIHuRef
CHM1_11254,352,227 - 54,352,336 (+)NCBICHM1_1
T2T-CHM13v2.01253,957,244 - 53,957,353 (+)NCBI
Mir196a-2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915102,881,785 - 102,881,869 (+)NCBIGRCm39mm39
GRCm39 Ensembl15102,881,785 - 102,881,869 (+)Ensembl
GRCm3815102,973,350 - 102,973,434 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15102,973,350 - 102,973,434 (+)EnsemblGRCm38mm10GRCm38
MGSCv3715102,803,781 - 102,803,865 (+)NCBIGRCm37mm9NCBIm37
Celera15105,134,275 - 105,134,359 (+)NCBICelera
Cytogenetic Map15F3NCBI
Mir196a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27134,110,400 - 134,110,509 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7134,110,400 - 134,110,509 (+)Ensembl
Rnor_6.07144,584,235 - 144,584,344 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7144,584,235 - 144,584,344 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07142,375,592 - 142,375,701 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47141,736,759 - 141,736,868 (+)NCBIRGSC3.4rn4RGSC3.4
Celera7130,536,584 - 130,536,693 (+)NCBICelera
Cytogenetic Map7q36NCBI
MIR196A-2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1271,270,718 - 1,270,776 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl271,270,691 - 1,270,800 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2744,978,848 - 44,978,906 (+)NCBI
ROS_Cfam_1.0271,274,383 - 1,274,441 (-)NCBI
UMICH_Zoey_3.1271,292,080 - 1,292,138 (-)NCBI
UNSW_CanFamBas_1.0271,273,603 - 1,273,661 (-)NCBI
UU_Cfam_GSD_1.02745,382,450 - 45,382,508 (+)NCBI
MIR196A-2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl519,204,442 - 19,204,548 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1519,204,442 - 19,204,548 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2519,654,956 - 19,655,062 (-)NCBISscrofa10.2Sscrofa10.2susScr3

Position Markers
STS-N31842  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371254,383,890 - 54,384,016UniSTSGRCh37
Build 361252,670,157 - 52,670,283RGDNCBI36
Celera1254,033,509 - 54,033,633RGD
Cytogenetic Map12q13.3UniSTS
Cytogenetic Map12q13.13UniSTS
HuRef1251,421,602 - 51,421,726UniSTS
GeneMap99-GB4 RH Map12234.38UniSTS
NCBI RH Map12423.0UniSTS

miRNA Target Status

Confirmed Targets
Gene TargetMature miRNAMethod NameResult TypeData TypeSupport TypePMID
RPS26hsa-miR-196a-3pMirtarbaseexternal_infoCLASHFunctional MTI (Weak)23622248
SPRR2Chsa-miR-196a-5pMirtarbaseexternal_infoLuciferase reporter assay//qRT-PCRFunctional MTI19342367
ANXA1hsa-miR-196a-5pMirtarbaseexternal_infoqRT-PCR//Luciferase reporter assay//Western blot//Functional MTI18663355
HOXB8hsa-miR-196a-5pMirtarbaseexternal_infoWestern blotFunctional MTI19418581
HOXB8hsa-miR-196a-5pMirtarbaseexternal_infoLuciferase reporter assayFunctional MTI18493311
HOXB8hsa-miR-196a-5pMirtarbaseexternal_infoLuciferase reporter assayFunctional MTI15105502
HOXB8hsa-miR-196a-5pMirtarbaseexternal_infoLuciferase reporter assay//Northern blot//Western Functional MTI17150553
HOXB8hsa-miR-196a-5pMirtarbaseexternal_infoCLASHFunctional MTI (Weak)23622248
HOXA7hsa-miR-196a-5pMirtarbaseexternal_infoSequencingFunctional MTI (Weak)20371350
HOXC8hsa-miR-196a-5pMirtarbaseexternal_infoLuciferase reporter assay//qRT-PCR//Western blot//Functional MTI19063684
HOXC8hsa-miR-196a-5pMirtarbaseexternal_infoLuciferase reporter assay//qRT-PCR//Reporter assayFunctional MTI21077158
HOXC8hsa-miR-196a-5pMirtarbaseexternal_infoImmunohistochemistry//Luciferase reporter assay//qFunctional MTI20736365
HOXC8hsa-miR-196a-5pMirtarbaseexternal_infoqRT-PCR//Western blotFunctional MTI22545021
HOXB7hsa-miR-196a-5pMirtarbaseexternal_infoImmunofluorescence//Luciferase reporter assay//qRTFunctional MTI20480203
BACH1hsa-miR-196a-5pMirtarbaseexternal_infoLuciferase reporter assay//qRT-PCR//Western blotFunctional MTI20127796
CDKN1Bhsa-miR-196a-5pMirtarbaseexternal_infoLuciferase reporter assayNon-Functional MTI17627278
HOXA5hsa-miR-196a-5pMirtarbaseexternal_infoLuciferase reporter assay//qRT-PCR//Western blotFunctional MTI22876840
LLGL1hsa-miR-196a-5pMirtarbaseexternal_infoqRT-PCRFunctional MTI (Weak)21077158
HOXC8hsa-miR-196a-5pTarbaseexternal_infoReporter GenePOSITIVE
NR4A1hsa-miR-196a-5pTarbaseexternal_infoSequencingPOSITIVE
LLGL1hsa-miR-196a-5pTarbaseexternal_infoqPCRPOSITIVE
HOXA5hsa-miR-196a-5pOncomiRDBexternal_infoNANA22876840
CDKN1Bhsa-miR-196a-5pOncomiRDBexternal_infoNANA22343731
HOXC8hsa-miR-196a-5pOncomiRDBexternal_infoNANA21077158
HOXC8hsa-miR-196a-5pOncomiRDBexternal_infoNANA20736365
ERGhsa-miR-196a-5pOncomiRDBexternal_infoNANA20570349
HOXB7hsa-miR-196a-5pOncomiRDBexternal_infoNANA20480203
KRT5hsa-miR-196a-5pOncomiRDBexternal_infoNANA19342367
ANXA1hsa-miR-196a-5pOncomiRDBexternal_infoNANA18663355

Predicted Targets
Summary Value
Count of predictions:27980
Count of gene targets:10856
Count of transcripts:20836
Interacting mature miRNAs:hsa-miR-196a-3p, hsa-miR-196a-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 sensory system adipose tissue appendage
High
Medium 2 1 2 1
Low 44 19 19 11 15 11 75 44 45 53 57 89 6 9 28
Below cutoff 62 85 28 6 35 4 149 51 89 24 59 50 3 36 96

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000385189
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1253,991,738 - 53,991,847 (+)Ensembl
RefSeq Acc Id: NR_029617
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381253,991,738 - 53,991,847 (+)NCBI
GRCh371254,385,522 - 54,385,631 (+)ENTREZGENE
HuRef1251,423,233 - 51,423,342 (+)ENTREZGENE
CHM1_11254,352,227 - 54,352,336 (+)NCBI
T2T-CHM13v2.01253,957,244 - 53,957,353 (+)NCBI
Sequence:

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 12q13.13(chr12:53224024-54222450)x1 copy number loss See cases [RCV000052812] Chr12:53224024..54222450 [GRCh38]
Chr12:53617808..54616234 [GRCh37]
Chr12:51904075..52902501 [NCBI36]
Chr12:12q13.13
pathogenic
GRCh38/hg38 12p13.33-q24.33(chr12:121271-133196807)x3 copy number gain See cases [RCV000139555] Chr12:121271..133196807 [GRCh38]
Chr12:282465..133773393 [GRCh37]
Chr12:100698..132283466 [NCBI36]
Chr12:12p13.33-q24.33
pathogenic
GRCh38/hg38 12q13.13(chr12:53841686-54136856)x3 copy number gain See cases [RCV000141162] Chr12:53841686..54136856 [GRCh38]
Chr12:54235470..54530640 [GRCh37]
Chr12:52521737..52816907 [NCBI36]
Chr12:12q13.13
likely benign
GRCh38/hg38 12q13.13-13.3(chr12:53420606-56202942)x3 copy number gain See cases [RCV000141435] Chr12:53420606..56202942 [GRCh38]
Chr12:53814390..56596726 [GRCh37]
Chr12:52100657..54882993 [NCBI36]
Chr12:12q13.13-13.3
pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:1-133851895)x3 copy number gain See cases [RCV000258805] Chr12:1..133851895 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic|likely pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902)x3 copy number gain See cases [RCV000510482] Chr12:173787..133777902 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902) copy number gain See cases [RCV000511643] Chr12:173787..133777902 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:621220-133779118)x3 copy number gain not provided [RCV000750253] Chr12:621220..133779118 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:191619-133777645)x3 copy number gain not provided [RCV000750246] Chr12:191619..133777645 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
Single allele deletion Neurodevelopmental disorder [RCV000787381] Chr12:53784698..54741363 [GRCh37]
Chr12:12q13.13
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:31568 AgrOrtholog
COSMIC MIR196A2 COSMIC
Ensembl Genes ENSG00000207924 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000385189 ENTREZGENE
GTEx ENSG00000207924 GTEx
HGNC ID HGNC:31568 ENTREZGENE
Human Proteome Map MIR196A2 Human Proteome Map
miRBase MI0000279 ENTREZGENE
NCBI Gene 406973 ENTREZGENE
OMIM 609687 OMIM
PharmGKB PA164722557 PharmGKB
RNAcentral URS00000D6378 RNACentral
  URS00000DA6A7 RNACentral
  URS00000E4877 RNACentral