MIR196A1 (microRNA 196a-1) - Rat Genome Database

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Gene: MIR196A1 (microRNA 196a-1) Homo sapiens
Analyze
Symbol: MIR196A1
Name: microRNA 196a-1
RGD ID: 1353314
HGNC Page HGNC:31567
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.
Type: ncrna
RefSeq Status: PROVISIONAL
Previously known as: mir-196a-1; MIRN196-1; MIRN196A1
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
GRCh381748,632,490 - 48,632,559 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1748,632,490 - 48,632,559 (-)EnsemblGRCh38hg38GRCh38
GRCh371746,709,852 - 46,709,921 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361744,064,850 - 44,064,919 (-)NCBINCBI36hg18NCBI36
Celera1743,164,015 - 43,164,084 (-)NCBI
Cytogenetic Map17q21.32NCBI
HuRef1742,078,730 - 42,078,799 (-)NCBIHuRef
CHM1_11746,775,846 - 46,775,915 (-)NCBICHM1_1
T2T-CHM13v2.01749,496,086 - 49,496,155 (-)NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Cellular Component
RISC complex  (IEA)

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:12554859   PMID:12624257   PMID:15105502   PMID:16381832   PMID:17604727   PMID:17616659   PMID:18663355   PMID:19063684   PMID:19418581   PMID:20127796   PMID:20229273   PMID:20480203  
PMID:20601442   PMID:20614181   PMID:20722507   PMID:20889907   PMID:21037258   PMID:21077158   PMID:22001830   PMID:22139073   PMID:22358059   PMID:22420029   PMID:22545021   PMID:22773844  
PMID:22859270   PMID:23470291   PMID:24007214   PMID:24048456   PMID:24120501   PMID:24377574   PMID:24379078   PMID:24463357   PMID:24568449   PMID:24622064   PMID:24727796   PMID:24817935  
PMID:24922658   PMID:25233933   PMID:25374225   PMID:25485932   PMID:25523631   PMID:25738504   PMID:25860510   PMID:26045752   PMID:26052033   PMID:26054667   PMID:26078942   PMID:26097603  
PMID:26261539   PMID:26683934   PMID:26782446   PMID:26843114   PMID:26936095   PMID:26940097   PMID:27105503   PMID:27267055   PMID:27462775   PMID:27591936   PMID:27619769   PMID:27621035  
PMID:27816459   PMID:27880728   PMID:27880730   PMID:28164681   PMID:28317323   PMID:28440476   PMID:28466015   PMID:28666797   PMID:28671039   PMID:28744327   PMID:29066350   PMID:29170131  
PMID:29286141   PMID:29636065   PMID:29793177   PMID:30249885   PMID:30267809   PMID:30383193   PMID:30485833   PMID:30521014   PMID:30850392   PMID:30904593   PMID:30988277   PMID:31352088  
PMID:31378890   PMID:31713780   PMID:32626994   PMID:32651705   PMID:32675397   PMID:32711415   PMID:32928012   PMID:33034957   PMID:33287939   PMID:33416178   PMID:33469841   PMID:33678493  
PMID:33892661   PMID:34166682   PMID:34191854   PMID:34196150   PMID:34339392   PMID:34435522   PMID:34463887   PMID:34951996   PMID:35163707   PMID:35317427   PMID:35655924  


Genomics

Comparative Map Data
MIR196A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381748,632,490 - 48,632,559 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1748,632,490 - 48,632,559 (-)EnsemblGRCh38hg38GRCh38
GRCh371746,709,852 - 46,709,921 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361744,064,850 - 44,064,919 (-)NCBINCBI36hg18NCBI36
Celera1743,164,015 - 43,164,084 (-)NCBI
Cytogenetic Map17q21.32NCBI
HuRef1742,078,730 - 42,078,799 (-)NCBIHuRef
CHM1_11746,775,846 - 46,775,915 (-)NCBICHM1_1
T2T-CHM13v2.01749,496,086 - 49,496,155 (-)NCBI
Mir196a-1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391196,155,990 - 96,156,091 (+)NCBIGRCm39mm39
GRCm39 Ensembl1196,155,990 - 96,156,091 (+)Ensembl
GRCm381196,265,164 - 96,265,265 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1196,265,164 - 96,265,265 (+)EnsemblGRCm38mm10GRCm38
MGSCv371196,126,478 - 96,126,579 (+)NCBIGRCm37mm9NCBIm37
Celera11105,916,213 - 105,916,314 (+)NCBICelera
Cytogenetic Map11DNCBI
Mir196c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21081,231,006 - 81,231,085 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1081,231,006 - 81,231,085 (+)Ensembl
Rnor_6.01084,113,578 - 84,113,657 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1084,113,578 - 84,113,657 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01083,916,623 - 83,916,702 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1079,997,352 - 79,997,431 (+)NCBICelera
Cytogenetic Map10q26NCBI
MIR196A-1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1924,895,666 - 24,895,756 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl924,895,666 - 24,895,756 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha924,359,563 - 24,359,653 (-)NCBI
ROS_Cfam_1.0925,690,134 - 25,690,224 (-)NCBI
ROS_Cfam_1.0 Ensembl925,690,134 - 25,690,224 (-)Ensembl
UMICH_Zoey_3.1924,458,223 - 24,458,313 (-)NCBI
UNSW_CanFamBas_1.0924,718,803 - 24,718,893 (-)NCBI
UU_Cfam_GSD_1.0924,847,103 - 24,847,193 (-)NCBI
MIR196A-1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1224,886,307 - 24,886,408 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11224,886,316 - 24,886,395 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21224,836,774 - 24,836,853 (+)NCBISscrofa10.2Sscrofa10.2susScr3

miRNA Target Status

Confirmed Targets
Gene TargetMature miRNAMethod NameResult TypeData TypeSupport TypePMID
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
NR4A1hsa-miR-196a-5pTarbaseexternal_infoSequencingPOSITIVE
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
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
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

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 124 9 7 19 8 7 11 13 43 39 43 2
Low 69 6 18 11 59 12 34 19 22 153 103 84 4 6 9
Below cutoff 17 4 3 6 7 10 9 5 5 8 1 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000388006
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1748,632,490 - 48,632,559 (-)Ensembl
RefSeq Acc Id: NR_029582
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381748,632,490 - 48,632,559 (-)NCBI
GRCh371746,709,852 - 46,709,921 (-)ENTREZGENE
HuRef1742,078,730 - 42,078,799 (-)ENTREZGENE
CHM1_11746,775,846 - 46,775,915 (-)NCBI
T2T-CHM13v2.01749,496,086 - 49,496,155 (-)NCBI
Sequence:

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 17q21.33-24.2(chr17:36449220-68170214)x3 copy number gain See cases [RCV000050957] Chr17:36449220..68170214 [GRCh38]
Chr17:48563237..65936105 [GRCh37]
Chr17:45918236..63677950 [NCBI36]
Chr17:17q21.33-24.2		 pathogenic
GRCh38/hg38 17q23.2-25.3(chr17:36449220-83086677)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|See cases [RCV000052483] Chr17:36449220..83086677 [GRCh38]
Chr17:58617905..81044553 [GRCh37]
Chr17:55972687..78637842 [NCBI36]
Chr17:17q23.2-25.3		 pathogenic
GRCh38/hg38 17q21.31-21.33(chr17:44955325-49381173)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052480]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052480]|See cases [RCV000052480] Chr17:44955325..49381173 [GRCh38]
Chr17:43032693..47458535 [GRCh37]
Chr17:40388219..44813534 [NCBI36]
Chr17:17q21.31-21.33		 pathogenic
GRCh38/hg38 17q21.32-21.33(chr17:48520885-49511208)x1 copy number loss See cases [RCV000053431] Chr17:48520885..49511208 [GRCh38]
Chr17:46598247..47588570 [GRCh37]
Chr17:43953246..44943569 [NCBI36]
Chr17:17q21.32-21.33		 pathogenic
GRCh38/hg38 17q23.1-25.1(chr17:36449220-75053130)x3 copy number gain See cases [RCV000137437] Chr17:36449220..75053130 [GRCh38]
Chr17:57595736..73049225 [GRCh37]
Chr17:54950518..70560820 [NCBI36]
Chr17:17q23.1-25.1		 pathogenic
GRCh38/hg38 17q21.32-21.33(chr17:47986886-49329397)x1 copy number loss See cases [RCV000142900] Chr17:47986886..49329397 [GRCh38]
Chr17:46064252..47406759 [GRCh37]
Chr17:43419251..44761758 [NCBI36]
Chr17:17q21.32-21.33		 pathogenic
GRCh38/hg38 17q21.32-21.33(chr17:48450628-49552921)x3 copy number gain See cases [RCV000143451] Chr17:48450628..49552921 [GRCh38]
Chr17:46527990..47630283 [GRCh37]
Chr17:43882989..44985282 [NCBI36]
Chr17:17q21.32-21.33		 uncertain significance
GRCh37/hg19 17q21.31-25.3(chr17:42580684-81085615)x3 copy number gain See cases [RCV000447823] Chr17:42580684..81085615 [GRCh37]
Chr17:17q21.31-25.3		 pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:526-81041938) copy number gain See cases [RCV000511439] Chr17:526..81041938 [GRCh37]
Chr17:17p13.3-q25.3		 pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:526-81041938)x3 copy number gain See cases [RCV000512441] Chr17:526..81041938 [GRCh37]
Chr17:17p13.3-q25.3		 pathogenic
GRCh37/hg19 17q21.32-22(chr17:46481089-51396368)x1 copy number loss not provided [RCV000513510] Chr17:46481089..51396368 [GRCh37]
Chr17:17q21.32-22		 likely pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:12344-81057996)x3 copy number gain not provided [RCV000739325] Chr17:12344..81057996 [GRCh37]
Chr17:17p13.3-q25.3		 pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:8547-81060040)x3 copy number gain not provided [RCV000739324] Chr17:8547..81060040 [GRCh37]
Chr17:17p13.3-q25.3		 pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:7214-81058310)x3 copy number gain not provided [RCV000739320] Chr17:7214..81058310 [GRCh37]
Chr17:17p13.3-q25.3		 pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:31567 AgrOrtholog
COSMIC MIR196A1 COSMIC
Ensembl Genes ENSG00000210741 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000388006 ENTREZGENE
GTEx ENSG00000210741 GTEx
HGNC ID HGNC:31567 ENTREZGENE
Human Proteome Map MIR196A1 Human Proteome Map
miRBase MI0000238 ENTREZGENE
NCBI Gene 406972 ENTREZGENE
OMIM 608632 OMIM
PharmGKB PA164722556 PharmGKB
RNAcentral URS00000DA6A7 RNACentral
  URS000014C145 RNACentral
  URS0000D5297E RNACentral