MIR346 (microRNA 346) - Rat Genome Database

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Gene: MIR346 (microRNA 346) Homo sapiens
Analyze
Symbol: MIR346
Name: microRNA 346
RGD ID: 1352152
HGNC Page HGNC
Description: Predicted to act upstream of or within cellular response to amino acid stimulus.
Type: ncrna
RefSeq Status: PROVISIONAL
Also known as: hsa-mir-346; miR-346; MIRN346; miRNA346
RGD Orthologs
Mouse
Rat
Dog
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 Ensembl1086,264,694 - 86,264,788 (-)EnsemblGRCh38hg38GRCh38
GRCh381086,264,694 - 86,264,788 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371088,024,451 - 88,024,545 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361088,014,430 - 88,014,524 (-)NCBINCBI36hg18NCBI36
Celera1082,019,715 - 82,019,809 (-)NCBI
Cytogenetic Map10q23.2NCBI
HuRef1081,873,792 - 81,873,886 (-)NCBIHuRef
CHM1_11088,306,192 - 88,306,286 (-)NCBICHM1_1
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

Biological Process

References

References - curated
1. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12554859   PMID:14691248   PMID:15634332   PMID:16381832   PMID:19342689   PMID:20889907   PMID:21037258   PMID:21611196   PMID:22002058   PMID:22838046   PMID:24023731   PMID:25192497  
PMID:25666935   PMID:26408183   PMID:26507454   PMID:26518874   PMID:27501413   PMID:27619846   PMID:27777383   PMID:27913185   PMID:28192819   PMID:28753968   PMID:28827075   PMID:28888578  
PMID:29107113   PMID:29295726   PMID:30053867   PMID:30216442   PMID:30470799   PMID:31298469   PMID:31494280   PMID:31953162   PMID:31972611   PMID:32131485   PMID:33299881   PMID:33537815  


Genomics

Comparative Map Data
MIR346
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1086,264,694 - 86,264,788 (-)EnsemblGRCh38hg38GRCh38
GRCh381086,264,694 - 86,264,788 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371088,024,451 - 88,024,545 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361088,014,430 - 88,014,524 (-)NCBINCBI36hg18NCBI36
Celera1082,019,715 - 82,019,809 (-)NCBI
Cytogenetic Map10q23.2NCBI
HuRef1081,873,792 - 81,873,886 (-)NCBIHuRef
CHM1_11088,306,192 - 88,306,286 (-)NCBICHM1_1
Mir346
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391434,616,566 - 34,616,663 (+)NCBIGRCm39mm39
GRCm39 Ensembl1434,616,566 - 34,616,663 (+)Ensembl
GRCm381434,894,609 - 34,894,706 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1434,894,609 - 34,894,706 (+)EnsemblGRCm38mm10GRCm38
MGSCv371435,707,795 - 35,707,892 (+)NCBIGRCm37mm9NCBIm37
Celera1431,153,100 - 31,153,197 (+)NCBICelera
Cytogenetic Map14BNCBI
Mir346
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21610,218,118 - 10,218,215 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1610,218,118 - 10,218,215 (+)Ensembl
Rnor_6.01611,250,054 - 11,250,151 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1611,250,054 - 11,250,151 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0169,574,933 - 9,575,030 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera165,002,049 - 5,002,146 (-)NCBICelera
Cytogenetic Map16p15NCBI
MIR346
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1434,073,335 - 34,073,429 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl434,073,335 - 34,073,429 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha434,063,133 - 34,063,227 (-)NCBI
ROS_Cfam_1.0434,404,379 - 34,404,473 (-)NCBI
UMICH_Zoey_3.1434,277,307 - 34,277,401 (-)NCBI
UNSW_CanFamBas_1.0434,447,229 - 34,447,323 (-)NCBI
UU_Cfam_GSD_1.0434,951,838 - 34,951,932 (-)NCBI

miRNA Target Status

Confirmed Targets
Gene TargetMature miRNAMethod NameResult TypeData TypeSupport TypePMID
EFEMP2hsa-miR-346Mirtarbaseexternal_infoMicroarray//qRT-PCRFunctional MTI (Weak)16822819
EFEMP2hsa-miR-346Mirtarbaseexternal_infoWestern blot;OtherFunctional MTI21611196
LIFhsa-miR-346Mirtarbaseexternal_infoELISA//Luciferase reporter assayFunctional MTI19011087
BTKhsa-miR-346Mirtarbaseexternal_infoLuciferase reporter assay//qRT-PCR//Northern blot/Functional MTI19342689
BDH2hsa-miR-346Mirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)16822819
IL18hsa-miR-346Mirtarbaseexternal_infoqRT-PCR//Luciferase reporter assay//Western blot//Non-Functional MTI19342689
TAP1hsa-miR-346Mirtarbaseexternal_infoImmunocytochemistry//In situ hybridization//qRT-PCFunctional MTI22002058
ZFP36hsa-miR-346Mirtarbaseexternal_infoWestern blot;qRT-PCR;OtherFunctional MTI21611196
HNRNPA3hsa-miR-346Mirtarbaseexternal_infoCLASHFunctional MTI (Weak)23622248
ZFP36hsa-miR-346Tarbaseexternal_infoqPCRPOSITIVE
ZFP36hsa-miR-346Tarbaseexternal_infoWesternblitPOSITIVE
ZFP36hsa-miR-346Tarbaseexternal_infoOtherPOSITIVE
LIFhsa-miR-346Mirecordsexternal_infoNANA19011087

Predicted Targets
Summary Value
Count of predictions:29061
Count of gene targets:12595
Count of transcripts:25721
Interacting mature miRNAs:hsa-miR-346
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
Low 3 5 9 4 4 4 7 1 11 2 5 8 2 4
Below cutoff 3 14 8 1 6 18 11 25 4 10 1 4 14

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000362234
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1086,264,694 - 86,264,788 (-)Ensembl
RefSeq Acc Id: NR_029907
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381086,264,694 - 86,264,788 (-)NCBI
GRCh371088,024,451 - 88,024,545 (-)RGD
Celera1082,019,715 - 82,019,809 (-)RGD
HuRef1081,873,792 - 81,873,886 (-)RGD
CHM1_11088,306,192 - 88,306,286 (-)NCBI
Sequence:

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 10q22.3-23.2(chr10:79719429-87358394)x1 copy number loss See cases [RCV000052534] Chr10:79719429..87358394 [GRCh38]
Chr10:81479185..89118151 [GRCh37]
Chr10:81149191..89108131 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79802022-87358394)x1 copy number loss See cases [RCV000052537] Chr10:79802022..87358394 [GRCh38]
Chr10:81561459..89118151 [GRCh37]
Chr10:81541288..89108131 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79882162-87068261)x1 copy number loss See cases [RCV000052539] Chr10:79882162..87068261 [GRCh38]
Chr10:81641918..88828018 [GRCh37]
Chr10:81631898..88817998 [NCBI36]
Chr10:10q22.3-23.2
pathogenic|conflicting data from submitters
GRCh38/hg38 10q22.3-23.2(chr10:79898516-86964367)x1 copy number loss See cases [RCV000052541] Chr10:79898516..86964367 [GRCh38]
Chr10:81658272..88724124 [GRCh37]
Chr10:81648252..88714104 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79898516-87358394)x1 copy number loss See cases [RCV000052542] Chr10:79898516..87358394 [GRCh38]
Chr10:81658272..89118151 [GRCh37]
Chr10:81648252..89108131 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79898516-87109827)x1 copy number loss See cases [RCV000052544] Chr10:79898516..87109827 [GRCh38]
Chr10:81658272..88869584 [GRCh37]
Chr10:81648252..88859564 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q23.1-23.31(chr10:84925492-88002064)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052546]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052546]|See cases [RCV000052546] Chr10:84925492..88002064 [GRCh38]
Chr10:86685248..89761821 [GRCh37]
Chr10:86675228..89751801 [NCBI36]
Chr10:10q23.1-23.31
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79881238-87182117)x3 copy number gain See cases [RCV000053558] Chr10:79881238..87182117 [GRCh38]
Chr10:81640994..88941874 [GRCh37]
Chr10:81630974..88931854 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q23.1-23.31(chr10:84434981-89150802)x3 copy number gain See cases [RCV000053559] Chr10:84434981..89150802 [GRCh38]
Chr10:86194737..90910559 [GRCh37]
Chr10:86184717..90900539 [NCBI36]
Chr10:10q23.1-23.31
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79925613-86951708)x1 copy number loss See cases [RCV000135348] Chr10:79925613..86951708 [GRCh38]
Chr10:81685369..88711465 [GRCh37]
Chr10:81675349..88701445 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79802022-87068261)x1 copy number loss See cases [RCV000136565] Chr10:79802022..87068261 [GRCh38]
Chr10:81561459..88828018 [GRCh37]
Chr10:81263385..88817998 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q11.23-23.2(chr10:50729367-87147204)x3 copy number gain See cases [RCV000138007] Chr10:50729367..87147204 [GRCh38]
Chr10:52489127..88906961 [GRCh37]
Chr10:52159133..88896941 [NCBI36]
Chr10:10q11.23-23.2
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79689360-87223773)x1 copy number loss See cases [RCV000141724] Chr10:79689360..87223773 [GRCh38]
Chr10:81449116..88983530 [GRCh37]
Chr10:81119122..88973510 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79881238-87180672)x1 copy number loss See cases [RCV000143178] Chr10:79881238..87180672 [GRCh38]
Chr10:81640994..88940429 [GRCh37]
Chr10:81630974..88930409 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79882162-87068261)x1 copy number loss See cases [RCV000148069] Chr10:79882162..87068261 [GRCh38]
Chr10:81641918..88828018 [GRCh37]
Chr10:81631898..88817998 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10q23.1-23.31(chr10:86766571-92609514)x1 copy number loss See cases [RCV000447104] Chr10:86766571..92609514 [GRCh37]
Chr10:10q23.1-23.31
pathogenic
GRCh37/hg19 10q22.3-23.2(chr10:81630468-88975551)x1 copy number loss See cases [RCV000447214] Chr10:81630468..88975551 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10q22.3-23.2(chr10:81892411-88722952)x1 copy number loss See cases [RCV000447520] Chr10:81892411..88722952 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10q23.1-25.1(chr10:85557432-105804295)x1 copy number loss Poly (ADP-Ribose) polymerase inhibitor response [RCV000431909] Chr10:85557432..105804295 [GRCh37]
Chr10:10q23.1-25.1
pathogenic|drug response
GRCh37/hg19 10q22.3-23.2(chr10:81630468-88973570)x3 copy number gain See cases [RCV000448704] Chr10:81630468..88973570 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10p15.3-q26.3(chr10:93297-135378918)x3 copy number gain See cases [RCV000448750] Chr10:93297..135378918 [GRCh37]
Chr10:10p15.3-q26.3
pathogenic
GRCh37/hg19 10q22.3-23.2(chr10:81597767-88951347)x1 copy number loss See cases [RCV000511644] Chr10:81597767..88951347 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10q23.1-23.2(chr10:82013260-89166455)x1 copy number loss See cases [RCV000511659] Chr10:82013260..89166455 [GRCh37]
Chr10:10q23.1-23.2
pathogenic
GRCh37/hg19 10q22.3-23.2(chr10:81617260-88980961)x1 copy number loss See cases [RCV000511693] Chr10:81617260..88980961 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10p15.3-q26.3(chr10:100027-135427143) copy number gain See cases [RCV000511389] Chr10:100027..135427143 [GRCh37]
Chr10:10p15.3-q26.3
pathogenic|uncertain significance
GRCh37/hg19 10p15.3-q26.3(chr10:100027-135427143)x3 copy number gain See cases [RCV000510861] Chr10:100027..135427143 [GRCh37]
Chr10:10p15.3-q26.3
pathogenic
GRCh37/hg19 10q11.21-26.3(chr10:42347406-135534747)x1 copy number loss Poly (ADP-Ribose) polymerase inhibitor response [RCV000626438] Chr10:42347406..135534747 [GRCh37]
Chr10:10q11.21-26.3
drug response
GRCh37/hg19 10q23.1-23.32(chr10:83379241-93219169)x1 copy number loss not provided [RCV000683284] Chr10:83379241..93219169 [GRCh37]
Chr10:10q23.1-23.32
pathogenic
GRCh37/hg19 10q22.3-23.2(chr10:81644079-88973306)x3 copy number gain not provided [RCV000683282] Chr10:81644079..88973306 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10q21.3-23.32(chr10:69040366-93194993)x3 copy number gain not provided [RCV000683289] Chr10:69040366..93194993 [GRCh37]
Chr10:10q21.3-23.32
pathogenic
GRCh37/hg19 10p15.3-q26.3(chr10:73232-135524321)x3 copy number gain not provided [RCV000749464] Chr10:73232..135524321 [GRCh37]
Chr10:10p15.3-q26.3
pathogenic
GRCh37/hg19 10p15.3-q26.3(chr10:98087-135477883)x3 copy number gain not provided [RCV000749465] Chr10:98087..135477883 [GRCh37]
Chr10:10p15.3-q26.3
pathogenic
GRCh37/hg19 10q22.3-23.2(chr10:81697811-88768847) copy number loss not provided [RCV000767565] Chr10:81697811..88768847 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10q22.3-23.2(chr10:81617260-88980961)x1 copy number loss not provided [RCV001006339] Chr10:81617260..88980961 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10q22.3-23.2(chr10:81617260-89146780)x1 copy number loss not provided [RCV001258450] Chr10:81617260..89146780 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10q23.2(chr10:87975634-88619777)x3 copy number gain not provided [RCV001258456] Chr10:87975634..88619777 [GRCh37]
Chr10:10q23.2
uncertain significance
Single allele deletion not provided [RCV001260503] Chr10:81585301..89101700 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10q22.3-23.2(chr10:81457752-89253430)x1 copy number loss not provided [RCV001258451] Chr10:81457752..89253430 [GRCh37]
Chr10:10q22.3-23.2
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:31780 AgrOrtholog
COSMIC MIR346 COSMIC
Ensembl Genes ENSG00000199104 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000362234 ENTREZGENE
GTEx ENSG00000199104 GTEx
HGNC ID HGNC:31780 ENTREZGENE
Human Proteome Map MIR346 Human Proteome Map
miRBase MI0000826 ENTREZGENE
NCBI Gene 442911 ENTREZGENE
OMIM 611190 OMIM
PharmGKB PA164722674 PharmGKB
RNAcentral URS0000134ADC RNACentral
  URS000075B886 RNACentral