MIR30C1 (microRNA 30c-1) - Rat Genome Database

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Gene: MIR30C1 (microRNA 30c-1) Homo sapiens
Analyze
Symbol: MIR30C1
Name: microRNA 30c-1
RGD ID: 1351898
HGNC Page HGNC:31626
Description: Enables high-density lipoprotein particle binding activity and mRNA base-pairing translational repressor activity. Involved in miRNA-mediated post-transcriptional gene silencing. Located in extracellular exosome.
Type: ncrna (Ensembl: miRNA)
RefSeq Status: PROVISIONAL
Previously known as: mir-30c-1; MIRN30C1
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
GRCh38140,757,284 - 40,757,372 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl140,757,284 - 40,757,372 (+)EnsemblGRCh38hg38GRCh38
GRCh37141,222,956 - 41,223,044 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36140,995,542 - 40,995,630 (+)NCBINCBI36Build 36hg18NCBI36
Celera139,505,156 - 39,505,244 (+)NCBICelera
Cytogenetic Map1p34.2NCBI
HuRef139,341,077 - 39,341,165 (+)NCBIHuRef
CHM1_1141,338,787 - 41,338,875 (+)NCBICHM1_1
T2T-CHM13v2.0140,626,494 - 40,626,582 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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:12007417   PMID:15325244   PMID:15634332   PMID:15978578   PMID:16381832   PMID:17604727   PMID:17616659   PMID:19048628   PMID:19138993   PMID:19851984   PMID:20490652   PMID:20732906  
PMID:20889907   PMID:21037258   PMID:22108846   PMID:22964638   PMID:23144934   PMID:23159078   PMID:23318178   PMID:23340433   PMID:23418453   PMID:23749231   PMID:24007526   PMID:24112779  
PMID:24129493   PMID:24148619   PMID:24199710   PMID:24452717   PMID:24595016   PMID:24623846   PMID:24802714   PMID:25119247   PMID:25340791   PMID:25521481   PMID:25692340   PMID:26002934  
PMID:26115089   PMID:26210453   PMID:26398116   PMID:26499781   PMID:26646931   PMID:26707189   PMID:26968781   PMID:27085140   PMID:27365390   PMID:27612589   PMID:27780851   PMID:27835588  
PMID:28056546   PMID:28062296   PMID:28222434   PMID:28423547   PMID:28443468   PMID:28466845   PMID:28610790   PMID:28697793   PMID:28798470   PMID:28901313   PMID:29016810   PMID:29164581  
PMID:29364496   PMID:29495977   PMID:29532993   PMID:29737469   PMID:30119891   PMID:30810945   PMID:30963631   PMID:31081087   PMID:31222863   PMID:31342628   PMID:31527801   PMID:31754292  
PMID:31894301   PMID:31904478   PMID:31923920   PMID:31926946   PMID:32096183   PMID:32391974   PMID:32412691   PMID:32432749   PMID:32583714   PMID:32602286   PMID:32860492   PMID:33058914  
PMID:33468212   PMID:33775270   PMID:33821429   PMID:33861889   PMID:34048811   PMID:34106501   PMID:34172072   PMID:34586620   PMID:34663825   PMID:34991623   PMID:35760371   PMID:35840740  
PMID:36040682   PMID:36180477   PMID:37125614  


Genomics

Comparative Map Data
MIR30C1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38140,757,284 - 40,757,372 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl140,757,284 - 40,757,372 (+)EnsemblGRCh38hg38GRCh38
GRCh37141,222,956 - 41,223,044 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36140,995,542 - 40,995,630 (+)NCBINCBI36Build 36hg18NCBI36
Celera139,505,156 - 39,505,244 (+)NCBICelera
Cytogenetic Map1p34.2NCBI
HuRef139,341,077 - 39,341,165 (+)NCBIHuRef
CHM1_1141,338,787 - 41,338,875 (+)NCBICHM1_1
T2T-CHM13v2.0140,626,494 - 40,626,582 (+)NCBIT2T-CHM13v2.0
Mir30c-1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394120,626,731 - 120,626,819 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4120,626,731 - 120,626,819 (-)EnsemblGRCm39 Ensembl
GRCm384120,769,534 - 120,769,622 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4120,769,534 - 120,769,622 (-)EnsemblGRCm38mm10GRCm38
MGSCv374120,442,139 - 120,442,227 (-)NCBIGRCm37MGSCv37mm9NCBIm37
Celera4119,487,732 - 119,487,820 (-)NCBICelera
Cytogenetic Map4D2.1NCBI
cM Map456.52NCBI
Mir30c1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85139,634,455 - 139,634,543 (-)NCBIGRCr8
mRatBN7.25134,349,237 - 134,349,325 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5134,349,237 - 134,349,325 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5137,076,728 - 137,076,816 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05138,833,199 - 138,833,287 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05138,853,814 - 138,853,902 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05139,699,877 - 139,699,965 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5139,699,877 - 139,699,965 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05143,494,757 - 143,494,845 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera5132,903,568 - 132,903,656 (-)NCBICelera
Cytogenetic Map5q36NCBI
MIR30C-1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1152,280,050 - 2,280,110 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl152,280,039 - 2,280,121 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha152,538,350 - 2,538,410 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0152,369,429 - 2,369,489 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl152,369,418 - 2,369,500 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1152,274,894 - 2,274,954 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0152,334,967 - 2,335,027 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0152,350,801 - 2,350,861 (-)NCBIUU_Cfam_GSD_1.0
MIR30C-1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6170,426,781 - 170,426,860 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16170,426,781 - 170,426,860 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26157,473,595 - 157,473,674 (-)NCBISscrofa10.2Sscrofa10.2susScr3


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1p34.2-34.1(chr1:40693289-44514104)x1 copy number loss See cases [RCV000050706] Chr1:40693289..44514104 [GRCh38]
Chr1:41158961..44979776 [GRCh37]
Chr1:40931548..44752363 [NCBI36]
Chr1:1p34.2-34.1
pathogenic
GRCh38/hg38 1p34.3-34.2(chr1:39360747-40900817)x3 copy number gain See cases [RCV000051815] Chr1:39360747..40900817 [GRCh38]
Chr1:39826419..41366489 [GRCh37]
Chr1:39599006..41139076 [NCBI36]
Chr1:1p34.3-34.2
pathogenic
GRCh38/hg38 1p34.3-33(chr1:39479787-47688131)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051817]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051817]|See cases [RCV000051817] Chr1:39479787..47688131 [GRCh38]
Chr1:39945459..48153803 [GRCh37]
Chr1:39718046..47926390 [NCBI36]
Chr1:1p34.3-33
pathogenic
GRCh38/hg38 1p34.3-34.1(chr1:38222737-45636176)x3 copy number gain See cases [RCV000051803] Chr1:38222737..45636176 [GRCh38]
Chr1:38688409..46101848 [GRCh37]
Chr1:38460996..45874435 [NCBI36]
Chr1:1p34.3-34.1
pathogenic
GRCh38/hg38 1p34.3-34.2(chr1:38108665-42327551)x1 copy number loss See cases [RCV000053805] Chr1:38108665..42327551 [GRCh38]
Chr1:38574337..42793222 [GRCh37]
Chr1:38346924..42565809 [NCBI36]
Chr1:1p34.3-34.2
pathogenic
GRCh38/hg38 1p34.2-34.1(chr1:40462415-44668040)x1 copy number loss See cases [RCV000053837] Chr1:40462415..44668040 [GRCh38]
Chr1:40928087..45133712 [GRCh37]
Chr1:40700674..44906299 [NCBI36]
Chr1:1p34.2-34.1
pathogenic
GRCh38/hg38 1p36.11-34.2(chr1:24381206-41401517)x3 copy number gain See cases [RCV000138891] Chr1:24381206..41401517 [GRCh38]
Chr1:24707696..41886350 [GRCh37]
Chr1:24580283..41658937 [NCBI36]
Chr1:1p36.11-34.2
pathogenic
GRCh37/hg19 1p34.2(chr1:40944820-42213560)x1 copy number loss See cases [RCV000240178] Chr1:40944820..42213560 [GRCh37]
Chr1:1p34.2
uncertain significance
GRCh37/hg19 1p36.12-12(chr1:20608823-120546301)x3 copy number loss not provided [RCV000762767] Chr1:20608823..120546301 [GRCh37]
Chr1:1p36.12-12
likely benign
GRCh37/hg19 1p34.2(chr1:41086977-41670357)x3 copy number gain See cases [RCV000446308] Chr1:41086977..41670357 [GRCh37]
Chr1:1p34.2
uncertain significance
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1p34.2(chr1:40962859-41375802)x1 copy number loss See cases [RCV000511219] Chr1:40962859..41375802 [GRCh37]
Chr1:1p34.2
uncertain significance
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44
pathogenic
NC_000001.10:g.(?_33241563)_(46663513_?)dup duplication Charcot-Marie-Tooth disease dominant intermediate C [RCV000708276] Chr1:33241563..46663513 [GRCh37]
Chr1:1p35.1-34.1
uncertain significance
GRCh37/hg19 1p36.33-q44(chr1:82154-249218992)x3 copy number gain not provided [RCV000736305] Chr1:82154..249218992 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1p36.22-21.1(chr1:103343285-103455144)x3 copy number gain Global developmental delay [RCV000787285] Chr1:103343285..103455144 [GRCh37]
Chr1:1p36.22-21.1
uncertain significance
NC_000001.10:g.(?_33241563)_(46663513_?)dup duplication Charcot-Marie-Tooth disease, dominant intermediate C [RCV001308684] Chr1:33241563..46663513 [GRCh37]
Chr1:1p35.1-34.1
uncertain significance
GRCh37/hg19 1p34.3-34.2(chr1:38679545-42556292) copy number loss not specified [RCV002053269] Chr1:38679545..42556292 [GRCh37]
Chr1:1p34.3-34.2
likely pathogenic
GRCh37/hg19 1p35.1-33(chr1:33285582-47891811) copy number gain not specified [RCV002052781] Chr1:33285582..47891811 [GRCh37]
Chr1:1p35.1-33
pathogenic
Single allele inversion Bilateral polymicrogyria [RCV003459046] Chr1:33246132..61045156 [GRCh38]
Chr1:1p35.1-31.3
likely pathogenic
miRNA Target Status

Confirmed Targets
Gene TargetMature miRNAMethod NameResult TypeData TypeSupport TypePMID
SMAD1hsa-miR-30c-5pMirtarbaseexternal_infoLuciferase reporter assay//Western blotFunctional MTI22253433
MUC17hsa-miR-30c-5pMirtarbaseexternal_infoImmunohistochemistry//Microarray//qRT-PCRFunctional MTI (Weak)20926598
UBE2Ihsa-miR-30c-5pMirtarbaseexternal_infoLuciferase reporter assay//qRT-PCR//Western blotFunctional MTI19223510
SERPINE1hsa-miR-30c-5pMirtarbaseexternal_infoLuciferase reporter assayFunctional MTI21175428
HSPA4hsa-miR-30c-5pMirtarbaseexternal_infoLuciferase reporter assay//qRT-PCRFunctional MTI22842562
TGIF2hsa-miR-30c-5pMirtarbaseexternal_infoqRT-PCR//Western blotFunctional MTI23469762
SOCS3hsa-miR-30c-5pMirtarbaseexternal_infoqRT-PCRFunctional MTI (Weak)23418453
VIMhsa-miR-30c-5pMirtarbaseexternal_infoLuciferase reporter assayFunctional MTI23224145
HMG20Ahsa-miR-30c-5pMirtarbaseexternal_infoCLASHFunctional MTI (Weak)23622248
TWF1hsa-miR-30c-5pOncomiRDBexternal_infoNANA23340433
TWF1hsa-miR-30c-5pOncomiRDBexternal_infoNANA23224145
CASP3hsa-miR-30c-5pOncomiRDBexternal_infoNANA22964638
KRAShsa-miR-30c-5pOncomiRDBexternal_infoNANA22701724
BCL2L11hsa-miR-30c-5pOncomiRDBexternal_infoNANA22157681
MTA1hsa-miR-30c-5pOncomiRDBexternal_infoNANA22139444
MYBhsa-miR-30c-5pOncomiRDBexternal_infoNANA21187425
UBE2Ihsa-miR-30c-5pOncomiRDBexternal_infoNANA20498642
HMBOX1hsa-miR-30c-1-3pMirtarbaseexternal_infoLuciferase reporter assay//Western blotFunctional MTI22320217
DYRK1Bhsa-miR-30c-1-3pMirtarbaseexternal_infoCLASHFunctional MTI (Weak)23622248
HMBOX1hsa-miR-30c-1-3pOncomiRDBexternal_infoNANA22320217

Predicted Targets
Summary Value
Count of predictions:54604
Count of gene targets:17233
Count of transcripts:37302
Interacting mature miRNAs:hsa-miR-30c-1-3p, hsa-miR-30c-5p
Prediction methods:Microtar, Miranda, Pita, Pita,Targetscan, 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 entire extraembryonic component
High
Medium 2 2
Low 42 8 34 25 177 27 39 22 41 38 70 54 3 1 4 3
Below cutoff 25 7 8 3 24 3 16 22 25 22 18 45 1 1 3

Sequence


RefSeq Acc Id: ENST00000385227
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl140,757,284 - 40,757,372 (+)Ensembl
RefSeq Acc Id: NR_029833
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38140,757,284 - 40,757,372 (+)NCBI
GRCh37141,222,956 - 41,223,044 (+)RGD
Celera139,505,156 - 39,505,244 (+)RGD
HuRef139,341,077 - 39,341,165 (+)ENTREZGENE
CHM1_1141,338,787 - 41,338,875 (+)NCBI
T2T-CHM13v2.0140,626,494 - 40,626,582 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:31626 AgrOrtholog
COSMIC MIR30C1 COSMIC
Ensembl Genes ENSG00000207962 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000385227 ENTREZGENE
GTEx ENSG00000207962 GTEx
HGNC ID HGNC:31626 ENTREZGENE
Human Proteome Map MIR30C1 Human Proteome Map
miRBase MI0000736 ENTREZGENE
NCBI Gene 407031 ENTREZGENE
OMIM 615151 OMIM
PharmGKB PA164722643 PharmGKB
RNAcentral URS000019907A RNACentral
  URS0000237FB8 RNACentral
  URS000075D43C RNACentral