pre-miRNA Information
pre-miRNA hsa-mir-190b   
Genomic Coordinates chr1: 154193665 - 154193743
Description Homo sapiens miR-190b stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-190b
Sequence 11| UGAUAUGUUUGAUAUUGGGUU |31
Evidence Not_experimental
Experiments
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol PGAM4   
Synonyms PGAM-B, PGAM1, PGAM3, dJ1000K24.1
Description phosphoglycerate mutase family member 4
Transcript NM_001029891   
Expression
Putative miRNA Targets on PGAM4
3'UTR of PGAM4
(miRNA target sites are highlighted)
>PGAM4|NM_001029891|3'UTR
   1 AGGCCAGCGGGGAGGATACTGTCCCCAGGAGCACCCTCCCTGCTGGTCTTGTCCCTCTGCCCCTCCCACCTGCACATGTC
  81 ACACTGACCACATCTGTAGACATCTTGAGTTGTAGCTGCAGATGGGGACCAGTGGCTCCCATTTTCATTTTAGCCATTTT
 161 GTCGCCTGCACCCACTCCCTTCATACAATCTAGTCAGAATAGCAGTTCTAGAGCACAGGTTCTCAGTCTAAGCTGTGGAA
 241 AAGCTCCCCTTATCCAACAGAGTTTAAAAGTAGTGACTTGGGTTTTTGTGAGTGCTTTGTTTACTAAGGACTTTGGGGAG
 321 GAACATGCTAAGCCACGACCAATGAGGAGAAGCAACAGAGCCTGTCTGTCCCCATGAGCAGAGTCTGTCCTCTGCTCTTC
 401 TGCAGTCAGGCCACTGCCTGGGGGCTCTAGTCATTCCAGTGGAAGATGAATGTAATCTGCATGGTGATGTGACAACTGTT
 481 TCCTCCTTGACCCCAGAGGATCTGGCTCTAGGTTGGGATCAATCCTGAATTTCGTTATGTGTTATATTTACTTTTATTAA
 561 AAAAGTATAGTATATATTAATAATACAAAACAATAACCCTTCTGGGGTTTCTTGTGGCGGTTGAAATAGTCCCACATGTG
 641 GTCATCAGAAAATAAGCCATTCCTCATACCAATATAGGATCAGCTCCTTGACCTCTGAGGGGCAGGAGTGCTTCCTGGTG
 721 TGTGTATTAGAATCCCTTCCTGCCTTGTTTCATGGCAGTGAAATGCCTCTTGGTCCTGTCCAAGTGTGTCTTTCACTGAT
 801 TTCTGAATCATGTTCTAGTTGCTTGACCCTGCCACATGGGCCCAGTGTTCATCTGAGCATAACTGTACTAAATCCTTTTA
 881 CCAGATCAGTATAATAAAGGAGTGATGTGCAAT
Target sites Provided by authors   Predicted by miRanda    DRVs    SNPs    DRVs & SNPs
miRNA-target interactions
(Predicted by miRanda)
ID Duplex structure Position Score MFE
1
miRNA  3' uuGGGUUAUAGUUUGUAUAGu 5'
            ||||    :: ||||:|| 
Target 5' ctCCCA--CCTGCACATGTCa 3'
63 - 81 127.00 -12.00
2
miRNA  3' uugggUUAUAGUUUGUAUAGu 5'
               |:||| : |:||||: 
Target 5' aaaaaAGTATAGTATATATTa 3'
559 - 579 124.00 -6.50
3
miRNA  3' uugggUUAU-AGUUUGUAUAgu 5'
               |||| ||  ||||:|  
Target 5' gttgaAATAGTCCCACATGTgg 3'
620 - 641 120.00 -5.90
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1177553917 3 dbSNP
rs782535693 6 dbSNP
rs370972288 8 dbSNP
rs782762847 9 dbSNP
rs1174605294 10 dbSNP
rs782136628 15 dbSNP
rs782775711 32 dbSNP
rs1377540587 35 dbSNP
rs190235986 41 dbSNP
rs782047376 45 dbSNP
rs781931947 46 dbSNP
rs1398452571 47 dbSNP
rs781831467 60 dbSNP
rs1446338988 61 dbSNP
rs1298921217 72 dbSNP
rs185437080 73 dbSNP
rs1217524801 78 dbSNP
rs1299153552 87 dbSNP
rs1311526577 89 dbSNP
rs1223948158 152 dbSNP
rs1264780416 154 dbSNP
rs1315764881 163 dbSNP
rs1197663460 164 dbSNP
rs1233052917 172 dbSNP
rs1481358257 216 dbSNP
rs1188919078 225 dbSNP
rs1267349498 242 dbSNP
rs1481042804 261 dbSNP
rs782057262 280 dbSNP
rs1421971021 282 dbSNP
rs1465385036 292 dbSNP
rs1171452596 294 dbSNP
rs782355542 326 dbSNP
rs1356463575 332 dbSNP
rs1434484876 336 dbSNP
rs1292999435 337 dbSNP
rs1346163707 339 dbSNP
rs1405484143 357 dbSNP
rs1285076590 366 dbSNP
rs1213753184 376 dbSNP
rs1273323389 380 dbSNP
rs782038018 390 dbSNP
rs782808962 401 dbSNP
rs1218819351 421 dbSNP
rs1264366365 422 dbSNP
rs782134806 428 dbSNP
rs1490351715 448 dbSNP
rs1202255253 459 dbSNP
rs781991422 466 dbSNP
rs1477721811 470 dbSNP
rs1187464416 483 dbSNP
rs782363641 491 dbSNP
rs1421986950 508 dbSNP
rs1403822563 513 dbSNP
rs782046653 513 dbSNP
rs782048834 527 dbSNP
rs1366310867 532 dbSNP
rs181072116 533 dbSNP
rs1304933235 534 dbSNP
rs189470519 538 dbSNP
rs1429850085 539 dbSNP
rs1270540650 540 dbSNP
rs1363743148 541 dbSNP
rs1226264320 543 dbSNP
rs1313857304 544 dbSNP
rs1359594768 545 dbSNP
rs1224029522 559 dbSNP
rs1284590345 565 dbSNP
rs1488240668 565 dbSNP
rs1217057299 577 dbSNP
rs1244194532 584 dbSNP
rs5913628 590 dbSNP
rs1471989474 605 dbSNP
rs1181523250 616 dbSNP
rs1386073651 618 dbSNP
rs1446565572 619 dbSNP
rs1156930914 629 dbSNP
rs1358611998 632 dbSNP
rs1400056818 663 dbSNP
rs1318811406 675 dbSNP
rs113125940 688 dbSNP
rs1346778479 693 dbSNP
rs1445509906 696 dbSNP
rs1335719937 718 dbSNP
rs1383063283 720 dbSNP
rs1247604682 722 dbSNP
rs1306469123 724 dbSNP
rs1349249863 726 dbSNP
rs1224853033 734 dbSNP
rs1286901693 735 dbSNP
rs1441100836 743 dbSNP
rs1203403019 774 dbSNP
rs1244049485 784 dbSNP
rs782304969 786 dbSNP
rs1462816868 787 dbSNP
rs1176943146 789 dbSNP
rs1379771599 796 dbSNP
rs1470531406 798 dbSNP
rs1159124383 818 dbSNP
rs1410032097 833 dbSNP
rs1412608290 845 dbSNP
rs1335822705 852 dbSNP
rs1406465986 859 dbSNP
rs782721181 882 dbSNP
rs1334679959 883 dbSNP
rs1442276810 890 dbSNP
rs1281825270 898 dbSNP
rs1343491534 904 dbSNP
rs1223343882 919 dbSNP
rs1197019875 926 dbSNP
rs1264160687 926 dbSNP
rs1326018020 926 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in GSM545216. RNA binding protein: AGO2. Condition:miR-124 transfection ...

- Hafner M; Landthaler M; Burger L; Khorshid et al., 2010, Cell.

Article - Hafner M; Landthaler M; Burger L; Khorshid et al.
- Cell, 2010
RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.
LinkOut: [PMID: 20371350]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 441531.0
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... "PAR-CLIP data was present in GSM714644. RNA binding protein: AGO2. Condition:completeT1 ...

- Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods.

Article - Kishore S; Jaskiewicz L; Burger L; Hausser et al.
- Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
CLIP-seq Support 1 for dataset GSM545216
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-124 transfection
Location of target site ENST00000334828.5 | 3UTR | CAUAACUGUACUAAAUCCUUUUUCCAUAUCAGUAUAAUAAAGGAGUGAUGUGCAAUAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM714644
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repA
Location of target site ENST00000334828.5 | 3UTR | UUCAUCUGAGCAUAACUGUACUAAAUCCUUUUUCCAUAUCAGUAUAAUAAAGGAGUGAUGUGCAAUAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
MiRNA-Target Expression Profile
Dataset Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
GSE28544 Breast cancer -0.604 8.9e-4 -0.521 4.5e-3 24 Click to see details
GSE42095 Differentiated embryonic stem cells -0.402 2.9e-2 -0.589 1.6e-3 23 Click to see details
GSE26953 Aortic valvular endothelial cells -0.176 2.1e-1 -0.175 2.1e-1 24 Click to see details
GSE28260 Renal cortex and medulla -0.17 2.9e-1 -0.258 2.0e-1 13 Click to see details
GSE38226 Liver fibrosis -0.082 3.6e-1 -0.112 3.1e-1 21 Click to see details
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
BRCA -0.239 0.02 -0.242 0.02 72 Click to see details
LIHC -0.295 0.12 -0.418 0.04 18 Click to see details
PRAD -0.256 0.12 -0.263 0.11 23 Click to see details
UCEC 0.315 0.13 0.275 0.16 15 Click to see details
HNSC -0.221 0.16 -0.232 0.14 23 Click to see details
LUSC -0.232 0.17 -0.347 0.07 19 Click to see details
KIRC -0.272 0.18 -0.297 0.16 13 Click to see details
THCA 0.038 0.43 -0.049 0.41 24 Click to see details
LUAD 0.074 0.43 0.048 0.46 8 Click to see details
KIRP 0.068 0.44 -0.321 0.24 7 Click to see details
CHOL -0.069 0.47 -0.400 0.3 4 Click to see details
STAD -0.033 0.48 0.100 0.44 5 Click to see details
ESCA -0.04 0.48 -0.800 0.1 4 Click to see details
KICH 0.004 0.5 -0.300 0.31 5 Click to see details
KICH 0.004 0.5 -0.300 0.31 5 Click to see details
KICH 0.004 0.5 -0.300 0.31 5 Click to see details
KICH 0.004 0.5 -0.300 0.31 5 Click to see details
KICH 0.004 0.5 -0.300 0.31 5 Click to see details
KICH 0.004 0.5 -0.300 0.31 5 Click to see details
60 hsa-miR-190b Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT054581 IGF1 insulin like growth factor 1 4 1
MIRT066966 ATXN7L3B ataxin 7 like 3B 2 2
MIRT192449 SPRED1 sprouty related EVH1 domain containing 1 2 2
MIRT250414 TNRC6A trinucleotide repeat containing 6A 2 2
MIRT306294 KLHL24 kelch like family member 24 2 2
MIRT355845 SGMS2 sphingomyelin synthase 2 2 4
MIRT437770 MTMR6 myotubularin related protein 6 1 1
MIRT437771 MTMR6 myotubularin related protein 6 1 1
MIRT437772 Mtmr6 myotubularin related protein 6 1 1
MIRT444672 CDKL2 cyclin dependent kinase like 2 2 2
MIRT446389 PCDHB11 protocadherin beta 11 2 2
MIRT446634 SDC3 syndecan 3 2 2
MIRT449410 TRIM5 tripartite motif containing 5 2 2
MIRT449560 GPC5 glypican 5 2 2
MIRT469928 PTPRJ protein tyrosine phosphatase, receptor type J 2 6
MIRT473736 MAP3K9 mitogen-activated protein kinase kinase kinase 9 2 2
MIRT474210 LDHA lactate dehydrogenase A 2 2
MIRT474583 KLF6 Kruppel like factor 6 2 2
MIRT476732 FOXN2 forkhead box N2 2 2
MIRT478455 DAB2 DAB2, clathrin adaptor protein 2 2
MIRT495327 ADAMTS8 ADAM metallopeptidase with thrombospondin type 1 motif 8 2 4
MIRT498615 MTRNR2L10 MT-RNR2-like 10 2 12
MIRT501734 OVOL1 ovo like transcriptional repressor 1 2 2
MIRT501849 MTRNR2L8 MT-RNR2-like 8 2 14
MIRT504678 CYGB cytoglobin 2 4
MIRT506517 MSANTD4 Myb/SANT DNA binding domain containing 4 with coiled-coils 2 6
MIRT507984 BCL2L13 BCL2 like 13 2 4
MIRT508444 ZNF608 zinc finger protein 608 2 4
MIRT511366 IL6ST interleukin 6 signal transducer 2 4
MIRT520515 TRA2B transformer 2 beta homolog 2 2
MIRT524571 CALML4 calmodulin like 4 2 4
MIRT531896 INVS inversin 2 4
MIRT533916 TATDN2 TatD DNase domain containing 2 2 2
MIRT537503 FAM13B family with sequence similarity 13 member B 2 2
MIRT541689 CCDC160 coiled-coil domain containing 160 2 8
MIRT544419 ZNF460 zinc finger protein 460 2 4
MIRT544615 CSDE1 cold shock domain containing E1 2 2
MIRT545076 IL7R interleukin 7 receptor 2 2
MIRT545849 ZNF264 zinc finger protein 264 2 4
MIRT547436 MED4 mediator complex subunit 4 2 2
MIRT550157 ZNF223 zinc finger protein 223 2 4
MIRT553948 STAMBP STAM binding protein 2 2
MIRT554395 SERP1 stress associated endoplasmic reticulum protein 1 2 2
MIRT555667 PGAM4 phosphoglycerate mutase family member 4 2 4
MIRT564193 PM20D2 peptidase M20 domain containing 2 2 2
MIRT566792 MKL2 MKL1/myocardin like 2 2 2
MIRT566843 LRRC58 leucine rich repeat containing 58 2 2
MIRT572516 KIAA0232 KIAA0232 2 2
MIRT607428 NOTCH2NL notch 2 N-terminal like 2 10
MIRT627779 RAB30 RAB30, member RAS oncogene family 2 2
MIRT635159 ENO4 enolase family member 4 2 2
MIRT642159 ADCYAP1R1 ADCYAP receptor type I 3 2
MIRT646205 DUSP10 dual specificity phosphatase 10 2 2
MIRT657007 KCNMB4 potassium calcium-activated channel subfamily M regulatory beta subunit 4 2 2
MIRT665817 TMEM161B transmembrane protein 161B 2 2
MIRT667488 MAP3K2 mitogen-activated protein kinase kinase kinase 2 2 2
MIRT707098 ZNF850 zinc finger protein 850 2 2
MIRT708719 PTPLAD2 3-hydroxyacyl-CoA dehydratase 4 1 1
MIRT735521 HUS1 HUS1 checkpoint clamp component 3 0
MIRT736644 AGPAT3 1-acylglycerol-3-phosphate O-acyltransferase 3 2 0
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-1 Anthocyanin NULL 145858 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Caffeic acid NULL 689043 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Catechin approved 9064 Microarray apoE−/− mice 22253797 2012 up-regulated
miR-1 Curcumin NULL 969516 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Ferulic acid NULL 445858 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Hesperidin NULL 10621 Microarray apoE−/− mice 22253797 2012 up-regulated
miR-1 Quercetin NULL 5280343 Microarray apoE−/− mice 22253797 2012 down-regulated
miR-1 Galactose NULL 6036 Quantitative real-time PCR lens 22736950 2012 up-regulated
miR-1 Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) NULL 8490 Microarray mouse brain 19270793 2009 down-regulated
miR-1 Trichostatin A (TSA) NULL 444732 Quantitative real-time PCR myocardial differentiation of mouse ES cells 19521018 2009 down-regulated
miR-1 Sulfonyl-hydrazone-1 (SHZ) NULL NULL Quantitative real-time PCR Murine broblast-derived Induced pluripotent stem cells 21445862 2011 up-regulated
miR-1 Cocaine NULL 446220 Next-generation sequencing ventral striatum 21708909 2011 up-regulated
miR-1 Atorvastatin approved 60823 Quantitative real-time PCR Cardiomyocyte 23860036 2013 down-regualted
miR-1 Glucose NULL 5793 Quantitative real-time PCR endothelial cells 24394957 2014 down-regulated
miR-1 Docosahexaenoic acid NULL 445580 Quantitative real-time PCR Caco-2 cells 24623846 2014 up-regulated
miR-1 Palmitic acid approved 985 Quantitative real-time PCR Caco-2 cells 24623846 2014 up-regulated
miR-1 17beta-estradiol (E2) approved 5757 Microarray MCF-7AKT breast cancer cells 19528081 2009 down-regulated
miR-1 Essential amino acids (EAA) NULL NULL Quantitative real-time PCR skeletal muscle of young adults 19828686 2009 up-regulated
miR-1 Hydrogen peroxide (H2O2) NULL 784 Quantitative real-time PCR Human umbilical vein endothelial cells 21527937 2011 down-regulated
miR-1 Trichostatin A (TSA) NULL 444732 Microarray apoptosis-resistant breast cancer cells 21971930 2011 up-regulated
miR-1 Arsenic trioxide approved 14888 Quantitative real-time PCR acute promyelocytic leukemia 22072212 2012 up-regulated
miR-1 5-Fluorouracil approved 3385 Microarray CNE cells 22614822 2012 up-regulated
miR-1 Bicalutamide approved 2375 Microarray prostate 22674191 2012 up-regulated
miR-1 Arsenic trioxide approved 14888 Quantitative real-time PCR cardia 22889704 2012 up-regulated
miR-1 Perfluorooctane sulfonate NULL 74483 Microarray zebrafish embryos 20878907 2011 up-regulated
miR-1 Quinidine approved 441074 Quantitative real-time PCR myocardial infarction (MI) rats 19775284 2009 up-regulated
miR-1 Tanshinone IIA NULL 164676 Quantitative real-time PCR myocardial infarction (MI) rats 19775284 2009 down-regulated
miR-1 Tanshinone IIA NULL 164676 Quantitative real-time PCR post-infarction rat cardiomyocytes 21220930 2011 down-regulated
miR-1 Isoproterenol approved 3779 Quantitative real-time PCR heart 22847192 2012 down-regulated
miR-1 Dexamethasone approved 5743 Microarray adrenals and granulosa cells 24205079 2014 up-regulated
miR-1 Thiourea (TU) NULL 737139 Quantitative real-time PCR skeletal muscle and heart 22142802 2012 up-regulated
miR-1 Thiourea (TU) NULL 737139 Quantitative real-time PCR skeletal muscle and heart 22142802 2012 down-regulated
miR-1 Isoproterenol approved 3779 Quantitative real-time PCR heart 22847192 2012 up-regulated
miR-190b Catechin approved 9064 Microarray apoE−/− mice 22253797 2012 up-regulated
miR-190b Atorvastatin approved 60823 Microarray PC3 prostate cancer cells 23936432 2013 up-regualted
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-190b Paclitaxel 36314 NSC125973 approved sensitive cell line (A2780)

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