pre-miRNA Information | |
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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 | |
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Mature miRNA | hsa-miR-190b |
Sequence | 11| UGAUAUGUUUGAUAUUGGGUU |31 |
Evidence | Not_experimental |
Experiments | |
Putative Targets |
miRNA Expression profile | |
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miRNAs in Extracellular Vesicles |
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Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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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
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miRNA-target interactions (Predicted by miRanda) |
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SNPs in gene 3'UTRs |
Experimental Support 1 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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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]
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Experimental Support 2 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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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]
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CLIP-seq Support 1 for dataset GSM545216 | |
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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 | |
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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 | ||||||||||||||||||||||||||||||||||||||||||
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MiRNA-Target Expression Profile (TCGA) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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60 hsa-miR-190b Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT054581 | IGF1 | insulin like growth factor 1 | ![]() |
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4 | 1 | ||||
MIRT066966 | ATXN7L3B | ataxin 7 like 3B | ![]() |
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2 | 2 | ||||||
MIRT192449 | SPRED1 | sprouty related EVH1 domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT250414 | TNRC6A | trinucleotide repeat containing 6A | ![]() |
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2 | 2 | ||||||
MIRT306294 | KLHL24 | kelch like family member 24 | ![]() |
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2 | 2 | ||||||
MIRT355845 | SGMS2 | sphingomyelin synthase 2 | ![]() |
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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 | ![]() |
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2 | 2 | ||||||
MIRT446389 | PCDHB11 | protocadherin beta 11 | ![]() |
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2 | 2 | ||||||
MIRT446634 | SDC3 | syndecan 3 | ![]() |
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2 | 2 | ||||||
MIRT449410 | TRIM5 | tripartite motif containing 5 | ![]() |
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2 | 2 | ||||||
MIRT449560 | GPC5 | glypican 5 | ![]() |
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2 | 2 | ||||||
MIRT469928 | PTPRJ | protein tyrosine phosphatase, receptor type J | ![]() |
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2 | 6 | ||||||
MIRT473736 | MAP3K9 | mitogen-activated protein kinase kinase kinase 9 | ![]() |
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2 | 2 | ||||||
MIRT474210 | LDHA | lactate dehydrogenase A | ![]() |
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2 | 2 | ||||||
MIRT474583 | KLF6 | Kruppel like factor 6 | ![]() |
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2 | 2 | ||||||
MIRT476732 | FOXN2 | forkhead box N2 | ![]() |
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2 | 2 | ||||||
MIRT478455 | DAB2 | DAB2, clathrin adaptor protein | ![]() |
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2 | 2 | ||||||
MIRT495327 | ADAMTS8 | ADAM metallopeptidase with thrombospondin type 1 motif 8 | ![]() |
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2 | 4 | ||||||
MIRT498615 | MTRNR2L10 | MT-RNR2-like 10 | ![]() |
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2 | 12 | ||||||
MIRT501734 | OVOL1 | ovo like transcriptional repressor 1 | ![]() |
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2 | 2 | ||||||
MIRT501849 | MTRNR2L8 | MT-RNR2-like 8 | ![]() |
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2 | 14 | ||||||
MIRT504678 | CYGB | cytoglobin | ![]() |
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2 | 4 | ||||||
MIRT506517 | MSANTD4 | Myb/SANT DNA binding domain containing 4 with coiled-coils | ![]() |
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2 | 6 | ||||||
MIRT507984 | BCL2L13 | BCL2 like 13 | ![]() |
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2 | 4 | ||||||
MIRT508444 | ZNF608 | zinc finger protein 608 | ![]() |
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2 | 4 | ||||||
MIRT511366 | IL6ST | interleukin 6 signal transducer | ![]() |
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2 | 4 | ||||||
MIRT520515 | TRA2B | transformer 2 beta homolog | ![]() |
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2 | 2 | ||||||
MIRT524571 | CALML4 | calmodulin like 4 | ![]() |
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2 | 4 | ||||||
MIRT531896 | INVS | inversin | ![]() |
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2 | 4 | ||||||
MIRT533916 | TATDN2 | TatD DNase domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT537503 | FAM13B | family with sequence similarity 13 member B | ![]() |
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2 | 2 | ||||||
MIRT541689 | CCDC160 | coiled-coil domain containing 160 | ![]() |
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2 | 8 | ||||||
MIRT544419 | ZNF460 | zinc finger protein 460 | ![]() |
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2 | 4 | ||||||
MIRT544615 | CSDE1 | cold shock domain containing E1 | ![]() |
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2 | 2 | ||||||
MIRT545076 | IL7R | interleukin 7 receptor | ![]() |
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2 | 2 | ||||||
MIRT545849 | ZNF264 | zinc finger protein 264 | ![]() |
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2 | 4 | ||||||
MIRT547436 | MED4 | mediator complex subunit 4 | ![]() |
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2 | 2 | ||||||
MIRT550157 | ZNF223 | zinc finger protein 223 | ![]() |
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2 | 4 | ||||||
MIRT553948 | STAMBP | STAM binding protein | ![]() |
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2 | 2 | ||||||
MIRT554395 | SERP1 | stress associated endoplasmic reticulum protein 1 | ![]() |
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2 | 2 | ||||||
MIRT555667 | PGAM4 | phosphoglycerate mutase family member 4 | ![]() |
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2 | 4 | ||||||
MIRT564193 | PM20D2 | peptidase M20 domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT566792 | MKL2 | MKL1/myocardin like 2 | ![]() |
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2 | 2 | ||||||
MIRT566843 | LRRC58 | leucine rich repeat containing 58 | ![]() |
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2 | 2 | ||||||
MIRT572516 | KIAA0232 | KIAA0232 | ![]() |
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2 | 2 | ||||||
MIRT607428 | NOTCH2NL | notch 2 N-terminal like | ![]() |
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2 | 10 | ||||||
MIRT627779 | RAB30 | RAB30, member RAS oncogene family | ![]() |
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2 | 2 | ||||||
MIRT635159 | ENO4 | enolase family member 4 | ![]() |
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2 | 2 | ||||||
MIRT642159 | ADCYAP1R1 | ADCYAP receptor type I | ![]() |
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3 | 2 | |||||
MIRT646205 | DUSP10 | dual specificity phosphatase 10 | ![]() |
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2 | 2 | ||||||
MIRT657007 | KCNMB4 | potassium calcium-activated channel subfamily M regulatory beta subunit 4 | ![]() |
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2 | 2 | ||||||
MIRT665817 | TMEM161B | transmembrane protein 161B | ![]() |
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2 | 2 | ||||||
MIRT667488 | MAP3K2 | mitogen-activated protein kinase kinase kinase 2 | ![]() |
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2 | 2 | ||||||
MIRT707098 | ZNF850 | zinc finger protein 850 | ![]() |
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2 | 2 | ||||||
MIRT708719 | PTPLAD2 | 3-hydroxyacyl-CoA dehydratase 4 | ![]() |
1 | 1 | |||||||
MIRT735521 | HUS1 | HUS1 checkpoint clamp component | ![]() |
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3 | 0 | |||||
MIRT736644 | AGPAT3 | 1-acylglycerol-3-phosphate O-acyltransferase 3 | ![]() |
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2 | 0 |
miRNA-Drug Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||
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