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 | SERP1 | ||||||||||||||||||||
Synonyms | RAMP4 | ||||||||||||||||||||
Description | stress associated endoplasmic reticulum protein 1 | ||||||||||||||||||||
Transcript | NM_014445 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on SERP1 | |||||||||||||||||||||
3'UTR of SERP1 (miRNA target sites are highlighted) |
>SERP1|NM_014445|3'UTR 1 AGTGACTGACCTTAAGATGTTTCCATTCTCCTGTGAATTTTAACTTGAACTCATTCCTGATGTTTGATACCCTGGTTGAA 81 AACAATTCAGTAAAGCATCCTGCCTCAGAATGACTTTCCTATCATGCTTCATGTGTCATTCCAAGGTTTCTTCATGAGTC 161 ATTCCAAGTTTTCTAGTCCATACCACAGTGCCTTGCAAAAAACACCACATGAATAAAGCAATAAAATTTGATTGTTAAGA 241 TACAGTAGTGGACCCTACTTATTCAGTCAATTAAGAGTAAGTTTTTTTATGTGGTTATTAAAACAGTATGAACAATTAGT 321 CTAACTCTGCATAGACAGGGTCTAGATTTTGTTAACCCAAATGTATAACTGCAGTTAGCTTAAATTACAATTTGAAGTCT 401 TGTGGTTTTTATATAGCTAGGCACTTTATTACTCTTTTGAACTGAAAGCACACTCCCTTATAGGTTCATGTAACTGTCCT 481 GTAATAAGGTGCTTATAAATGGAACAACTACACAGCCTAGTTTTGCCACAACCTTTAGCATCTAAAAAGTTTTAAAAGCT 561 TCTAAATGTCTAATATAAAGGGAGATGCTTATAGCCACAACATCTATTTTACCAATATTGTTTCCATTACACTACCTTGG 641 ATTTTGCATGAGTGAGTATAGTAACCCAAGATGCCATAAAAAAAAAACTTGATCGTTTTCTGACTTAATCAGTTACTGTG 721 GTTTCACTAAAAGCTACCGTGGTGGAGTGAAGTCAGTCAGGGAAGGTTTGTTTATGTTACATTTATTTCACCAGAACTAT 801 TTTAATATATCAAAGGGGTTTACTATGCCAAACAAAATTCTAGGGAAAAATACTGCTAAAAATGGATGCCTCATCAGAAC 881 ATGCTGTTGAGTCCAATGTGCCATAAGACATTTTAGCATGTTAAATAGCACTTTTAATAGCAAAAAAAGGCACATCAACT 961 GCGAAGTTATCCTTAGTTTGCAAATGCTTTTTCTAGATTAATGATTTTTCAATCATTAGGGTACTAGACACATCAGCCTA 1041 AAGTGGCATCTGGAATTGAATGGATTTACTGATAATGATCAGTCTTTAGTCTTCCCTTTGTTATATGACTTTATAGGTTA 1121 TGATTGATCAAATTTACGTTTTACTAATGGTAAGGGTGAGGGTCATAGGGCAGGTTTTGGGTTTTCTAGTACTGTTGAAA 1201 ACTGCAAGTATTGGCTATTTGTATACTTAGCCATAACTTGGTGAAAAAAAACCTGAGCAGTGTCTATGTATTAATGCGTT 1281 GGAAAGAAAGCTGCTTGTGTTTGCTTTGTTAATTGCCTCAGGATATTTCTTTTAAAATAAGCTGTTTTAAGAGGAACAGA 1361 AGGGAAATCTGCTACCTAGTCTATACACAGCGTGAACCTCACAGGGGGCTTCTGATACCCTCAAACATGGAGAACAGTAA 1441 GGGAGCAGAGTGGTTAAGGACTTTCAGGAACTTAACTATTCTGGAATAAGGAATGAATCAACTGACCTTGGGCCAGCAGG 1521 TTTTTAACTAAATTGTTACTTGCCTTTCTCACCCAGTTAATCAGTCTCTGTACTTGTTTCCCTTTTTGAAACAAGTGTCT 1601 TGGTTAACTAATTCTGTTTTATGGTTGTGCTAAATTCATAGCAGGTGCCTTATTCTTTGCTTTTAGTCAAACCATTCCAT 1681 ATCAGAATTTTCCTTGGTTTACTATAGATATTTGGCTTTAAGTTGTTGTTTGTGTTTTTTAATGTACAATGTTCTGATAA 1761 ATTTGACTGTTAAATTGCTATAGCTAGCAATCATTTTACATATGTAAAATTGCATTCCCTTTGTATTTCATGTGTAATTC 1841 ACCAATTAAGTGCAGTTTATATTCAGGTTGGATTATGCATGTTTAGGTAAACGAAAGCTGTGTCTTACTTGATTTATTCT 1921 TTAAAAATAAAGTTCCCTGAATATTTGATGCTTTTCTTCTAAACGGAAATGATTTTACAGTTATCTGAGTGTACCTTTTA 2001 TAGTTAGTAGAAAATGATTTTAAAGAATGTTTAGTATTGTACTTAAATGGTATGCAGAGGCACAGATGTAAGGTTTATAA 2081 CTGGAAATAGGTGGTAAGAAAAATATATAGAAAGCACAATGATTTGAATATTTTTCCACTTAGGATTTCCTAATCTCCTT 2161 GTCATCCAATTCAAGCTCAAGATGAAGCACAATTCTTTGATCTCCCTTTGCCAGTTGAATTTTATAGATCATCTAATGTT 2241 GAGCACAGTATGAGAATAAATATTGGGGTTGTCAACATTACTCAGTTACTCTTTGTGGTTTAACTCTAACATTTCAACAA 2321 GTTGTCAATTAATTGTATCTGTTGGGTTGTATATAATGTTGCTCAAAATAATTAAGTGGACTTCCAAAAATAAGATTTCC 2401 ATTGTAACAGGATGCATTGTGATGGGCTTTGACTTACATTAAAGAAATGTGGATAGTCAACTGCAAAAAAAAAA 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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DRVs in gene 3'UTRs | |||||||||||||||||||||
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 | ||||||
Disease | 27230.0 | ||||||
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. |
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miRNA-target interactions (Provided by authors) |
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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 GSM714644 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / completeT1, repA |
Location of target site | ENST00000239944.2 | 3UTR | UCAAACCAUUCCAUAUCAGAAUUUUCCUUGGUUUACUAUAG |
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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