pre-miRNA Information | |
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pre-miRNA | hsa-mir-4291 |
Genomic Coordinates | chr9: 93819357 - 93819421 |
Description | Homo sapiens miR-4291 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||||||||
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Mature miRNA | hsa-miR-4291 | ||||||||||||
Sequence | 11| UUCAGCAGGAACAGCU |26 | ||||||||||||
Evidence | Experimental | ||||||||||||
Experiments | SOLiD | ||||||||||||
SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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Human miRNA Tissue Atlas | |
Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | TRIM37 | ||||||||||||||||||||
Synonyms | MUL, POB1, TEF3 | ||||||||||||||||||||
Description | tripartite motif containing 37 | ||||||||||||||||||||
Transcript | NM_015294 | ||||||||||||||||||||
Other Transcripts | NM_001005207 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on TRIM37 | |||||||||||||||||||||
3'UTR of TRIM37 (miRNA target sites are highlighted) |
>TRIM37|NM_015294|3'UTR 1 TTGCCAAATCAAGAGAACTGACTTGCAAGCTACCTTGACCCTGAATTTTGCTGTAGTTGGTGCTCAAATTTGTCATCAGT 81 CAGATAATCAGATTTGGTCTTATTTCTTCATTATCTCGACCTGAAATAGTAATTTGGAAACTGTTGGAAGGTGGCACAGT 161 TTAGTCTAAGACAGCAGTAGTACATGGGAAAAACAGTATGGGAAGAGTTCTTTGTAATGTAAGGAAATAACAATGTAGTT 241 CTCTATTAATTTAGCAAATTTGTACATTCACAAAAGGCAGTTTGTCTACTACAGCAGAAGGCTGGTTAACTGCCAGAAAA 321 TGTACCTCCAGGCCCTGCATGCCGTCAGTAACCCGCCCGGCATTGGTGCTCTACTGTCTTTGGCTAGAGCTTAGTTGTGT 401 TTAAATAATCATCTTTATATTTGGGGTTTTAATTACAGTTCCATTAGTGCCTGTAGATTAGTGAACAGAAAATTGCTTTG 481 GAAGAGATTCTGCCCTGTAGACACTATGTGAATAACTGAAGTAACACTAGACTGAATCTCCTTTTTGGAGTATGTATCTT 561 CTCTCACTTGTTCAAGTACAGGCACACTGTTCAACCGCATGGTATCTTTCTGTTGTGTGACTTCTACAAATGTAATTTTA 641 AATGAAATTAAGTTAACATGGATTCATTACGTTCCTGGCCCTGTAGACACGTGTAAGATTATTTAAAATTCTTTCATTTT 721 TTTCTGCCTCTTACTATACGACTGTAGTGCAACAAATATTTTAAAGCCCCCTTTTCTTCTTTATTTTCATTAGTTGTACA 801 TTGATTTCAGTGTCAACACATTTAAAGATTCATTCATGTTGCACAGTGGCTTACATGAACGTGAAACTGTGATATAAGGT 881 TTTCTTTCATACTCATAATTAGCCCAAAACAGTTGCCAAACTTTGCCATTGTGCTCCTGCATTTGTGTTTGAGCTGCTAT 961 ATATTTGTGGAAATTACACTGAAAGTTGACTAAGAGACTATTGAAAAAGCATGAATAATTAAATATACATGTGAGAGACA 1041 TCTCATCTGCTGTATTTTACTTAGTGAATATTGTTCACTCTTCCGTGTCTGATGTCTTGCTGAATGCTGTGACTCATAGT 1121 TTACTTTTGTTCAAAATAGTTTGCACTTTTTGTTAATAAAATCAACTTGAGAAAATAAAAA 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 | MCF7 |
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 SRR1045082. RNA binding protein: AGO2. Condition:Untreated
... - Farazi TA; Ten Hoeve JJ; Brown M; et al., 2014, Genome biology. |
Article |
- Farazi TA; Ten Hoeve JJ; Brown M; et al. - Genome biology, 2014
BACKGROUND: Various microRNAs (miRNAs) are up- or downregulated in tumors. However, the repression of cognate miRNA targets responsible for the phenotypic effects of this dysregulation in patients remains largely unexplored. To define miRNA targets and associated pathways, together with their relationship to outcome in breast cancer, we integrated patient-paired miRNA-mRNA expression data with a set of validated miRNA targets and pathway inference. RESULTS: To generate a biochemically-validated set of miRNA-binding sites, we performed argonaute-2 photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (AGO2-PAR-CLIP) in MCF7 cells. We then defined putative miRNA-target interactions using a computational model, which ranked and selected additional TargetScan-predicted interactions based on features of our AGO2-PAR-CLIP binding-site data. We subselected modeled interactions according to the abundance of their constituent miRNA and mRNA transcripts in tumors, and we took advantage of the variability of miRNA expression within molecular subtypes to detect miRNA repression. Interestingly, our data suggest that miRNA families control subtype-specific pathways; for example, miR-17, miR-19a, miR-25, and miR-200b show high miRNA regulatory activity in the triple-negative, basal-like subtype, whereas miR-22 and miR-24 do so in the HER2 subtype. An independent dataset validated our findings for miR-17 and miR-25, and showed a correlation between the expression levels of miR-182 targets and overall patient survival. Pathway analysis associated miR-17, miR-19a, and miR-200b with leukocyte transendothelial migration. CONCLUSIONS: We combined PAR-CLIP data with patient expression data to predict regulatory miRNAs, revealing potential therapeutic targets and prognostic markers in breast cancer.
LinkOut: [PMID: 24398324]
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CLIP-seq Support 1 for dataset SRR1045082 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | MCF7 / Untreated |
Location of target site | ENST00000262294.7 | 3UTR | CUGAAUGCUGUGACUCAUAGUUUACUUUUGUUCAAAAUAGUUUGCACUUUUUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 24398324 / SRX388831 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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82 hsa-miR-4291 Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT102445 | CALU | calumenin | ![]() |
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2 | 4 | ||||||
MIRT108677 | ZBTB33 | zinc finger and BTB domain containing 33 | ![]() |
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2 | 4 | ||||||
MIRT125969 | SHOC2 | SHOC2, leucine rich repeat scaffold protein | ![]() |
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2 | 6 | ||||||
MIRT179018 | PAFAH1B2 | platelet activating factor acetylhydrolase 1b catalytic subunit 2 | ![]() |
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2 | 4 | ||||||
MIRT379033 | CDK6 | cyclin dependent kinase 6 | ![]() |
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2 | 6 | ||||||
MIRT442473 | CPEB4 | cytoplasmic polyadenylation element binding protein 4 | ![]() |
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2 | 2 | ||||||
MIRT442910 | PCBD2 | pterin-4 alpha-carbinolamine dehydratase 2 | ![]() |
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2 | 2 | ||||||
MIRT442979 | ZNF736 | zinc finger protein 736 | ![]() |
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2 | 2 | ||||||
MIRT445663 | TNFSF15 | TNF superfamily member 15 | ![]() |
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2 | 2 | ||||||
MIRT446237 | FZD6 | frizzled class receptor 6 | ![]() |
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2 | 2 | ||||||
MIRT448860 | FAM49B | family with sequence similarity 49 member B | ![]() |
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2 | 2 | ||||||
MIRT455559 | TRAF1 | TNF receptor associated factor 1 | ![]() |
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2 | 2 | ||||||
MIRT459704 | ZNF641 | zinc finger protein 641 | ![]() |
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2 | 2 | ||||||
MIRT460608 | FEM1A | fem-1 homolog A | ![]() |
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2 | 2 | ||||||
MIRT462251 | LAMA4 | laminin subunit alpha 4 | ![]() |
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2 | 2 | ||||||
MIRT462469 | FIZ1 | FLT3 interacting zinc finger 1 | ![]() |
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2 | 2 | ||||||
MIRT466656 | TAF1D | TATA-box binding protein associated factor, RNA polymerase I subunit D | ![]() |
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2 | 6 | ||||||
MIRT466841 | STX6 | syntaxin 6 | ![]() |
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2 | 2 | ||||||
MIRT471403 | PDP2 | pyruvate dehyrogenase phosphatase catalytic subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT471517 | PCGF3 | polycomb group ring finger 3 | ![]() |
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2 | 2 | ||||||
MIRT471681 | PABPN1 | poly(A) binding protein nuclear 1 | ![]() |
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2 | 2 | ||||||
MIRT472858 | MTHFD2 | methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase | ![]() |
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2 | 2 | ||||||
MIRT474813 | KIAA0226 | RUN and cysteine rich domain containing beclin 1 interacting protein | ![]() |
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2 | 2 | ||||||
MIRT474931 | KCTD15 | potassium channel tetramerization domain containing 15 | ![]() |
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2 | 2 | ||||||
MIRT475814 | HDGF | heparin binding growth factor | ![]() |
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2 | 2 | ||||||
MIRT480434 | C17orf49 | chromosome 17 open reading frame 49 | ![]() |
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2 | 2 | ||||||
MIRT480903 | BCL2L2-PABPN1 | BCL2L2-PABPN1 readthrough | ![]() |
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2 | 2 | ||||||
MIRT481478 | ARL8B | ADP ribosylation factor like GTPase 8B | ![]() |
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2 | 2 | ||||||
MIRT484982 | UBE2V1 | ubiquitin conjugating enzyme E2 V1 | ![]() |
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2 | 8 | ||||||
MIRT485019 | TMEM189-UBE2V1 | TMEM189-UBE2V1 readthrough | ![]() |
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2 | 8 | ||||||
MIRT485036 | TMEM189 | transmembrane protein 189 | ![]() |
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2 | 8 | ||||||
MIRT495074 | HEYL | hes related family bHLH transcription factor with YRPW motif-like | ![]() |
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2 | 2 | ||||||
MIRT496004 | CD180 | CD180 molecule | ![]() |
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2 | 2 | ||||||
MIRT500675 | TRIM37 | tripartite motif containing 37 | ![]() |
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2 | 2 | ||||||
MIRT504544 | ZNF417 | zinc finger protein 417 | ![]() |
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2 | 6 | ||||||
MIRT506782 | KLHL15 | kelch like family member 15 | ![]() |
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2 | 6 | ||||||
MIRT507256 | FGF2 | fibroblast growth factor 2 | ![]() |
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2 | 6 | ||||||
MIRT507386 | EN2 | engrailed homeobox 2 | ![]() |
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2 | 2 | ||||||
MIRT512505 | BTBD19 | BTB domain containing 19 | ![]() |
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2 | 2 | ||||||
MIRT516903 | CTSB | cathepsin B | ![]() |
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2 | 2 | ||||||
MIRT528124 | PPP1R10 | protein phosphatase 1 regulatory subunit 10 | ![]() |
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2 | 2 | ||||||
MIRT528874 | ATF3 | activating transcription factor 3 | ![]() |
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2 | 2 | ||||||
MIRT536091 | MBOAT2 | membrane bound O-acyltransferase domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT541079 | RLIM | ring finger protein, LIM domain interacting | ![]() |
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2 | 2 | ||||||
MIRT541099 | RAF1 | Raf-1 proto-oncogene, serine/threonine kinase | ![]() |
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2 | 2 | ||||||
MIRT545360 | LIN7C | lin-7 homolog C, crumbs cell polarity complex component | ![]() |
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2 | 2 | ||||||
MIRT545831 | ZNF367 | zinc finger protein 367 | ![]() |
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2 | 4 | ||||||
MIRT547115 | PHLPP2 | PH domain and leucine rich repeat protein phosphatase 2 | ![]() |
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2 | 2 | ||||||
MIRT547312 | NPTN | neuroplastin | ![]() |
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2 | 2 | ||||||
MIRT547959 | HIGD1A | HIG1 hypoxia inducible domain family member 1A | ![]() |
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2 | 4 | ||||||
MIRT549943 | RPL7L1 | ribosomal protein L7 like 1 | ![]() |
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2 | 2 | ||||||
MIRT550749 | ENTPD1 | ectonucleoside triphosphate diphosphohydrolase 1 | ![]() |
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2 | 2 | ||||||
MIRT565145 | TUBB2A | tubulin beta 2A class IIa | ![]() |
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2 | 2 | ||||||
MIRT571050 | POLQ | DNA polymerase theta | ![]() |
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2 | 2 | ||||||
MIRT571361 | ZNF45 | zinc finger protein 45 | ![]() |
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2 | 2 | ||||||
MIRT610133 | FOXI2 | forkhead box I2 | ![]() |
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2 | 2 | ||||||
MIRT613145 | DSE | dermatan sulfate epimerase | ![]() |
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2 | 2 | ||||||
MIRT613379 | ABCC12 | ATP binding cassette subfamily C member 12 | ![]() |
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2 | 2 | ||||||
MIRT615752 | C6 | complement C6 | ![]() |
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2 | 2 | ||||||
MIRT616460 | ADRA2B | adrenoceptor alpha 2B | ![]() |
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2 | 2 | ||||||
MIRT616719 | FEM1B | fem-1 homolog B | ![]() |
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2 | 2 | ||||||
MIRT618312 | IPP | intracisternal A particle-promoted polypeptide | ![]() |
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2 | 2 | ||||||
MIRT631491 | RASSF4 | Ras association domain family member 4 | ![]() |
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2 | 2 | ||||||
MIRT643134 | PLCXD2 | phosphatidylinositol specific phospholipase C X domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT643482 | DISC1 | disrupted in schizophrenia 1 | ![]() |
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2 | 2 | ||||||
MIRT649715 | TWSG1 | twisted gastrulation BMP signaling modulator 1 | ![]() |
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2 | 2 | ||||||
MIRT653542 | SLC38A7 | solute carrier family 38 member 7 | ![]() |
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2 | 2 | ||||||
MIRT666307 | SLC22A3 | solute carrier family 22 member 3 | ![]() |
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2 | 2 | ||||||
MIRT692005 | NAP1L4 | nucleosome assembly protein 1 like 4 | ![]() |
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2 | 2 | ||||||
MIRT696838 | ARL2BP | ADP ribosylation factor like GTPase 2 binding protein | ![]() |
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2 | 2 | ||||||
MIRT698204 | TMEM248 | transmembrane protein 248 | ![]() |
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2 | 2 | ||||||
MIRT703316 | GDPD5 | glycerophosphodiester phosphodiesterase domain containing 5 | ![]() |
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2 | 2 | ||||||
MIRT709376 | FAM13A | family with sequence similarity 13 member A | ![]() |
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2 | 2 | ||||||
MIRT710112 | MED23 | mediator complex subunit 23 | ![]() |
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2 | 2 | ||||||
MIRT711975 | HOMER2 | homer scaffolding protein 2 | ![]() |
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2 | 2 | ||||||
MIRT712275 | PPIP5K2 | diphosphoinositol pentakisphosphate kinase 2 | ![]() |
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2 | 2 | ||||||
MIRT714108 | TMED9 | transmembrane p24 trafficking protein 9 | ![]() |
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2 | 2 | ||||||
MIRT719113 | MAML1 | mastermind like transcriptional coactivator 1 | ![]() |
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2 | 2 | ||||||
MIRT719727 | SLC39A11 | solute carrier family 39 member 11 | ![]() |
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2 | 2 | ||||||
MIRT720018 | TFAP2C | transcription factor AP-2 gamma | ![]() |
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2 | 2 | ||||||
MIRT720358 | ZBTB8B | zinc finger and BTB domain containing 8B | ![]() |
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2 | 2 | ||||||
MIRT720372 | NUDT3 | nudix hydrolase 3 | ![]() |
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2 | 2 |
miRNA-Drug Associations | ||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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