pre-miRNA Information | |
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pre-miRNA | hsa-mir-4301 |
Genomic Coordinates | chr11: 113450023 - 113450088 |
Description | Homo sapiens miR-4301 stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | |||||||||||||||||||
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Mature miRNA | hsa-miR-4301 | ||||||||||||||||||
Sequence | 11| UCCCACUACUUCACUUGUGA |30 | ||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||
Experiments | SOLiD | ||||||||||||||||||
SNPs in miRNA |
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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 | OSBPL1A | ||||||||||||||||||||
Synonyms | ORP-1, ORP1, OSBPL1B | ||||||||||||||||||||
Description | oxysterol binding protein like 1A | ||||||||||||||||||||
Transcript | NM_018030 | ||||||||||||||||||||
Other Transcripts | NM_080597 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on OSBPL1A | |||||||||||||||||||||
3'UTR of OSBPL1A (miRNA target sites are highlighted) |
>OSBPL1A|NM_018030|3'UTR 1 AATGCATACAAGTCAGGGTGTTTGGCTAATCTACAAATAAGTCTTAAACCTATGTTTTTAAATTTTTTTCCCTTGGTTTC 81 TACTTATCTTTTAAAAAAAAAAATGAAAAAACACTCATGAGATAACTGCATTTCACCCAACAAAAGCAGGGTATAAGGCG 161 ATATTGGTGATGAAAGTCTTAGGAAAAATGCATAATTTTGCTATAAAATGTACTTATTTGGAATACTATTTTATATAGAG 241 GTAAGAGAACACTGCTGGGGAATATGCTTTTTATGGTTGCTGTTGCCATATTTACTGAAGGTTTATACCTAAATGTAACT 321 TTAGCTTTATGGAACTATATAGTAATCCCAAATCAAGTTATTTTGAATATTTTTATGCTGTCATGCTTGAATGTTTTAGA 401 TGTAACCTTTGACATATTTAGAACTCTCCTCCTATACAATGTTTATTCTCAGATATAGAGGTTATGTCATTTTATAAAGA 481 CTTCATTGATAAGATGGCTTTTATTCATACTAATCCTCCCAATGTTACCCCTTCCATCTTCCAAGAAGAAAAAAAATGCC 561 TGAATATTCAGAATAGATATTTCTGATTTGAAAATTCTAAAGAATTAAACTGGAAAAGTATTTCATTTACTTAGTGCTCT 641 GAATTTACTTTTACAGTTTTCTGCAGTCAGTATCATTAAAATGGTTAAGTTTACATTTGAACTGAAAATATGTATAAAAT 721 CTAGCAATTCACAAAAATGCCCTAGAAATATAGATTTTAATCACCATTACATAATGACAAACCTTGTTAAATGCTTCCAC 801 TTCCAGTGGCAAATGCCACTAGGGAAAGTAAGTTGCACTCATGTAAGTATCAAACTATATAAAAGGAGGCCTTGTGCATT 881 TCAAGTTTGCAAAGTACCTGTGTACTTAAAATATGTGTGGAGACCTACTGTACAGTAGTTTTGCCCCTTTAATTGGGGCA 961 CATTCATCTTAAATCTTATAGTATTTATCCACCCAAACCCCAGACTGAGATACTGCTCCCAGGGGCCTAGGTAGCTGCCA 1041 GTCCGTGATTTTAATTGCTGTCTTGAAGTTAACAAGTGTTATAATGAAATAATCTACCTGATGCTAAATAAAGGCTTTAG 1121 AATGTTCCCCAAAAAAAAAAAAAAAAAAAAAAAA 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 | 114876.0 | ||||||
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 GSM714645. 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 GSM714645 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / completeT1, repB |
Location of target site | ENST00000319481.3 | 3UTR | AGUGGGAAUAGUUUAAAAA |
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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83 hsa-miR-4301 Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT081134 | LDLR | low density lipoprotein receptor | 2 | 4 | ||||||||
MIRT090911 | ARHGEF26 | Rho guanine nucleotide exchange factor 26 | 2 | 2 | ||||||||
MIRT229436 | MECP2 | methyl-CpG binding protein 2 | 2 | 2 | ||||||||
MIRT274717 | CPSF6 | cleavage and polyadenylation specific factor 6 | 2 | 2 | ||||||||
MIRT350957 | BACH1 | BTB domain and CNC homolog 1 | 2 | 2 | ||||||||
MIRT386722 | NUFIP2 | NUFIP2, FMR1 interacting protein 2 | 2 | 2 | ||||||||
MIRT446022 | PEX3 | peroxisomal biogenesis factor 3 | 2 | 2 | ||||||||
MIRT481303 | ATP5G3 | ATP synthase, H+ transporting, mitochondrial Fo complex subunit C3 (subunit 9) | 2 | 14 | ||||||||
MIRT483959 | ZNF354B | zinc finger protein 354B | 2 | 6 | ||||||||
MIRT495667 | TUBAL3 | tubulin alpha like 3 | 2 | 2 | ||||||||
MIRT496554 | TBX15 | T-box 15 | 2 | 2 | ||||||||
MIRT497702 | ARL6IP6 | ADP ribosylation factor like GTPase 6 interacting protein 6 | 2 | 2 | ||||||||
MIRT498105 | RMND5A | required for meiotic nuclear division 5 homolog A | 2 | 2 | ||||||||
MIRT512535 | SEMA4D | semaphorin 4D | 2 | 2 | ||||||||
MIRT512556 | MFN2 | mitofusin 2 | 2 | 6 | ||||||||
MIRT521465 | RABGAP1 | RAB GTPase activating protein 1 | 2 | 6 | ||||||||
MIRT526236 | C2orf15 | chromosome 2 open reading frame 15 | 2 | 2 | ||||||||
MIRT526743 | HLA-DOB | major histocompatibility complex, class II, DO beta | 2 | 2 | ||||||||
MIRT527578 | BRD7 | bromodomain containing 7 | 2 | 4 | ||||||||
MIRT528038 | WT1 | Wilms tumor 1 | 2 | 2 | ||||||||
MIRT528267 | GPRIN2 | G protein regulated inducer of neurite outgrowth 2 | 2 | 2 | ||||||||
MIRT528505 | HTR7 | 5-hydroxytryptamine receptor 7 | 2 | 4 | ||||||||
MIRT528758 | RPS27 | ribosomal protein S27 | 2 | 6 | ||||||||
MIRT528999 | IPO9 | importin 9 | 2 | 2 | ||||||||
MIRT529701 | MRPL30 | mitochondrial ribosomal protein L30 | 2 | 2 | ||||||||
MIRT529781 | C17orf82 | chromosome 17 open reading frame 82 | 2 | 2 | ||||||||
MIRT533797 | TMEM119 | transmembrane protein 119 | 2 | 6 | ||||||||
MIRT535308 | PHF12 | PHD finger protein 12 | 2 | 2 | ||||||||
MIRT535917 | MKL2 | MKL1/myocardin like 2 | 2 | 2 | ||||||||
MIRT544892 | OSBPL1A | oxysterol binding protein like 1A | 2 | 2 | ||||||||
MIRT555423 | PPIC | peptidylprolyl isomerase C | 2 | 2 | ||||||||
MIRT562068 | KLHL15 | kelch like family member 15 | 2 | 2 | ||||||||
MIRT565623 | SLC31A1 | solute carrier family 31 member 1 | 2 | 2 | ||||||||
MIRT565661 | SIX1 | SIX homeobox 1 | 2 | 2 | ||||||||
MIRT570138 | IL1RL2 | interleukin 1 receptor like 2 | 2 | 2 | ||||||||
MIRT571045 | YRDC | yrdC N6-threonylcarbamoyltransferase domain containing | 2 | 2 | ||||||||
MIRT621232 | LMAN1 | lectin, mannose binding 1 | 2 | 2 | ||||||||
MIRT622272 | SH3TC2 | SH3 domain and tetratricopeptide repeats 2 | 2 | 2 | ||||||||
MIRT623844 | GAN | gigaxonin | 2 | 2 | ||||||||
MIRT626158 | NFYA | nuclear transcription factor Y subunit alpha | 2 | 2 | ||||||||
MIRT626464 | CMKLR1 | chemerin chemokine-like receptor 1 | 2 | 2 | ||||||||
MIRT632087 | ALDH1A2 | aldehyde dehydrogenase 1 family member A2 | 2 | 2 | ||||||||
MIRT637243 | FAM26E | calcium homeostasis modulator family member 5 | 2 | 2 | ||||||||
MIRT642710 | FGFR1OP2 | FGFR1 oncogene partner 2 | 2 | 2 | ||||||||
MIRT643611 | KANSL3 | KAT8 regulatory NSL complex subunit 3 | 2 | 2 | ||||||||
MIRT644270 | PAFAH1B1 | platelet activating factor acetylhydrolase 1b regulatory subunit 1 | 2 | 2 | ||||||||
MIRT645470 | SPIN3 | spindlin family member 3 | 2 | 2 | ||||||||
MIRT649193 | DNPEP | aspartyl aminopeptidase | 2 | 2 | ||||||||
MIRT650776 | POP4 | POP4 homolog, ribonuclease P/MRP subunit | 2 | 2 | ||||||||
MIRT651345 | ZC2HC1C | zinc finger C2HC-type containing 1C | 2 | 2 | ||||||||
MIRT652237 | TRAPPC3L | trafficking protein particle complex 3 like | 2 | 2 | ||||||||
MIRT652587 | TIMM8A | translocase of inner mitochondrial membrane 8A | 2 | 2 | ||||||||
MIRT654591 | PURA | purine rich element binding protein A | 2 | 2 | ||||||||
MIRT654649 | PTAFR | platelet activating factor receptor | 2 | 2 | ||||||||
MIRT656842 | KLF7 | Kruppel like factor 7 | 2 | 2 | ||||||||
MIRT657209 | IKZF2 | IKAROS family zinc finger 2 | 2 | 2 | ||||||||
MIRT658513 | ETV3 | ETS variant 3 | 2 | 2 | ||||||||
MIRT659448 | CNNM2 | cyclin and CBS domain divalent metal cation transport mediator 2 | 2 | 2 | ||||||||
MIRT668816 | CYLD | CYLD lysine 63 deubiquitinase | 2 | 2 | ||||||||
MIRT669067 | CELSR3 | cadherin EGF LAG seven-pass G-type receptor 3 | 2 | 2 | ||||||||
MIRT677711 | ELOF1 | elongation factor 1 homolog | 2 | 4 | ||||||||
MIRT687146 | PTPN12 | protein tyrosine phosphatase, non-receptor type 12 | 2 | 2 | ||||||||
MIRT698498 | THOC2 | THO complex 2 | 2 | 2 | ||||||||
MIRT707930 | PPP1R3D | protein phosphatase 1 regulatory subunit 3D | 4 | 2 | ||||||||
MIRT708737 | FAM71F2 | family with sequence similarity 71 member F2 | 2 | 2 | ||||||||
MIRT710031 | POLL | DNA polymerase lambda | 2 | 2 | ||||||||
MIRT712175 | STK4 | serine/threonine kinase 4 | 2 | 2 | ||||||||
MIRT715297 | MAPK1 | mitogen-activated protein kinase 1 | 2 | 2 | ||||||||
MIRT716892 | AGPAT6 | glycerol-3-phosphate acyltransferase 4 | 2 | 2 | ||||||||
MIRT717378 | RBM41 | RNA binding motif protein 41 | 2 | 2 | ||||||||
MIRT718082 | CLIC5 | chloride intracellular channel 5 | 2 | 2 | ||||||||
MIRT718721 | ANKRD18A | ankyrin repeat domain 18A | 2 | 2 | ||||||||
MIRT719152 | DPYSL5 | dihydropyrimidinase like 5 | 2 | 2 | ||||||||
MIRT719224 | CAMK4 | calcium/calmodulin dependent protein kinase IV | 2 | 2 | ||||||||
MIRT719528 | SRCIN1 | SRC kinase signaling inhibitor 1 | 2 | 2 | ||||||||
MIRT719861 | KLF2 | Kruppel like factor 2 | 2 | 2 | ||||||||
MIRT720326 | CAMK2G | calcium/calmodulin dependent protein kinase II gamma | 2 | 2 | ||||||||
MIRT721596 | SREBF1 | sterol regulatory element binding transcription factor 1 | 2 | 2 | ||||||||
MIRT722020 | NEBL | nebulette | 2 | 2 | ||||||||
MIRT722484 | QSOX1 | quiescin sulfhydryl oxidase 1 | 2 | 2 | ||||||||
MIRT722614 | TEAD1 | TEA domain transcription factor 1 | 2 | 2 | ||||||||
MIRT723664 | RPTN | repetin | 2 | 2 | ||||||||
MIRT723939 | SVOP | SV2 related protein | 2 | 2 |
miRNA-Drug Associations | ||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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