pre-miRNA Information | |
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pre-miRNA | hsa-mir-4666a |
Genomic Coordinates | chr1: 228462074 - 228462152 |
Description | Homo sapiens miR-4666a stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | ||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-4666a-5p | |||||||||||||||||||||||||||
Sequence | 10| AUACAUGUCAGAUUGUAUGCC |30 | |||||||||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||||||||
Experiments | Illumina | |||||||||||||||||||||||||||
SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | FKBP9 | ||||||||||||||||||||
Synonyms | FKBP60, FKBP63, PPIase | ||||||||||||||||||||
Description | FK506 binding protein 9 | ||||||||||||||||||||
Transcript | NM_007270 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on FKBP9 | |||||||||||||||||||||
3'UTR of FKBP9 (miRNA target sites are highlighted) |
>FKBP9|NM_007270|3'UTR 1 ACCTGGCATGAACCAGATGGTGCCAGGGAGTACGTGACACCAAGCCACCTGTGTGGCAAGACGTGCAGTGAGGGTGCAAG 81 GGTCTCTCAGAAGTTGCATCATTAGCCAGTAGTAGGTGGGTCACATAGTACCTGGTGTACACATCGGGGTGGGTTGATAT 161 ATGGGGTGAGAAGTTTGGGCTGATCGCCAGTGATAGTAAACAAAATCTGTGCAGAGGGCCTTAGCATGGGATGTGTCCAG 241 TATTGAAAAGGCTGCACTGCCAACCATGATTTGTGAGCCTTCTGGGAAATTTTGTTATTAAAGGAATATATAGTGTCAGA 321 CGGAAGTTATAATCATCTTGGAGGAACCATAAGAAAAGGTGTCCAGGGTATCTATATAAAGAGGGTTAAATTTTTTTTTA 401 ACTTGCTGGTTAAAACATTTTAGAAATATTCTAGAGATGGGCAGGAGAGTCAAAGGGCTTGCTTGCCCCAGCAGAGTTCC 481 CAGCAGACAGCCATGGCTCTTCCCAGCAGCCTGTGCAAATTCTGATGATGGCCCCACCCCCGCACACGCACACGCACATC 561 ATGCTTTTCCAGCTCATCACACCCCGCCCCACTATGGGCCTACCATTAATAGTGTATAACTTGGAGGTTAAAAGAGCCTT 641 TTGGACAGAAAACTGGGCCAGGAAAAGGCATCTCAGACCACAAATAGAGAATTTGATTCCTCATTTGCCACATAAGTCAT 721 CTGCTTAGCTTTTCCTTTCCTTTTTTTTTTTTTTTTTTTTTCTGGAGGCAGAGTCTCCCTTTGTCGCCAGGCTGGAGTGC 801 AGTGGTGCCATCTCGGCTCACTGCAGCACTGTCTCGGCTCACTGCAGCCTCCGCCTCCCGTATTCAAGCGATTCTCCTGT 881 CTCAGCCTCCTGAGTAGCTGGGACTACAGGTGTGCACCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGT 961 TTCACTGTGTTGGCCAGGATGGTCTCAATCTCGACCTCGTGATCCGCCCACCTTGGCCTCCCAAAGTGTTGGGATTACAG 1041 GCGTGACTCACCATGCCCAGCCACTTAGTTTTTTCTTATTCCCACCTTTCTATCCCATAGAACACTCTTTTTTATCTTCC 1121 CTGAACCATATTGATGAGATAAATAGGGCTGGGGGCTGGGCCCCGCTGGTCACTCAACAGAGTATTTCCCTTGGCCGAGA 1201 TGGAAGTTTTGTCCCAATAGATGAGCTGCTGAGCATCAACAAGGTGACATTTTTCTGCTGCCCATTTGTGTCCTGGAGAC 1281 GGTGGTACCCTGAAGGCAGAGGCCAGCTGCCGCAAGACAGCAATGACAGTCCACCTGCCGACCTGATTCCTGCATCATGG 1361 AATAACCACATGGCTACCTTCTATCCTCTGTTCCCAAATGGTGGTGGCACTTATCCTGAAGTCGTCAATGATTTCCCTTT 1441 GAAACTACTTTATTTTACTAATTTAAACTATTTTGTACTGATGTAGCCCTGAGGTAGTTCATGAAAATGCTGTGCACTCA 1521 TTCCATGGAATAAATGTTGGAAAGCTGATCTTTTCTGATATAAAATGTTGAATGATATTAAAAAAAAAAAAAAAAAA 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 | HEK293S | ||||||
Location of target site | 3'UTR | ||||||
Tools used in this research | TargetScan , miRTarCLIP , Piranha | ||||||
Original Description (Extracted from the article) |
...
HITS-CLIP data was present in GSM1084068. RNA binding protein: AGO2. Condition:CLIP_noemetine_SigmaAb
HITS-CLIP data was present in GSM1084073. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep1_AbnovaAb
... - Karginov FV; Hannon GJ, 2013, Genes & development. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Karginov FV; Hannon GJ - Genes & development, 2013
When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Argonaute 2 (Ago2)/microRNA (miRNA) machinery has been shown to participate in stress-induced translational up-regulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (UTR) and coding sequence (CDS) sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2-binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA sequencing (RNA-seq). Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian miRNAs in mediating the translational component of the stress response.
LinkOut: [PMID: 23824327]
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CLIP-seq Support 1 for dataset GSM1084068 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_noemetine_SigmaAb |
Location of target site | ENST00000242209.4 | 3UTR | CAUGUAUAGAGAAACUGUGUGUGUGUGUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM1084073 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_hippuristanol_rep1_AbnovaAb |
Location of target site | ENST00000242209.4 | 3UTR | UAUAGAGAAACUGUGUGUGUGUGUGGU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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83 hsa-miR-4666a-5p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT057266 | FAM35A | family with sequence similarity 35 member A | ![]() |
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2 | 2 | ||||||
MIRT059969 | PATL1 | PAT1 homolog 1, processing body mRNA decay factor | ![]() |
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2 | 6 | ||||||
MIRT079031 | TNRC6C | trinucleotide repeat containing 6C | ![]() |
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2 | 2 | ||||||
MIRT079631 | DNAJB4 | DnaJ heat shock protein family (Hsp40) member B4 | ![]() |
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2 | 2 | ||||||
MIRT086974 | LANCL1 | LanC like 1 | ![]() |
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2 | 2 | ||||||
MIRT091804 | GOLGA4 | golgin A4 | ![]() |
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2 | 2 | ||||||
MIRT229501 | EIF1AX | eukaryotic translation initiation factor 1A, X-linked | ![]() |
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2 | 4 | ||||||
MIRT255972 | WDR17 | WD repeat domain 17 | ![]() |
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2 | 2 | ||||||
MIRT262975 | ADO | 2-aminoethanethiol dioxygenase | ![]() |
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2 | 2 | ||||||
MIRT264774 | PAFAH1B2 | platelet activating factor acetylhydrolase 1b catalytic subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT334169 | CCND1 | cyclin D1 | ![]() |
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2 | 6 | ||||||
MIRT345868 | SRSF2 | serine and arginine rich splicing factor 2 | ![]() |
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2 | 2 | ||||||
MIRT452477 | DDX4 | DEAD-box helicase 4 | ![]() |
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2 | 2 | ||||||
MIRT455764 | TSPAN6 | tetraspanin 6 | ![]() |
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2 | 4 | ||||||
MIRT461627 | DCAF15 | DDB1 and CUL4 associated factor 15 | ![]() |
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2 | 4 | ||||||
MIRT465169 | TRPV2 | transient receptor potential cation channel subfamily V member 2 | ![]() |
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2 | 4 | ||||||
MIRT468950 | RPS14 | ribosomal protein S14 | ![]() |
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2 | 6 | ||||||
MIRT483236 | C2orf72 | chromosome 2 open reading frame 72 | ![]() |
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2 | 8 | ||||||
MIRT498544 | TMEM30B | transmembrane protein 30B | ![]() |
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2 | 2 | ||||||
MIRT500633 | TXNIP | thioredoxin interacting protein | ![]() |
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2 | 4 | ||||||
MIRT504113 | GPR158 | G protein-coupled receptor 158 | ![]() |
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2 | 2 | ||||||
MIRT504428 | ZNF85 | zinc finger protein 85 | ![]() |
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2 | 6 | ||||||
MIRT505036 | ZNF451 | zinc finger protein 451 | ![]() |
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2 | 2 | ||||||
MIRT506526 | MRPL17 | mitochondrial ribosomal protein L17 | ![]() |
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2 | 6 | ||||||
MIRT508773 | GSG1 | germ cell associated 1 | ![]() |
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2 | 2 | ||||||
MIRT517297 | ELF4 | E74 like ETS transcription factor 4 | ![]() |
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2 | 6 | ||||||
MIRT519353 | OBFC1 | STN1, CST complex subunit | ![]() |
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2 | 4 | ||||||
MIRT523891 | ENPP6 | ectonucleotide pyrophosphatase/phosphodiesterase 6 | ![]() |
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2 | 6 | ||||||
MIRT527509 | ZNF134 | zinc finger protein 134 | ![]() |
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2 | 2 | ||||||
MIRT531218 | IFNGR2 | interferon gamma receptor 2 | ![]() |
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2 | 2 | ||||||
MIRT535957 | MOGAT1 | monoacylglycerol O-acyltransferase 1 | ![]() |
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2 | 2 | ||||||
MIRT537229 | GALNT7 | polypeptide N-acetylgalactosaminyltransferase 7 | ![]() |
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2 | 4 | ||||||
MIRT537337 | FKBP5 | FK506 binding protein 5 | ![]() |
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2 | 2 | ||||||
MIRT539125 | ARHGEF17 | Rho guanine nucleotide exchange factor 17 | ![]() |
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2 | 2 | ||||||
MIRT539910 | ISPD | isoprenoid synthase domain containing | ![]() |
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2 | 2 | ||||||
MIRT541527 | MGAT4C | MGAT4 family member C | ![]() |
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2 | 2 | ||||||
MIRT546119 | USP25 | ubiquitin specific peptidase 25 | ![]() |
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2 | 2 | ||||||
MIRT548846 | CERCAM | cerebral endothelial cell adhesion molecule | ![]() |
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2 | 2 | ||||||
MIRT549892 | LINC00955 | long intergenic non-protein coding RNA 955 | ![]() |
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2 | 2 | ||||||
MIRT549898 | ADH4 | alcohol dehydrogenase 4 (class II), pi polypeptide | ![]() |
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2 | 2 | ||||||
MIRT550763 | ENOX2 | ecto-NOX disulfide-thiol exchanger 2 | ![]() |
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2 | 4 | ||||||
MIRT553200 | UBE2A | ubiquitin conjugating enzyme E2 A | ![]() |
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2 | 2 | ||||||
MIRT553970 | SRSF10 | serine and arginine rich splicing factor 10 | ![]() |
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2 | 2 | ||||||
MIRT554092 | SMU1 | DNA replication regulator and spliceosomal factor | ![]() |
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2 | 2 | ||||||
MIRT555208 | PROX1 | prospero homeobox 1 | ![]() |
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2 | 4 | ||||||
MIRT555834 | PAX5 | paired box 5 | ![]() |
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2 | 4 | ||||||
MIRT556865 | JAZF1 | JAZF zinc finger 1 | ![]() |
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2 | 2 | ||||||
MIRT558594 | CREBL2 | cAMP responsive element binding protein like 2 | ![]() |
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2 | 2 | ||||||
MIRT559690 | AGO2 | argonaute 2, RISC catalytic component | ![]() |
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2 | 4 | ||||||
MIRT563312 | ORC4 | origin recognition complex subunit 4 | ![]() |
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2 | 2 | ||||||
MIRT563585 | FAM229B | family with sequence similarity 229 member B | ![]() |
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2 | 2 | ||||||
MIRT563853 | ALYREF | Aly/REF export factor | ![]() |
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2 | 4 | ||||||
MIRT565146 | TUBB2A | tubulin beta 2A class IIa | ![]() |
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2 | 2 | ||||||
MIRT565769 | SEPHS1 | selenophosphate synthetase 1 | ![]() |
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2 | 2 | ||||||
MIRT568317 | BACH1 | BTB domain and CNC homolog 1 | ![]() |
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2 | 2 | ||||||
MIRT575387 | Unc5b | unc-5 netrin receptor B | ![]() |
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2 | 4 | ||||||
MIRT607728 | BDH1 | 3-hydroxybutyrate dehydrogenase 1 | ![]() |
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2 | 8 | ||||||
MIRT612691 | PLXNA4 | plexin A4 | ![]() |
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2 | 4 | ||||||
MIRT615916 | GDPD1 | glycerophosphodiester phosphodiesterase domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT629792 | P2RY1 | purinergic receptor P2Y1 | ![]() |
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2 | 2 | ||||||
MIRT632119 | FKBP9 | FK506 binding protein 9 | ![]() |
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2 | 2 | ||||||
MIRT645554 | ZDHHC15 | zinc finger DHHC-type containing 15 | ![]() |
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2 | 4 | ||||||
MIRT651479 | WWC3 | WWC family member 3 | ![]() |
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2 | 2 | ||||||
MIRT654138 | RPH3A | rabphilin 3A | ![]() |
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2 | 6 | ||||||
MIRT655191 | PHAX | phosphorylated adaptor for RNA export | ![]() |
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2 | 2 | ||||||
MIRT665543 | UNC5B | unc-5 netrin receptor B | ![]() |
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2 | 5 | ||||||
MIRT668057 | GRIK3 | glutamate ionotropic receptor kainate type subunit 3 | ![]() |
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2 | 2 | ||||||
MIRT678978 | CERS4 | ceramide synthase 4 | ![]() |
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2 | 4 | ||||||
MIRT679124 | RBM3 | RNA binding motif (RNP1, RRM) protein 3 | ![]() |
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2 | 2 | ||||||
MIRT686776 | AZF1 | azoospermia factor 1 | ![]() |
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2 | 2 | ||||||
MIRT687144 | PTPN12 | protein tyrosine phosphatase, non-receptor type 12 | ![]() |
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2 | 2 | ||||||
MIRT691453 | C21orf58 | chromosome 21 open reading frame 58 | ![]() |
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2 | 2 | ||||||
MIRT691469 | FAM98B | family with sequence similarity 98 member B | ![]() |
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2 | 2 | ||||||
MIRT697031 | UHRF1BP1 | UHRF1 binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT698401 | TM9SF3 | transmembrane 9 superfamily member 3 | ![]() |
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2 | 2 | ||||||
MIRT702056 | RNMT | RNA guanine-7 methyltransferase | ![]() |
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2 | 2 | ||||||
MIRT705903 | ADAM9 | ADAM metallopeptidase domain 9 | ![]() |
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2 | 2 | ||||||
MIRT707491 | MMADHC | methylmalonic aciduria and homocystinuria, cblD type | ![]() |
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2 | 2 | ||||||
MIRT708080 | KLHL23 | kelch like family member 23 | ![]() |
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2 | 2 | ||||||
MIRT709738 | TRIM27 | tripartite motif containing 27 | ![]() |
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2 | 2 | ||||||
MIRT710056 | RWDD2A | RWD domain containing 2A | ![]() |
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2 | 2 | ||||||
MIRT710226 | KCNK1 | potassium two pore domain channel subfamily K member 1 | ![]() |
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2 | 2 | ||||||
MIRT712043 | STYK1 | serine/threonine/tyrosine kinase 1 | ![]() |
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2 | 2 |