pre-miRNA Information | |
---|---|
pre-miRNA | hsa-mir-4742 |
Genomic Coordinates | chr1: 224398227 - 224398311 |
Description | Homo sapiens miR-4742 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Mature miRNA | hsa-miR-4742-5p | ||||||||||||||||||||||||
Sequence | 1| UCAGGCAAAGGGAUAUUUACAGA |23 | ||||||||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||||||||
Experiments | Illumina | ||||||||||||||||||||||||
SNPs in miRNA |
|
||||||||||||||||||||||||
Putative Targets |
Gene Information | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene Symbol | LRRC40 | ||||||||||||||||||||
Synonyms | dJ677H15.1 | ||||||||||||||||||||
Description | leucine rich repeat containing 40 | ||||||||||||||||||||
Transcript | NM_017768 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on LRRC40 | |||||||||||||||||||||
3'UTR of LRRC40 (miRNA target sites are highlighted) |
>LRRC40|NM_017768|3'UTR 1 CATGGAGTTGCTTTATAACCCTTGTCATGTATTATTAACCCTGGTTAATTCTAAGGAGGATGTAACATTTGTTTTAGTAT 81 CATCTTAAAAGGTGATTATTGTAATTGATCTTGTAGTTTCCCAGTATCACCTACCTGTTGGTATAATTAGCCTGGGCCAT 161 ATTCACTGCCAGTAAATATTTTTACATTTTTATTTAAGATTTTTGTAAGGTGTTGTATACATTTGTAATGGTGATAACCA 241 CAATGTGTTCATACATTTGTTCTAAATGTTTTGCTTATGATTTATCCTGCTAACTTTCATTTTCTTATAGCAAGCAGTTT 321 TTTCAAAAATGAATTTTTATTTAATGTGGTTCAGTATTATAATAACAAAGCATTTTTGTAGAACTGGTTTTTTTTCTCAT 401 TTATTTTTGTATTCCATACAATGTGACCAATTGACTTGAATATGACTAGCCAGTTTCTATGTTTTTGTTAGATATAAAAT 481 TAAATCGAATTTTGTTGAATACTGTTCTTTGGCATTTAAAAAATAAGACCTTCTTATCTTGGGCCACATGTCAAAAGAAA 561 AAGGAAACAAAAATATATTAAAAATAAGACTTTTCATTACCCATGATAGGACTTTTGTGATATGGCTAATCTCAGTACAC 641 ATTTCAACTTAAAACCTTTTTATTTACAGCACCATAATTTTAAAATTTACTTGCAATCTTGGTAAGACTAAACTTGCAGT 721 GTTTTTCTAAAAGGGAATTTGATAGGTAAACTTGATTTAATAAAAATTAAATATCATTTTTGTTTACACCAAAATTATCA 801 GAAGTAGGTTGATTAGTCATTATAACACTTACCATATGATTCTATTAAGAAGTCAATTCAGTAGCATGTATATCAATTTA 881 TATAGATAGGTAGATAGCTTTTGGATGATTGAGGCATGCTTATATTATGAAAAAAATTGCTAATAAAGATAAATACTACA 961 TGTTCAGAATAAAAGTTACATTTTTCAAATATTGATTAAAAAAAAAAAAAA Target sites
Provided by authors
Predicted by miRanda
DRVs
SNPs
DRVs & SNPs
|
||||||||||||||||||||
miRNA-target interactions (Predicted by miRanda) |
|
||||||||||||||||||||
DRVs in gene 3'UTRs | |||||||||||||||||||||
SNPs in gene 3'UTRs |
Experimental Support 1 for Functional miRNA-Target Interaction | |
---|---|
miRNA:Target | ---- |
Validation Method |
|
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 GSM1084067. RNA binding protein: AGO2. Condition:CLIP_emetine_SantaCruzAb
HITS-CLIP data was present in GSM1084082. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep2_SigmaAb
... - Karginov FV; Hannon GJ, 2013, Genes & development. |
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]
|
CLIP-seq Support 1 for dataset GSM1084067 | |
---|---|
Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_emetine_SantaCruzAb |
Location of target site | ENST00000370952.3 | 3UTR | GCAAAAAAAAAAAAAAUU |
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 GSM1084082 | |
---|---|
Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_nohippuristanol_rep2_SigmaAb |
Location of target site | ENST00000370952.3 | 3UTR | AAAUGCAAAAAAAAAAAAAAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
---|---|---|---|---|---|---|---|
|
MiRNA-Target Expression Profile (TCGA) | |||||||
---|---|---|---|---|---|---|---|
|
70 hsa-miR-4742-5p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
![]() |
![]() |
|||||||
Strong evidence | Less strong evidence | |||||||||||
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
|||||
MIRT065632 | CLIC4 | chloride intracellular channel 4 | ![]() |
![]() |
2 | 4 | ||||||
MIRT068170 | TXLNA | taxilin alpha | ![]() |
![]() |
2 | 2 | ||||||
MIRT119024 | TSN | translin | ![]() |
![]() |
2 | 2 | ||||||
MIRT165212 | GRAMD3 | GRAM domain containing 2B | ![]() |
![]() |
2 | 2 | ||||||
MIRT175254 | PSAT1 | phosphoserine aminotransferase 1 | ![]() |
![]() |
2 | 4 | ||||||
MIRT213228 | REST | RE1 silencing transcription factor | ![]() |
![]() |
2 | 6 | ||||||
MIRT296337 | PARD6B | par-6 family cell polarity regulator beta | ![]() |
![]() |
2 | 2 | ||||||
MIRT316776 | FOXC1 | forkhead box C1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT453943 | XRCC6 | X-ray repair cross complementing 6 | ![]() |
![]() |
2 | 6 | ||||||
MIRT454599 | RPL13A | ribosomal protein L13a | ![]() |
![]() |
2 | 2 | ||||||
MIRT458485 | RMI1 | RecQ mediated genome instability 1 | ![]() |
![]() |
2 | 6 | ||||||
MIRT458650 | SGPP2 | sphingosine-1-phosphate phosphatase 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT459240 | ADRBK1 | G protein-coupled receptor kinase 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT461008 | SYT7 | synaptotagmin 7 | ![]() |
![]() |
2 | 2 | ||||||
MIRT462026 | RIF1 | replication timing regulatory factor 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT462103 | TMEM214 | transmembrane protein 214 | ![]() |
![]() |
2 | 2 | ||||||
MIRT463255 | ZIC5 | Zic family member 5 | ![]() |
![]() |
2 | 4 | ||||||
MIRT465190 | TRPS1 | transcriptional repressor GATA binding 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT470507 | PPP1R11 | protein phosphatase 1 regulatory inhibitor subunit 11 | ![]() |
![]() |
2 | 2 | ||||||
MIRT472356 | TSPAN1 | tetraspanin 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT473260 | MIDN | midnolin | ![]() |
![]() |
2 | 2 | ||||||
MIRT477527 | EIF4G2 | eukaryotic translation initiation factor 4 gamma 2 | ![]() |
![]() |
2 | 4 | ||||||
MIRT485182 | PTP4A1 | protein tyrosine phosphatase type IVA, member 1 | ![]() |
![]() |
2 | 4 | ||||||
MIRT486461 | MDM2 | MDM2 proto-oncogene | ![]() |
![]() |
2 | 2 | ||||||
MIRT492760 | PER1 | period circadian clock 1 | ![]() |
![]() |
2 | 8 | ||||||
MIRT496703 | TRIM39 | tripartite motif containing 39 | ![]() |
![]() |
2 | 2 | ||||||
MIRT497227 | MORC2 | MORC family CW-type zinc finger 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT499582 | INTU | inturned planar cell polarity protein | ![]() |
![]() |
2 | 4 | ||||||
MIRT504081 | C9orf40 | chromosome 9 open reading frame 40 | ![]() |
![]() |
2 | 6 | ||||||
MIRT505484 | SRSF2 | serine and arginine rich splicing factor 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT513255 | FBXO17 | F-box protein 17 | ![]() |
![]() |
2 | 2 | ||||||
MIRT525061 | FRK | fyn related Src family tyrosine kinase | ![]() |
![]() |
2 | 2 | ||||||
MIRT528798 | RAB32 | RAB32, member RAS oncogene family | ![]() |
![]() |
2 | 2 | ||||||
MIRT534357 | SFT2D2 | SFT2 domain containing 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT538731 | CAPN1 | calpain 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT550792 | WARS2 | tryptophanyl tRNA synthetase 2, mitochondrial | ![]() |
![]() |
2 | 2 | ||||||
MIRT553994 | SRPR | SRP receptor alpha subunit | ![]() |
![]() |
2 | 4 | ||||||
MIRT568102 | CDKN1B | cyclin dependent kinase inhibitor 1B | ![]() |
![]() |
2 | 2 | ||||||
MIRT570107 | SLC18B1 | solute carrier family 18 member B1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT570823 | RPL7L1 | ribosomal protein L7 like 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT572004 | HMGB1 | high mobility group box 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT572352 | PCYT2 | phosphate cytidylyltransferase 2, ethanolamine | ![]() |
![]() |
2 | 2 | ||||||
MIRT609716 | TMEM132C | transmembrane protein 132C | ![]() |
![]() |
2 | 2 | ||||||
MIRT613982 | LRRC40 | leucine rich repeat containing 40 | ![]() |
![]() |
2 | 2 | ||||||
MIRT620740 | CCL16 | C-C motif chemokine ligand 16 | ![]() |
![]() |
2 | 2 | ||||||
MIRT625074 | C15orf41 | chromosome 15 open reading frame 41 | ![]() |
![]() |
2 | 4 | ||||||
MIRT627941 | NNT | nicotinamide nucleotide transhydrogenase | ![]() |
![]() |
2 | 2 | ||||||
MIRT629941 | IGSF6 | immunoglobulin superfamily member 6 | ![]() |
![]() |
2 | 2 | ||||||
MIRT633396 | FBXW8 | F-box and WD repeat domain containing 8 | ![]() |
![]() |
2 | 2 | ||||||
MIRT635846 | ZNF264 | zinc finger protein 264 | ![]() |
![]() |
2 | 2 | ||||||
MIRT638086 | ZNF652 | zinc finger protein 652 | ![]() |
![]() |
2 | 2 | ||||||
MIRT643996 | TCHP | trichoplein keratin filament binding | ![]() |
![]() |
2 | 2 | ||||||
MIRT660020 | C1GALT1 | core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT660161 | BRCC3 | BRCA1/BRCA2-containing complex subunit 3 | ![]() |
![]() |
2 | 2 | ||||||
MIRT668887 | CSRP1 | cysteine and glycine rich protein 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT676729 | METTL14 | methyltransferase like 14 | ![]() |
![]() |
2 | 2 | ||||||
MIRT677210 | MURC | caveolae associated protein 4 | ![]() |
![]() |
2 | 2 | ||||||
MIRT685949 | PTGIS | prostaglandin I2 synthase | ![]() |
![]() |
2 | 2 | ||||||
MIRT687816 | ITPRIPL2 | inositol 1,4,5-trisphosphate receptor interacting protein like 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT689900 | SOD2 | superoxide dismutase 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT698214 | TMEM248 | transmembrane protein 248 | ![]() |
![]() |
2 | 2 | ||||||
MIRT698279 | TMEM2 | transmembrane protein 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT698758 | STK4 | serine/threonine kinase 4 | ![]() |
![]() |
2 | 2 | ||||||
MIRT698789 | STK38 | serine/threonine kinase 38 | ![]() |
![]() |
2 | 2 | ||||||
MIRT703152 | GPR137C | G protein-coupled receptor 137C | ![]() |
![]() |
2 | 2 | ||||||
MIRT704408 | CTPS1 | CTP synthase 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT705067 | C4orf32 | family with sequence similarity 241 member A | ![]() |
![]() |
2 | 2 | ||||||
MIRT710201 | FLVCR1 | feline leukemia virus subgroup C cellular receptor 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT714495 | HSPA4 | heat shock protein family A (Hsp70) member 4 | ![]() |
![]() |
2 | 2 | ||||||
MIRT720082 | TNRC6B | trinucleotide repeat containing 6B | ![]() |
![]() |
2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|