pre-miRNA Information | |
---|---|
pre-miRNA | hsa-mir-6509 |
Genomic Coordinates | chr7: 135206994 - 135207078 |
Description | Homo sapiens miR-6509 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | ||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Mature miRNA | hsa-miR-6509-3p | |||||||||||||||||||||||||||||||||
Sequence | 52| UUCCACUGCCACUACCUAAUUU |73 | |||||||||||||||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||||||||||||||
Experiments | Illumina | |||||||||||||||||||||||||||||||||
SNPs in miRNA |
|
|||||||||||||||||||||||||||||||||
Putative Targets |
miRNA Expression profile | |
---|---|
Human miRNA Tissue Atlas | |
Circulating MicroRNA Expression Profiling |
Gene Information | |
---|---|
Gene Symbol | RPLP1 |
Synonyms | LP1, P1, RPP1 |
Description | ribosomal protein lateral stalk subunit P1 |
Transcript | NM_001003 |
Other Transcripts | NM_213725 |
Expression | |
Putative miRNA Targets on RPLP1 | |
3'UTR of RPLP1 (miRNA target sites are highlighted) |
>RPLP1|NM_001003|3'UTR 1 ACCTCTTTTATAACATGTTCAATAAAAAGCTGAACTTT Target sites
Provided by authors
Predicted by miRanda
DRVs
SNPs
DRVs & SNPs
|
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 GSM1084064. RNA binding protein: AGO2. Condition:CLIP_noemetine_AbnovaAb
HITS-CLIP data was present in GSM1084065. RNA binding protein: AGO2. Condition:CLIP_emetine_AbnovaAb
HITS-CLIP data was present in GSM1084066. RNA binding protein: AGO2. Condition:CLIP_noemetine_SantaCruzAb
HITS-CLIP data was present in GSM1084067. RNA binding protein: AGO2. Condition:CLIP_emetine_SantaCruzAb
HITS-CLIP data was present in GSM1084068. RNA binding protein: AGO2. Condition:CLIP_noemetine_SigmaAb
HITS-CLIP data was present in GSM1084069. RNA binding protein: AGO2. Condition:CLIP_emetine_SigmaAb
HITS-CLIP data was present in GSM1084078. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep2_AbnovaAb
HITS-CLIP data was present in GSM1084079. RNA binding protein: AGO2. Condition:CLIP_hippuristanol_rep2_AbnovaAb
HITS-CLIP data was present in GSM1084080. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep2_SantaCruzAb
... - 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 GSM1084064 | |
---|---|
Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_noemetine_AbnovaAb |
Location of target site | ENST00000260379.6 | 3UTR | AGUGGAAAAAAAAAAA |
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 GSM1084065 | |
---|---|
Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_emetine_AbnovaAb |
Location of target site | ENST00000260379.6 | 3UTR | AAGUGGAAAAAAAAAAAGAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 for dataset GSM1084066 | |
---|---|
Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_noemetine_SantaCruzAb |
Location of target site | ENST00000260379.6 | 3UTR | AAGUGGAAAAAAAAAAAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
CLIP-seq Support 4 for dataset GSM1084067 | |
---|---|
Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_emetine_SantaCruzAb |
Location of target site | ENST00000260379.6 | 3UTR | AGUGGAAAAAAAAAAAGAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
CLIP-seq Support 5 for dataset GSM1084068 | |
---|---|
Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_noemetine_SigmaAb |
Location of target site | ENST00000260379.6 | 3UTR | AAGUGGAAAAAAAAAAAGA |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
CLIP-seq Support 6 for dataset GSM1084069 | |
---|---|
Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_emetine_SigmaAb |
Location of target site | ENST00000260379.6 | 3UTR | CAAAGUGGAAAAAAAAAAAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
CLIP-seq Support 7 for dataset GSM1084078 | |
---|---|
Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_nohippuristanol_rep2_AbnovaAb |
Location of target site | ENST00000260379.6 | 3UTR | AAGUGGAAAAAAAAAAAGAUUC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
CLIP-seq Support 8 for dataset GSM1084079 | |
---|---|
Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_hippuristanol_rep2_AbnovaAb |
Location of target site | ENST00000260379.6 | 3UTR | AAGUGGAAAAAAAAAAAGAUU |
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) | |||||||
---|---|---|---|---|---|---|---|
|
82 hsa-miR-6509-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
![]() |
![]() |
|||||||
Strong evidence | Less strong evidence | |||||||||||
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
|||||
MIRT055374 | PDCD4 | programmed cell death 4 | ![]() |
![]() |
2 | 4 | ||||||
MIRT378341 | MARCKS | myristoylated alanine rich protein kinase C substrate | ![]() |
![]() |
2 | 2 | ||||||
MIRT444668 | CDKL2 | cyclin dependent kinase like 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT446953 | CD248 | CD248 molecule | ![]() |
![]() |
2 | 2 | ||||||
MIRT460332 | CAMK4 | calcium/calmodulin dependent protein kinase IV | ![]() |
![]() |
2 | 6 | ||||||
MIRT464078 | VPS4A | vacuolar protein sorting 4 homolog A | ![]() |
![]() |
2 | 2 | ||||||
MIRT464586 | UBN2 | ubinuclein 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT468482 | SESN3 | sestrin 3 | ![]() |
![]() |
2 | 2 | ||||||
MIRT468962 | RPRD2 | regulation of nuclear pre-mRNA domain containing 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT475455 | HSPA8 | heat shock protein family A (Hsp70) member 8 | ![]() |
![]() |
2 | 2 | ||||||
MIRT482403 | ADRB1 | adrenoceptor beta 1 | ![]() |
![]() |
2 | 10 | ||||||
MIRT486992 | ZFAND2B | zinc finger AN1-type containing 2B | ![]() |
![]() |
2 | 2 | ||||||
MIRT489397 | TUBB2A | tubulin beta 2A class IIa | ![]() |
![]() |
2 | 2 | ||||||
MIRT526319 | UGT2A1 | UDP glucuronosyltransferase family 2 member A1 complex locus | ![]() |
![]() |
2 | 2 | ||||||
MIRT526560 | UGT2A2 | UDP glucuronosyltransferase family 2 member A2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT526732 | ZNF138 | zinc finger protein 138 | ![]() |
![]() |
2 | 8 | ||||||
MIRT531581 | STXBP5L | syntaxin binding protein 5 like | ![]() |
![]() |
2 | 2 | ||||||
MIRT532011 | NOX5 | NADPH oxidase 5 | ![]() |
![]() |
2 | 2 | ||||||
MIRT533407 | TXLNG | taxilin gamma | ![]() |
![]() |
2 | 2 | ||||||
MIRT533436 | TRPC5 | transient receptor potential cation channel subfamily C member 5 | ![]() |
![]() |
2 | 2 | ||||||
MIRT533866 | TBL1XR1 | transducin beta like 1 X-linked receptor 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT539254 | ANKRD50 | ankyrin repeat domain 50 | ![]() |
![]() |
2 | 2 | ||||||
MIRT541451 | C15orf48 | chromosome 15 open reading frame 48 | ![]() |
![]() |
2 | 2 | ||||||
MIRT566794 | MIER3 | MIER family member 3 | ![]() |
![]() |
2 | 2 | ||||||
MIRT569294 | SURF6 | surfeit 6 | ![]() |
![]() |
2 | 2 | ||||||
MIRT571336 | RABGEF1 | RAB guanine nucleotide exchange factor 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT572802 | PPP3CB | protein phosphatase 3 catalytic subunit beta | ![]() |
![]() |
2 | 2 | ||||||
MIRT572813 | MYO1C | myosin IC | ![]() |
![]() |
2 | 2 | ||||||
MIRT574219 | DMRT2 | doublesex and mab-3 related transcription factor 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT607259 | GRAMD1B | GRAM domain containing 1B | ![]() |
![]() |
2 | 4 | ||||||
MIRT609307 | CHD4 | chromodomain helicase DNA binding protein 4 | ![]() |
![]() |
2 | 2 | ||||||
MIRT615459 | REPS1 | RALBP1 associated Eps domain containing 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT616861 | RPLP1 | ribosomal protein lateral stalk subunit P1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT619415 | NOS1AP | nitric oxide synthase 1 adaptor protein | ![]() |
![]() |
2 | 2 | ||||||
MIRT619652 | COX19 | COX19, cytochrome c oxidase assembly factor | ![]() |
![]() |
2 | 2 | ||||||
MIRT625325 | TNFRSF13B | TNF receptor superfamily member 13B | ![]() |
![]() |
2 | 2 | ||||||
MIRT638980 | ARFIP2 | ADP ribosylation factor interacting protein 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT639458 | ZNF429 | zinc finger protein 429 | ![]() |
![]() |
2 | 2 | ||||||
MIRT640550 | SMCR8 | Smith-Magenis syndrome chromosome region, candidate 8 | ![]() |
![]() |
2 | 2 | ||||||
MIRT641473 | B4GALNT3 | beta-1,4-N-acetyl-galactosaminyltransferase 3 | ![]() |
![]() |
2 | 2 | ||||||
MIRT642720 | ATXN3 | ataxin 3 | ![]() |
![]() |
2 | 2 | ||||||
MIRT643048 | SMN1 | survival of motor neuron 1, telomeric | ![]() |
![]() |
2 | 2 | ||||||
MIRT644921 | SMN2 | survival of motor neuron 2, centromeric | ![]() |
![]() |
2 | 2 | ||||||
MIRT645875 | ZNF275 | zinc finger protein 275 | ![]() |
![]() |
2 | 2 | ||||||
MIRT649824 | LIPG | lipase G, endothelial type | ![]() |
![]() |
2 | 2 | ||||||
MIRT649851 | GYS2 | glycogen synthase 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT649972 | TRAFD1 | TRAF-type zinc finger domain containing 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT650675 | ZNF259 | ZPR1 zinc finger | ![]() |
1 | 1 | |||||||
MIRT651319 | ZCCHC2 | zinc finger CCHC-type containing 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT652876 | TAB1 | TGF-beta activated kinase 1 (MAP3K7) binding protein 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT652881 | SYVN1 | synoviolin 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT654144 | RPAP2 | RNA polymerase II associated protein 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT657080 | JMY | junction mediating and regulatory protein, p53 cofactor | ![]() |
![]() |
2 | 2 | ||||||
MIRT657181 | INO80C | INO80 complex subunit C | ![]() |
![]() |
2 | 2 | ||||||
MIRT657830 | GJD3 | gap junction protein delta 3 | ![]() |
![]() |
2 | 2 | ||||||
MIRT657897 | GDF7 | growth differentiation factor 7 | ![]() |
![]() |
2 | 2 | ||||||
MIRT659631 | CDKN2AIP | CDKN2A interacting protein | ![]() |
![]() |
2 | 2 | ||||||
MIRT663115 | SPTA1 | spectrin alpha, erythrocytic 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT664739 | METTL16 | methyltransferase like 16 | ![]() |
![]() |
2 | 2 | ||||||
MIRT667551 | LRAT | lecithin retinol acyltransferase | ![]() |
![]() |
2 | 2 | ||||||
MIRT668552 | ERCC1 | ERCC excision repair 1, endonuclease non-catalytic subunit | ![]() |
![]() |
2 | 2 | ||||||
MIRT682893 | XIAP | X-linked inhibitor of apoptosis | ![]() |
![]() |
2 | 2 | ||||||
MIRT683092 | PRRG4 | proline rich and Gla domain 4 | ![]() |
![]() |
2 | 2 | ||||||
MIRT683102 | TIMM10B | translocase of inner mitochondrial membrane 10B | ![]() |
![]() |
2 | 2 | ||||||
MIRT697648 | WNK1 | WNK lysine deficient protein kinase 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT709158 | ZNF419 | zinc finger protein 419 | ![]() |
![]() |
2 | 2 | ||||||
MIRT713220 | RCAN2 | regulator of calcineurin 2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT713277 | LAIR1 | leukocyte associated immunoglobulin like receptor 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT715008 | CYP1B1 | cytochrome P450 family 1 subfamily B member 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT715051 | SYNJ2BP | synaptojanin 2 binding protein | ![]() |
![]() |
2 | 2 | ||||||
MIRT715696 | PNMAL2 | paraneoplastic Ma antigen family member 8B | ![]() |
![]() |
2 | 2 | ||||||
MIRT717250 | TMEM246 | transmembrane protein 246 | ![]() |
![]() |
2 | 2 | ||||||
MIRT717322 | PGK1 | phosphoglycerate kinase 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT717587 | MTHFD1L | methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like | ![]() |
![]() |
2 | 2 | ||||||
MIRT718122 | CHST4 | carbohydrate sulfotransferase 4 | ![]() |
![]() |
2 | 2 | ||||||
MIRT718418 | CALN1 | calneuron 1 | ![]() |
![]() |
2 | 2 | ||||||
MIRT718750 | ZNF490 | zinc finger protein 490 | ![]() |
![]() |
2 | 2 | ||||||
MIRT720048 | PPP1R3F | protein phosphatase 1 regulatory subunit 3F | ![]() |
![]() |
2 | 2 | ||||||
MIRT721497 | THRB | thyroid hormone receptor beta | ![]() |
![]() |
2 | 2 | ||||||
MIRT722531 | EPRS | glutamyl-prolyl-tRNA synthetase | ![]() |
![]() |
2 | 2 | ||||||
MIRT723279 | KRTAP21-2 | keratin associated protein 21-2 | ![]() |
![]() |
2 | 2 | ||||||
MIRT724813 | MSX2 | msh homeobox 2 | ![]() |
![]() |
2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|