pre-miRNA Information
pre-miRNA hsa-mir-6839   
Genomic Coordinates chr7: 64679064 - 64679176
Description Homo sapiens miR-6839 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-6839-3p
Sequence 92| UUGGGUUUUCUCUUCAAUCCAG |113
Evidence Experimental
Experiments Meta-analysis
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN15661209 19 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1426245091 3 dbSNP
rs533324498 6 dbSNP
rs1169594864 16 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol MED7   
Synonyms ARC34, CRSP33, CRSP9
Description mediator complex subunit 7
Transcript NM_001100816   
Other Transcripts NM_004270   
Expression
Putative miRNA Targets on MED7
3'UTR of MED7
(miRNA target sites are highlighted)
>MED7|NM_001100816|3'UTR
   1 AAGATGTTTCTTTTTCTTTTTTTCCTTTTGATAATAGCATCATATATTAGTTCATTTTCTTTTGGACAGTCTTAAGAGAA
  81 GTTTCACTAAAAATGTAAACAGCTTTAATCTTGACTCCAAATTTTTCAATTATGAGATGTCATAGGCAGTAATTTCGCTG
 161 TATAACAAGCATAGACAAATGAGTGTCCCTGCACTAAGAAGAATCACTTTAAAAAGCAAAGTGTTAGCTGCTGTTGTATG
 241 GGACATTCCTATGTTTTAGAGTTGCAGTAAAACTTTGATGATAACCTCAAAAAAAAAAAAAAAAAA
Target sites Provided by authors   Predicted by miRanda    DRVs    SNPs    DRVs & SNPs
miRNA-target interactions
(Predicted by miRanda)
ID Duplex structure Position Score MFE
1
miRNA  3' gaccuAACUUCUCUUUUGGGUu 5'
               |||| ||  || |:|| 
Target 5' aaactTTGATGA-TAACCTCAa 3'
270 - 290 108.00 -7.40
2
miRNA  3' gaccuaACUUCUCUUUUGGGUu 5'
                | |||||||: ::|| 
Target 5' acagtcTTAAGAGAAGTTTCAc 3'
66 - 87 92.00 -9.40
3
miRNA  3' gaccuaacuucUCUUUUGGGUu 5'
                     ||||:| :|| 
Target 5' tccctgcactaAGAAGAATCAc 3'
186 - 207 91.00 -5.90
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN26984150 16 COSMIC
COSN30460609 16 COSMIC
COSN31526153 16 COSMIC
COSN26984151 17 COSMIC
COSN30182798 35 COSMIC
COSN31495528 36 COSMIC
COSN30189392 37 COSMIC
COSN30154928 46 COSMIC
COSN30522886 89 COSMIC
COSN30511900 116 COSMIC
COSN22208279 156 COSMIC
COSN18806911 180 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs746321069 3 dbSNP
rs1232442914 4 dbSNP
rs1222386068 6 dbSNP
rs774853668 9 dbSNP
rs1453346557 10 dbSNP
rs1275472565 11 dbSNP
rs1173435028 14 dbSNP
rs759613123 14 dbSNP
rs770361852 17 dbSNP
rs748793891 23 dbSNP
rs1043892 24 dbSNP
rs1043894 25 dbSNP
rs1354172244 29 dbSNP
rs553002745 34 dbSNP
rs1373076585 35 dbSNP
rs1008006735 37 dbSNP
rs1412262575 45 dbSNP
rs1344768476 46 dbSNP
rs1435907389 53 dbSNP
rs879886222 54 dbSNP
rs894007902 59 dbSNP
rs1232053098 66 dbSNP
rs1274147159 69 dbSNP
rs1345534685 71 dbSNP
rs1263679496 75 dbSNP
rs1243961810 82 dbSNP
rs1053865228 86 dbSNP
rs937781922 90 dbSNP
rs1208846832 92 dbSNP
rs1249297162 94 dbSNP
rs1294869047 95 dbSNP
rs1407724598 108 dbSNP
rs890904092 110 dbSNP
rs904924678 113 dbSNP
rs1198856887 117 dbSNP
rs1041428924 118 dbSNP
rs1378701437 127 dbSNP
rs9007 129 dbSNP
rs574191904 132 dbSNP
rs771151158 137 dbSNP
rs908198262 144 dbSNP
rs557515581 148 dbSNP
rs537370276 156 dbSNP
rs1322781609 157 dbSNP
rs369252857 158 dbSNP
rs1388666955 162 dbSNP
rs747432582 171 dbSNP
rs1331554029 174 dbSNP
rs185611895 180 dbSNP
rs1235150813 182 dbSNP
rs879261479 187 dbSNP
rs919780803 191 dbSNP
rs975219950 192 dbSNP
rs1269598635 197 dbSNP
rs1332101723 202 dbSNP
rs1208663668 206 dbSNP
rs1268670236 206 dbSNP
rs557800004 207 dbSNP
rs1453791159 208 dbSNP
rs949514107 213 dbSNP
rs1251608625 217 dbSNP
rs866001715 221 dbSNP
rs534556910 226 dbSNP
rs1458835086 236 dbSNP
rs1161735404 241 dbSNP
rs964799073 248 dbSNP
rs1457482478 249 dbSNP
rs565781190 251 dbSNP
rs1391405627 253 dbSNP
rs987570737 259 dbSNP
rs1347654221 273 dbSNP
rs767779387 273 dbSNP
rs1410791267 274 dbSNP
rs1182067212 276 dbSNP
rs982877545 280 dbSNP
rs1439115632 283 dbSNP
rs1264616473 286 dbSNP
rs768405631 288 dbSNP
rs549144057 290 dbSNP
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 GSM1084076. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep1_SigmaAb HITS-CLIP data was present in GSM1084078. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep2_AbnovaAb ...

- 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 ENST00000286317.5 | 3UTR | CAAGGGGUGGAGGUUGCAGUGAGCC
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 GSM1084076
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_nohippuristanol_rep1_SigmaAb
Location of target site ENST00000286317.5 | 3UTR | CAAGGGGUGGAGGUU
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 GSM1084078
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_nohippuristanol_rep2_AbnovaAb
Location of target site ENST00000286317.5 | 3UTR | CAAGGGGUGGAGGUUGCAGUGAGC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
MiRNA-Target Expression Profile
Dataset Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
62 hsa-miR-6839-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT059162 TXNIP thioredoxin interacting protein 2 2
MIRT064872 ZBTB18 zinc finger and BTB domain containing 18 2 2
MIRT065802 HOXC8 homeobox C8 2 4
MIRT106005 SDCBP syndecan binding protein 2 2
MIRT275773 TFDP1 transcription factor Dp-1 2 2
MIRT314032 PAPD7 poly(A) RNA polymerase D7, non-canonical 2 2
MIRT360277 HIST1H2BE histone cluster 1 H2B family member e 2 8
MIRT360301 HIST1H2BH histone cluster 1 H2B family member h 2 2
MIRT450086 OR2A4 olfactory receptor family 2 subfamily A member 4 2 2
MIRT468815 RSRC2 arginine and serine rich coiled-coil 2 2 6
MIRT475093 IRF2BP2 interferon regulatory factor 2 binding protein 2 2 4
MIRT477575 EIF1AD eukaryotic translation initiation factor 1A domain containing 2 2
MIRT483926 LCORL ligand dependent nuclear receptor corepressor like 2 6
MIRT504381 HIST1H1C histone cluster 1 H1 family member c 2 4
MIRT506970 HNRNPUL1 heterogeneous nuclear ribonucleoprotein U like 1 2 6
MIRT507028 HIST1H3B histone cluster 1 H3 family member b 2 6
MIRT511561 HIST3H2BB histone cluster 3 H2B family member b 2 4
MIRT511650 HIST1H3D histone cluster 1 H3 family member d 2 6
MIRT511696 HIST1H2BL histone cluster 1 H2B family member l 2 4
MIRT511737 HIST1H2BB histone cluster 1 H2B family member b 2 6
MIRT511746 HIST1H2BA histone cluster 1 H2B family member a 2 8
MIRT515260 CSNK1E casein kinase 1 epsilon 2 2
MIRT516220 RAB3B RAB3B, member RAS oncogene family 2 4
MIRT523281 HIST1H1E histone cluster 1 H1 family member e 2 2
MIRT524121 DMXL1 Dmx like 1 2 2
MIRT530744 GPR82 G protein-coupled receptor 82 2 2
MIRT532214 CCDC117 coiled-coil domain containing 117 2 2
MIRT546182 TPRG1L tumor protein p63 regulated 1 like 2 2
MIRT558638 CNNM2 cyclin and CBS domain divalent metal cation transport mediator 2 2 2
MIRT559562 ARF1 ADP ribosylation factor 1 2 4
MIRT560680 HIST1H1T histone cluster 1 H1 family member t 2 2
MIRT570746 AAK1 AP2 associated kinase 1 2 2
MIRT609518 RAB3IP RAB3A interacting protein 2 2
MIRT612583 SYNGAP1 synaptic Ras GTPase activating protein 1 2 4
MIRT615733 RIOK3 RIO kinase 3 2 2
MIRT616068 SIX1 SIX homeobox 1 2 2
MIRT617903 SGCD sarcoglycan delta 2 2
MIRT620851 SERPING1 serpin family G member 1 2 2
MIRT625107 SLC1A5 solute carrier family 1 member 5 2 2
MIRT625120 NUP93 nucleoporin 93 2 2
MIRT625893 LINC00632 long intergenic non-protein coding RNA 632 2 2
MIRT626569 MED7 mediator complex subunit 7 2 2
MIRT626694 ZFP14 ZFP14 zinc finger protein 2 4
MIRT626808 PRR11 proline rich 11 2 2
MIRT628131 HM13 histocompatibility minor 13 2 2
MIRT636596 DCAF5 DDB1 and CUL4 associated factor 5 2 2
MIRT649866 SLFN12L schlafen family member 12 like 2 2
MIRT652133 TRPM7 transient receptor potential cation channel subfamily M member 7 2 2
MIRT652663 TIMELESS timeless circadian clock 2 2
MIRT658335 FAM83D family with sequence similarity 83 member D 2 2
MIRT660615 ANKS4B ankyrin repeat and sterile alpha motif domain containing 4B 2 2
MIRT666304 SLC22A3 solute carrier family 22 member 3 2 2
MIRT668528 ERGIC2 ERGIC and golgi 2 2 2
MIRT692510 PARD3 par-3 family cell polarity regulator 2 2
MIRT694784 DHFRL1 dihydrofolate reductase 2 2 2
MIRT700510 PTPN14 protein tyrosine phosphatase, non-receptor type 14 2 2
MIRT701438 NFYA nuclear transcription factor Y subunit alpha 2 2
MIRT710155 MTRF1L mitochondrial translational release factor 1 like 2 2
MIRT711436 DLC1 DLC1 Rho GTPase activating protein 2 2
MIRT716979 GPR155 G protein-coupled receptor 155 2 2
MIRT720155 POU2F2 POU class 2 homeobox 2 2 2
MIRT722512 DSTYK dual serine/threonine and tyrosine protein kinase 2 2

Error report submission