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 FAM83D   
Synonyms C20orf129, CHICA, dJ616B8.3
Description family with sequence similarity 83 member D
Transcript NM_030919   
Expression
Putative miRNA Targets on FAM83D
3'UTR of FAM83D
(miRNA target sites are highlighted)
>FAM83D|NM_030919|3'UTR
   1 CTGCTCCGTGTTCAGACTCCTGGTTTCTTCCAGGCTTACAGTGGACATCATCAGCTTCCTGCTTTAAAAAATATCTTATG
  81 TCCCTAATTGCCTTTCTTTTACCTGACTTTGTCACCTTTGTTGTCTTTGAATTCTTTAGGCTGCATATTATTTTACATGC
 161 TTTGTTTTGTCATGTATATACCAGGTATTGGTTTTATGGTTTAAACACTATGGATACAGGGGTTTGTTTTGCACAATTTT
 241 AATAGTCATGCACTACATAATGATGTTTTGGTCAATGACAGACCACGTATATGTTGGCAGTCTCATAAGATTATAATACT
 321 GTATTTTTACTATACCTTTTCTGTGTTTAGATACAAATACCATTATGTTACAGTTGCCTACAGTATTCAGTGCAGTAACA
 401 TGATGTACAGGTTTGTAGCCTGTTTTGCATTTTTCTTAGGTTGTATGCTCTTCTGTTTTAAAGGTTTGAATCACCAGCAT
 481 TTTTGTGATCAAAATCCTATTTAGAAAAAATAAAACTACTTTCTGTTTATCTCTTTAGAAAAAAAAAAAAAAAAAA
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' catttTTGTGATCAAAATCCta 3'
478 - 499 113.00 -6.70
2
miRNA  3' gaCCUAACUUCUCU-UUUG-GGUu 5'
            | :||  ||| | |||: ||| 
Target 5' ctGTGTT-TAGATACAAATACCAt 3'
341 - 363 103.00 -7.50
3
miRNA  3' gaCCUAACU-UCUCUUUUG-GGUu 5'
            || || | :|   |||| |:| 
Target 5' ttGGTTTTATGGTTTAAACACTAt 3'
188 - 211 100.00 -7.00
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN26975915 9 COSMIC
COSN28759833 20 COSMIC
COSN31578456 20 COSMIC
COSN31503669 29 COSMIC
COSN30659164 52 COSMIC
COSN30472141 59 COSMIC
COSN26975916 72 COSMIC
COSN27851001 83 COSMIC
COSN30635817 117 COSMIC
COSN25811420 145 COSMIC
COSN28646215 275 COSMIC
COSN28647418 290 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1259406476 8 dbSNP
rs747020087 9 dbSNP
rs1208467923 14 dbSNP
rs1269853312 18 dbSNP
rs768943338 19 dbSNP
rs776696039 20 dbSNP
rs1388813537 22 dbSNP
rs762308879 25 dbSNP
rs765694697 31 dbSNP
rs1160155076 36 dbSNP
rs965114522 40 dbSNP
rs1158690585 41 dbSNP
rs773915243 42 dbSNP
rs763571491 47 dbSNP
rs766732469 49 dbSNP
rs751906746 58 dbSNP
rs6028220 60 dbSNP
rs1054902390 62 dbSNP
rs916221417 69 dbSNP
rs1468679985 72 dbSNP
rs1187504944 75 dbSNP
rs1455219808 80 dbSNP
rs1246827813 103 dbSNP
rs1220159958 106 dbSNP
rs1449574227 113 dbSNP
rs1259472904 115 dbSNP
rs1219252912 148 dbSNP
rs762268544 157 dbSNP
rs949041868 176 dbSNP
rs1046307694 181 dbSNP
rs1193822035 183 dbSNP
rs902469446 185 dbSNP
rs572923114 188 dbSNP
rs999357292 198 dbSNP
rs1238557756 208 dbSNP
rs1367784961 211 dbSNP
rs1373787102 212 dbSNP
rs952444179 213 dbSNP
rs142770945 216 dbSNP
rs1167250058 217 dbSNP
rs893871989 221 dbSNP
rs1395272561 227 dbSNP
rs1006905729 228 dbSNP
rs1420107316 230 dbSNP
rs1359620582 237 dbSNP
rs1018324657 239 dbSNP
rs1156582816 243 dbSNP
rs1456977357 248 dbSNP
rs1436559618 256 dbSNP
rs965313914 258 dbSNP
rs151031091 263 dbSNP
rs1387611347 266 dbSNP
rs767724986 267 dbSNP
rs1130247 275 dbSNP
rs548175476 280 dbSNP
rs928873260 282 dbSNP
rs984289196 285 dbSNP
rs1214873696 286 dbSNP
rs1314522128 287 dbSNP
rs140956081 288 dbSNP
rs149955259 295 dbSNP
rs1365521329 300 dbSNP
rs990534753 301 dbSNP
rs916336089 302 dbSNP
rs949030685 303 dbSNP
rs1046131632 305 dbSNP
rs923866553 306 dbSNP
rs1280373882 307 dbSNP
rs947485114 308 dbSNP
rs1258518081 321 dbSNP
rs1340099152 336 dbSNP
rs1296179933 337 dbSNP
rs935267673 342 dbSNP
rs1733 344 dbSNP
rs1255189469 356 dbSNP
rs893601607 362 dbSNP
rs1170736287 366 dbSNP
rs1477318329 372 dbSNP
rs1260569330 373 dbSNP
rs1006684646 401 dbSNP
rs1484401254 405 dbSNP
rs117006760 406 dbSNP
rs187707520 410 dbSNP
rs1418736816 411 dbSNP
rs549562754 416 dbSNP
rs1260133654 420 dbSNP
rs901303583 421 dbSNP
rs1219315494 446 dbSNP
rs1472271316 448 dbSNP
rs1019564384 450 dbSNP
rs1157201695 454 dbSNP
rs370020282 455 dbSNP
rs901093733 476 dbSNP
rs998130508 481 dbSNP
rs1026090740 496 dbSNP
rs887136168 497 dbSNP
rs1402339189 500 dbSNP
rs1331504054 505 dbSNP
rs952329533 520 dbSNP
rs1302679416 522 dbSNP
rs1464642960 522 dbSNP
rs569403439 526 dbSNP
rs1166571915 532 dbSNP
rs983893894 534 dbSNP
rs41276986 545 dbSNP
rs755152591 555 dbSNP
rs1355550428 562 dbSNP
rs550584699 563 dbSNP
rs1482597728 565 dbSNP
rs980682753 577 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 GSM1084065. RNA binding protein: AGO2. Condition:CLIP_emetine_AbnovaAb ...

- Karginov FV; Hannon GJ, 2013, Genes & development.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' gaccuaacuUCUC--UUUUGGGUu 5'
                   ||||  ::|:|::: 
Target 5' ---------AGAGGCGGAGCUUGc 3'
1 - 15
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 GSM1084065
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_emetine_AbnovaAb
Location of target site ENST00000217429.4 | 3UTR | AGAGGCGGAGCUUGCAGUGAGC
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

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