pre-miRNA Information
pre-miRNA hsa-mir-6787   
Genomic Coordinates chr17: 82236668 - 82236728
Description Homo sapiens miR-6787 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-6787-5p
Sequence 6| UGGCGGGGGUAGAGCUGGCUGC |27
Evidence Experimental
Experiments Meta-analysis
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs778888046 4 dbSNP
rs772018061 5 dbSNP
rs760886644 6 dbSNP
rs776925052 7 dbSNP
rs760060985 8 dbSNP
rs1432528063 9 dbSNP
rs778772390 10 dbSNP
rs924024166 11 dbSNP
rs201523090 13 dbSNP
rs1451075810 17 dbSNP
rs1378844609 18 dbSNP
Putative Targets

Gene Information
Gene Symbol VGF   
Synonyms SCG7, SgVII
Description VGF nerve growth factor inducible
Transcript NM_003378   
Expression
Putative miRNA Targets on VGF
3'UTR of VGF
(miRNA target sites are highlighted)
>VGF|NM_003378|3'UTR
   1 CTGCCCTTCCCGGTCCCGCCCCCGCGCGCCCCCGCCGCGCGCGCGCGCCGGCGCCCCCCTCCGTGTTGCCCGCTCCCCCT
  81 CGGTGTTTGCATGCGCCCCGGCCCTGCCCCTTGGCCCTGCCCCTGTCCCCGGGCTGCGTCGGGACCTGCCAGACCCCCCT
 161 CCCGGGTCCTGAGCCCGAACTCCCAGAGCTCACCCGCGGGTGACCGGGGGCCAGCCCAGGAGGGCGGGTGGTTTGTGCGA
 241 GTTCCCTTGCCACGCGGGGCCCCGGCCCCATCAAGTCCCTCTGGGGACGTCCCCGTCGGAAACCGGAAAAAGCAGTTCCA
 321 GTTAATTGTGTGAAGTGTGTCTGTCTCCAGCCCTTCGGGCCTCCCACGAGCCCCTCCAGCCTCTCCAAGTCGCTGTGAAT
 401 TGACCCCTTCTTTCCTTTCTCTGTTGTAAATACCCCTCACGGAGGAAATAGTTTTGCTAAGAAATAAAAGTGACTATTTT
 481 ATTAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
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' cgucGGUCGAGAUGGGGGCGGu 5'
              || || | :|||||||| 
Target 5' cgccCCCGCGC-GCCCCCGCCg 3'
17 - 37 157.00 -27.20
2
miRNA  3' cgucGGUCGAGAUG-------GGGGCGGu 5'
              ||:|| ||:|       |||:||| 
Target 5' cgccCCGGCCCTGCCCCTTGGCCCTGCCc 3'
94 - 122 138.00 -23.64
3
miRNA  3' cgUCGGUCGAGA----UG--GGGGCGGu 5'
            ||:|  ||||    ||  |||||:| 
Target 5' caAGTC-CCTCTGGGGACGTCCCCGTCg 3'
272 - 298 135.00 -24.60
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30529835 2 COSMIC
COSN27004601 19 COSMIC
COSN27004602 20 COSMIC
COSN30646161 36 COSMIC
COSN24310986 113 COSMIC
COSN30670199 206 COSMIC
COSN30541763 230 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs957958709 1 dbSNP
rs1487721484 3 dbSNP
rs770089706 5 dbSNP
rs574477804 11 dbSNP
rs1032220775 12 dbSNP
rs1284094424 18 dbSNP
rs762359570 19 dbSNP
rs771811708 19 dbSNP
rs752200712 26 dbSNP
rs972871257 28 dbSNP
rs1301231332 30 dbSNP
rs1318021589 32 dbSNP
rs1228011232 33 dbSNP
rs1329913517 34 dbSNP
rs764988113 36 dbSNP
rs745345037 38 dbSNP
rs759227426 39 dbSNP
rs778522822 40 dbSNP
rs776590939 41 dbSNP
rs1215476799 43 dbSNP
rs1300074477 43 dbSNP
rs867998937 43 dbSNP
rs902335415 45 dbSNP
rs1463004810 47 dbSNP
rs1030453096 49 dbSNP
rs770611627 49 dbSNP
rs1343522333 50 dbSNP
rs760707757 50 dbSNP
rs773019846 50 dbSNP
rs1304009681 51 dbSNP
rs768837064 51 dbSNP
rs1367644777 54 dbSNP
rs1455691595 55 dbSNP
rs1472638408 56 dbSNP
rs559485433 58 dbSNP
rs1365129064 59 dbSNP
rs1378339714 59 dbSNP
rs1305434578 60 dbSNP
rs749383214 60 dbSNP
rs1350911554 71 dbSNP
rs1431771833 71 dbSNP
rs1238754377 72 dbSNP
rs1267161168 73 dbSNP
rs1181023391 75 dbSNP
rs1438141311 79 dbSNP
rs1490735125 80 dbSNP
rs1219191617 82 dbSNP
rs1214849300 84 dbSNP
rs1470271067 87 dbSNP
rs773827695 89 dbSNP
rs1266798365 95 dbSNP
rs756747525 101 dbSNP
rs753777397 103 dbSNP
rs1198564472 105 dbSNP
rs1378361641 106 dbSNP
rs1281461021 109 dbSNP
rs1040031502 110 dbSNP
rs944456574 111 dbSNP
rs777866017 116 dbSNP
rs1231403854 120 dbSNP
rs1330289862 121 dbSNP
rs1422983470 125 dbSNP
rs1485132172 125 dbSNP
rs1323078588 126 dbSNP
rs755905793 130 dbSNP
rs912940238 132 dbSNP
rs989391610 138 dbSNP
rs752605591 140 dbSNP
rs1319829064 141 dbSNP
rs957593474 142 dbSNP
rs926112477 150 dbSNP
rs980344767 154 dbSNP
rs1386545585 155 dbSNP
rs1170421293 156 dbSNP
rs970270933 157 dbSNP
rs1377419315 158 dbSNP
rs867236981 159 dbSNP
rs775479850 160 dbSNP
rs1288641250 161 dbSNP
rs1455873600 161 dbSNP
rs1024274088 163 dbSNP
rs757510647 164 dbSNP
rs770032327 164 dbSNP
rs1447636042 168 dbSNP
rs540842583 172 dbSNP
rs1198945577 173 dbSNP
rs1344502331 177 dbSNP
rs961763231 179 dbSNP
rs1281329144 180 dbSNP
rs1236153454 186 dbSNP
rs928793428 189 dbSNP
rs1245059724 193 dbSNP
rs767612486 195 dbSNP
rs1309581616 197 dbSNP
rs1296738804 199 dbSNP
rs1435785181 201 dbSNP
rs1327665200 206 dbSNP
rs1331705775 208 dbSNP
rs759842912 209 dbSNP
rs868168937 210 dbSNP
rs1402413522 211 dbSNP
rs751763107 211 dbSNP
rs1394715444 222 dbSNP
rs1175161565 225 dbSNP
rs1339199256 226 dbSNP
rs1436938721 232 dbSNP
rs1375070928 239 dbSNP
rs1388760804 242 dbSNP
rs766434888 245 dbSNP
rs1384389936 248 dbSNP
rs1015646103 255 dbSNP
rs1445120373 257 dbSNP
rs1283277017 261 dbSNP
rs916309784 263 dbSNP
rs990487246 280 dbSNP
rs1058351 281 dbSNP
rs957657609 291 dbSNP
rs1032293874 297 dbSNP
rs1204252492 298 dbSNP
rs978410886 304 dbSNP
rs1440813989 307 dbSNP
rs576697919 308 dbSNP
rs34907591 312 dbSNP
rs887658951 312 dbSNP
rs1049352650 318 dbSNP
rs1242973339 321 dbSNP
rs1030563995 324 dbSNP
rs1476512033 329 dbSNP
rs1368339065 335 dbSNP
rs73712100 342 dbSNP
rs184655571 356 dbSNP
rs1244003273 371 dbSNP
rs1040063529 373 dbSNP
rs539407810 378 dbSNP
rs1400652910 381 dbSNP
rs575223120 385 dbSNP
rs1456589971 386 dbSNP
rs1412304964 387 dbSNP
rs1006187896 388 dbSNP
rs887772194 391 dbSNP
rs944319016 402 dbSNP
rs1422206923 408 dbSNP
rs369818277 408 dbSNP
rs529022474 408 dbSNP
rs1275861496 410 dbSNP
rs748792118 421 dbSNP
rs758982088 431 dbSNP
rs1223869373 433 dbSNP
rs1190963020 437 dbSNP
rs1342768751 449 dbSNP
rs907397954 454 dbSNP
rs1052911358 460 dbSNP
rs1285051005 466 dbSNP
rs1355574746 472 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions C8166
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in GSM1462572. RNA binding protein: AGO2. Condition:C8166 NL4-3 ...

- Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' cguCGGUCGAGAUGGGGGCGGu 5'
             |||:|| |  ||||| || 
Target 5' cgcGCCGGCGC--CCCCCUCCg 3'
12 - 31
2
miRNA  3' cgucggucgagaugGGGGCGgu 5'
                        | ||||  
Target 5' --------------CGCCGCgc 3'
1 - 8
Article - Whisnant AW; Bogerd HP; Flores O; Ho P; et al.
- mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
CLIP-seq Support 1 for dataset GSM1462572
Method / RBP PAR-CLIP / AGO2
Cell line / Condition C8166 / C8166 NL4-3
Location of target site ENST00000249330.2 | 3UTR | CGCCGCGCGCGCGCGCCGGCGCCCCCCUCCG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23592263 / GSE59944
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
90 hsa-miR-6787-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT449091 XPO6 exportin 6 2 2
MIRT449991 PSMG1 proteasome assembly chaperone 1 2 2
MIRT454608 MYADM myeloid associated differentiation marker 2 2
MIRT456116 VAV3 vav guanine nucleotide exchange factor 3 2 6
MIRT457064 TOR4A torsin family 4 member A 2 2
MIRT461023 SDF4 stromal cell derived factor 4 2 2
MIRT467197 SPRY4 sprouty RTK signaling antagonist 4 2 2
MIRT471711 OTUB1 OTU deubiquitinase, ubiquitin aldehyde binding 1 2 2
MIRT472566 NACC1 nucleus accumbens associated 1 2 2
MIRT476079 GRB2 growth factor receptor bound protein 2 2 2
MIRT480150 CALR calreticulin 2 2
MIRT483027 KHSRP KH-type splicing regulatory protein 2 4
MIRT483498 STMN3 stathmin 3 2 4
MIRT483728 THSD4 thrombospondin type 1 domain containing 4 2 2
MIRT484550 BARHL1 BarH like homeobox 1 2 6
MIRT484684 PACSIN1 protein kinase C and casein kinase substrate in neurons 1 2 2
MIRT486059 CTDNEP1 CTD nuclear envelope phosphatase 1 2 2
MIRT486116 INO80E INO80 complex subunit E 2 2
MIRT486313 SIPA1 signal-induced proliferation-associated 1 2 2
MIRT486525 CLCN7 chloride voltage-gated channel 7 2 2
MIRT486857 DPF1 double PHD fingers 1 2 2
MIRT487352 PHF15 jade family PHD finger 2 1 1
MIRT487582 FAM83H family with sequence similarity 83 member H 2 4
MIRT487792 GPR20 G protein-coupled receptor 20 2 4
MIRT488104 POU3F1 POU class 3 homeobox 1 2 2
MIRT488786 POFUT2 protein O-fucosyltransferase 2 2 2
MIRT489361 SYNGR1 synaptogyrin 1 2 4
MIRT489387 RAB11B RAB11B, member RAS oncogene family 2 2
MIRT489680 SCAMP4 secretory carrier membrane protein 4 2 2
MIRT489731 GNAI2 G protein subunit alpha i2 2 4
MIRT489750 TACC3 transforming acidic coiled-coil containing protein 3 2 2
MIRT490029 PCSK4 proprotein convertase subtilisin/kexin type 4 2 2
MIRT490379 LHFPL3 LHFPL tetraspan subfamily member 3 2 2
MIRT490580 SLC47A1 solute carrier family 47 member 1 2 2
MIRT490753 SRCIN1 SRC kinase signaling inhibitor 1 2 2
MIRT491187 JUND JunD proto-oncogene, AP-1 transcription factor subunit 2 4
MIRT491301 VGF VGF nerve growth factor inducible 2 2
MIRT491462 HOXB8 homeobox B8 2 2
MIRT491702 PDZD4 PDZ domain containing 4 2 2
MIRT491724 RTN4R reticulon 4 receptor 2 2
MIRT491737 SEMA3F semaphorin 3F 2 2
MIRT491984 UNK unkempt family zinc finger 2 2
MIRT492844 NRGN neurogranin 2 2
MIRT492936 NEUROD2 neuronal differentiation 2 2 4
MIRT493713 H2AFX H2A histone family member X 2 2
MIRT494623 ASB6 ankyrin repeat and SOCS box containing 6 2 4
MIRT494703 ARHGAP31 Rho GTPase activating protein 31 2 2
MIRT495602 NKX2-5 NK2 homeobox 5 2 2
MIRT495750 PDE4C phosphodiesterase 4C 2 4
MIRT500367 ZNF385A zinc finger protein 385A 2 2
MIRT501161 SLC10A7 solute carrier family 10 member 7 2 6
MIRT501702 PCGF3 polycomb group ring finger 3 2 6
MIRT504922 PDRG1 p53 and DNA damage regulated 1 2 2
MIRT517945 TRIM59 tripartite motif containing 59 2 2
MIRT524212 DDI2 DNA damage inducible 1 homolog 2 2 6
MIRT531186 SIGLEC12 sialic acid binding Ig like lectin 12 (gene/pseudogene) 2 2
MIRT531972 C12orf49 chromosome 12 open reading frame 49 2 2
MIRT558055 EVI5L ecotropic viral integration site 5 like 2 2
MIRT560482 LACE1 AFG1 like ATPase 2 2
MIRT563217 FXN frataxin 2 2
MIRT569095 FSCN1 fascin actin-bundling protein 1 2 2
MIRT569522 AP5Z1 adaptor related protein complex 5 zeta 1 subunit 2 2
MIRT569531 CTTN cortactin 2 2
MIRT569848 RGS5 regulator of G protein signaling 5 2 2
MIRT570738 ANKRD52 ankyrin repeat domain 52 2 2
MIRT574140 MARVELD1 MARVEL domain containing 1 2 2
MIRT615994 DHTKD1 dehydrogenase E1 and transketolase domain containing 1 2 2
MIRT628493 ZNF556 zinc finger protein 556 2 2
MIRT633451 KLLN killin, p53-regulated DNA replication inhibitor 2 2
MIRT649054 SLC1A2 solute carrier family 1 member 2 2 2
MIRT649340 HEXA hexosaminidase subunit alpha 2 2
MIRT670226 PTCHD1 patched domain containing 1 2 2
MIRT670666 KIAA1551 KIAA1551 2 2
MIRT671452 CDH7 cadherin 7 2 2
MIRT671729 ZNF451 zinc finger protein 451 2 2
MIRT690285 ZNF154 zinc finger protein 154 2 2
MIRT700575 PRSS22 protease, serine 22 2 2
MIRT701411 NKRF NFKB repressing factor 2 2
MIRT711877 VASP vasodilator stimulated phosphoprotein 2 2
MIRT712082 UNC13A unc-13 homolog A 2 2
MIRT712523 CYTH2 cytohesin 2 2 2
MIRT712751 GMDS GDP-mannose 4,6-dehydratase 2 2
MIRT714681 PRX periaxin 2 2
MIRT714718 VPS8 VPS8, CORVET complex subunit 2 2
MIRT717508 HRNR hornerin 2 2
MIRT717650 THBS2 thrombospondin 2 2 2
MIRT719592 PIAS4 protein inhibitor of activated STAT 4 2 2
MIRT720521 PTGR2 prostaglandin reductase 2 2 2
MIRT721295 C3orf36 chromosome 3 open reading frame 36 2 2
MIRT724922 VPS18 VPS18, CORVET/HOPS core subunit 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-6787 Ceritinib 57379345 NSC776422 approved sensitive High Non-Small Cell Lung Cancer cell line (H3122, H2228)
hsa-miR-6787-5p Dabrafenib 44462760 NSC764134 approved resistant High Melanoma cell line (A375, IGR37, 501Mel)
hsa-miR-6787-5p Vemurafenib 42611257 NSC761431 approved resistant High Melanoma cell line (A375, IGR37, 501Mel)
hsa-miR-6787-5p Cisplatin 5460033 NSC119875 approved sensitive cell line
hsa-miR-6787-5p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-6787-5p Tamoxifen 2733525 NSC180973 approved sensitive cell line (LCC2)
hsa-miR-6787-5p Osimertinib 71496458 NSC779217 approved sensitive cell line (H1975)
hsa-miR-6787-5p Paclitaxel 36314 NSC125973 approved resistant cell line (A2780)
hsa-miR-6787-5p Cisplatin 5460033 NSC119875 approved resistant cell line (A2780)
hsa-miR-6787-5p Docetaxel+Cisplatin+5-Fluorouracil resistant tissue (hypopharyngeal squamous cell carcinoma)

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