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 PCSK4   
Synonyms PC4, SPC5
Description proprotein convertase subtilisin/kexin type 4
Transcript NM_017573   
Expression
Putative miRNA Targets on PCSK4
3'UTR of PCSK4
(miRNA target sites are highlighted)
>PCSK4|NM_017573|3'UTR
   1 AGTTGTCAGCTCAGAAAGCGACCTTGCCCCCGCCTGGGTCCCTGACAGGCACTGCTGCCATGCTGCCTCCCCAGGCTGGC
  81 CCCAGAGGAGCGAGCACCAGCACCCGACGCCTGGCCTGCCAGGGATGGGCCCCGTGGAACCCCGAAGCCTGGCGGGAGAG
 161 AGAGAGAGAGAAGTCTCCTCTGCATTTTGGGTTTGGGCGGGAGTGGGCTGGGGGGAGAGGCTGGAGCACCCCAAAAGCCA
 241 GGGGAAAGTGGAGGGAGAGAAACGTGACACTGTCCGCCTCGGGCACCGCGTCCAACCTCAGAGTTTGCAAATAAAGGTTG
 321 CTTAGAAGGTGAAAAAAAAAAAAA
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' aaAGCGACCT-TGCCCCCGCCt 3'
15 - 35 167.00 -25.80
2
miRNA  3' cgUCGGUCGAGAU-G-GGG--GCGGu 5'
            ||| ||| | | | |||  |||| 
Target 5' ggAGCGAGCACCAGCACCCGACGCCt 3'
87 - 112 120.00 -22.70
3
miRNA  3' cguCGGUCGAGA-UGGGGGCGgu 5'
             |||||   | : |||||:  
Target 5' cctGCCAGGGATGGGCCCCGTgg 3'
115 - 137 115.00 -20.10
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30118179 26 COSMIC
COSN30163527 44 COSMIC
COSN29585004 156 COSMIC
COSN5802009 198 COSMIC
COSN32058085 199 COSMIC
COSN6667128 277 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs779469225 4 dbSNP
rs202135990 9 dbSNP
rs779756459 11 dbSNP
rs749628323 19 dbSNP
rs777989832 22 dbSNP
rs1291221331 27 dbSNP
rs756292775 28 dbSNP
rs767440720 31 dbSNP
rs368872756 32 dbSNP
rs1195480340 34 dbSNP
rs1248729671 36 dbSNP
rs766389320 38 dbSNP
rs1363115151 39 dbSNP
rs762891125 41 dbSNP
rs1417765989 43 dbSNP
rs773093162 44 dbSNP
rs1364567254 45 dbSNP
rs764985735 46 dbSNP
rs1038376492 56 dbSNP
rs1474514440 60 dbSNP
rs556132251 61 dbSNP
rs543853655 69 dbSNP
rs1462141701 74 dbSNP
rs763056915 75 dbSNP
rs571019020 78 dbSNP
rs980586496 83 dbSNP
rs112631650 88 dbSNP
rs917835446 91 dbSNP
rs940620316 92 dbSNP
rs908507349 95 dbSNP
rs992107720 102 dbSNP
rs558207755 103 dbSNP
rs2656884 105 dbSNP
rs763721595 106 dbSNP
rs2656883 108 dbSNP
rs1486813705 109 dbSNP
rs1211601799 114 dbSNP
rs1351169306 115 dbSNP
rs959106818 129 dbSNP
rs554715722 133 dbSNP
rs536552031 134 dbSNP
rs1428278553 139 dbSNP
rs1168861481 141 dbSNP
rs184247620 143 dbSNP
rs1436215371 147 dbSNP
rs1029793348 151 dbSNP
rs994340424 153 dbSNP
rs897423056 154 dbSNP
rs1362641700 156 dbSNP
rs1019885611 157 dbSNP
rs1293179366 158 dbSNP
rs1158940180 161 dbSNP
rs1038747933 162 dbSNP
rs1413522513 165 dbSNP
rs1345776385 166 dbSNP
rs1005578563 168 dbSNP
rs1185228749 170 dbSNP
rs370258871 172 dbSNP
rs747484931 172 dbSNP
rs769926039 172 dbSNP
rs890150243 172 dbSNP
rs1455277224 173 dbSNP
rs1491539358 173 dbSNP
rs1474609598 177 dbSNP
rs1256377137 179 dbSNP
rs1201830489 180 dbSNP
rs995981484 181 dbSNP
rs1259987419 184 dbSNP
rs1452980239 185 dbSNP
rs1286850500 190 dbSNP
rs1216404350 198 dbSNP
rs1047852 199 dbSNP
rs1270068411 208 dbSNP
rs368548596 210 dbSNP
rs1316796194 211 dbSNP
rs1354934823 212 dbSNP
rs1275647709 223 dbSNP
rs947860266 225 dbSNP
rs1398017327 229 dbSNP
rs917720691 231 dbSNP
rs1251980909 241 dbSNP
rs1476838434 245 dbSNP
rs1360293256 246 dbSNP
rs878980714 247 dbSNP
rs1408099886 253 dbSNP
rs1418388644 255 dbSNP
rs1156818834 257 dbSNP
rs1047066483 263 dbSNP
rs1461765989 264 dbSNP
rs191278790 275 dbSNP
rs1392484731 276 dbSNP
rs1047854 277 dbSNP
rs1280173518 280 dbSNP
rs370465752 281 dbSNP
rs991980382 287 dbSNP
rs958852492 288 dbSNP
rs528565566 289 dbSNP
rs186833293 290 dbSNP
rs1368554917 296 dbSNP
rs1480013136 301 dbSNP
rs867902242 303 dbSNP
rs548362508 321 dbSNP
rs770798240 328 dbSNP
rs759342986 329 dbSNP
rs113906426 332 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' --------------CCCCGCCu 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 ENST00000300954.5 | 3UTR | CCCCGCCUGGGUCCC
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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