pre-miRNA Information
pre-miRNA hsa-mir-4697   
Genomic Coordinates chr11: 133898504 - 133898581
Description Homo sapiens miR-4697 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4697-5p
Sequence 10| AGGGGGCGCAGUCACUGACGUG |31
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs549326907 2 dbSNP
rs897782230 7 dbSNP
rs748950280 8 dbSNP
rs978998780 15 dbSNP
rs968922289 19 dbSNP
rs3802919 20 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol TACC3   
Synonyms ERIC-1, ERIC1
Description transforming acidic coiled-coil containing protein 3
Transcript NM_006342   
Expression
Putative miRNA Targets on TACC3
3'UTR of TACC3
(miRNA target sites are highlighted)
>TACC3|NM_006342|3'UTR
   1 CCTCCACGGAGCCGCTGTCCCCGCCCCCCTGCTCCCGTCTGTCTGTCCTGTCTGATTCTCTTAGGTGTCATGTTCTTTTT
  81 TCTGTCTTGTCTTCAACTTTTTTAAAAACTAGATTGCTTTGAAAACATGACTCAATAAAAGTTTCCTTTCAATTTAAACA
 161 CTGAAAAAAAAAAAA
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' gugCAGUCACUGACGCGGGGGa 5'
             | |: || |  ||||||| 
Target 5' ggaGCCGCTGTCCCCGCCCCCc 3'
8 - 29 151.00 -17.30
2
miRNA  3' gugcagucACUGACGCGGGGGa 5'
                  || || :|:|::| 
Target 5' cttttttcTGTCT-TGTCTTCa 3'
75 - 95 85.00 -7.30
3
miRNA  3' gugcagucacugacgcGGGGGa 5'
                          ||:|| 
Target 5' ----------------CCTCCa 3'
1 - 6 84.00 -6.90
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN26997743 3 COSMIC
COSN31491746 15 COSMIC
COSN30140368 24 COSMIC
COSN31487703 82 COSMIC
COSN27181723 83 COSMIC
COSN31560597 104 COSMIC
COSN28560234 105 COSMIC
COSN1291877 156 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1272688761 1 dbSNP
rs1346569434 1 dbSNP
rs767320506 1 dbSNP
rs999589670 2 dbSNP
rs755331935 3 dbSNP
rs1445578590 5 dbSNP
rs372676821 8 dbSNP
rs1359678620 9 dbSNP
rs748297490 14 dbSNP
rs770095009 15 dbSNP
rs879161211 17 dbSNP
rs1195678191 18 dbSNP
rs1251880804 20 dbSNP
rs989480123 21 dbSNP
rs1185899368 22 dbSNP
rs376061018 23 dbSNP
rs199702094 24 dbSNP
rs752588395 24 dbSNP
rs372428037 25 dbSNP
rs377098346 26 dbSNP
rs1388339707 29 dbSNP
rs1461548777 30 dbSNP
rs760414105 31 dbSNP
rs1398572180 32 dbSNP
rs1412734017 36 dbSNP
rs756045719 37 dbSNP
rs763751716 37 dbSNP
rs201530808 38 dbSNP
rs1218220346 42 dbSNP
rs761244590 42 dbSNP
rs1454229704 44 dbSNP
rs1173293301 46 dbSNP
rs1237658718 48 dbSNP
rs764795119 48 dbSNP
rs1375924162 49 dbSNP
rs374553386 52 dbSNP
rs1227563754 53 dbSNP
rs918377112 59 dbSNP
rs376674701 64 dbSNP
rs1437778230 68 dbSNP
rs763799289 69 dbSNP
rs1381177416 73 dbSNP
rs1414081609 73 dbSNP
rs544101337 76 dbSNP
rs1438188187 80 dbSNP
rs776257404 82 dbSNP
rs1370468646 83 dbSNP
rs1380148753 87 dbSNP
rs1048055341 103 dbSNP
rs1474068477 104 dbSNP
rs8389 105 dbSNP
rs1208839615 106 dbSNP
rs1257767096 114 dbSNP
rs574796578 118 dbSNP
rs774278718 123 dbSNP
rs540574807 128 dbSNP
rs1315484827 132 dbSNP
rs1229895420 134 dbSNP
rs866164362 136 dbSNP
rs1474745291 139 dbSNP
rs1204468913 144 dbSNP
rs956782984 145 dbSNP
rs1361297319 146 dbSNP
rs560489902 147 dbSNP
rs1041709413 153 dbSNP
rs532580351 154 dbSNP
rs1407540735 159 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' gugcagucaCUGACGCGGGGGa 5'
                   | |  :|:|||| 
Target 5' ---------GCCGCUGUCCCCg 3'
1 - 13
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 ENST00000313288.4 | 3UTR | GCCGCUGUCCCCGCC
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
67 hsa-miR-4697-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT441332 C19orf26 CACN beta subunit associated regulatory protein 2 4
MIRT451390 FARSA phenylalanyl-tRNA synthetase alpha subunit 2 2
MIRT452310 EIF5AL1 eukaryotic translation initiation factor 5A-like 1 2 2
MIRT455043 MEN1 menin 1 2 2
MIRT455256 DDX39B DExD-box helicase 39B 2 10
MIRT461279 COX10 COX10, heme A:farnesyltransferase cytochrome c oxidase assembly factor 2 2
MIRT464945 TXLNA taxilin alpha 2 4
MIRT468043 SIK1 salt inducible kinase 1 2 2
MIRT472523 NACC1 nucleus accumbens associated 1 2 2
MIRT472929 MSN moesin 2 2
MIRT473247 MIDN midnolin 2 2
MIRT475828 HDGF heparin binding growth factor 2 2
MIRT478744 CS citrate synthase 2 2
MIRT480081 CALR calreticulin 2 2
MIRT483482 STMN3 stathmin 3 2 4
MIRT483643 QSOX2 quiescin sulfhydryl oxidase 2 2 4
MIRT483721 THSD4 thrombospondin type 1 domain containing 4 2 2
MIRT484539 BARHL1 BarH like homeobox 1 2 6
MIRT486041 WSCD1 WSC domain containing 1 2 4
MIRT486142 SIX5 SIX homeobox 5 2 6
MIRT486498 MYH11 myosin heavy chain 11 2 2
MIRT486977 STEAP3 STEAP3 metalloreductase 2 4
MIRT487279 AGPAT6 glycerol-3-phosphate acyltransferase 4 2 4
MIRT487742 MIB2 mindbomb E3 ubiquitin protein ligase 2 2 2
MIRT487987 RXRB retinoid X receptor beta 2 2
MIRT488338 PAX2 paired box 2 2 2
MIRT488668 WWP2 WW domain containing E3 ubiquitin protein ligase 2 2 4
MIRT488752 FXYD1 FXYD domain containing ion transport regulator 1 2 2
MIRT488812 TBC1D28 TBC1 domain family member 28 2 2
MIRT489380 RAB11B RAB11B, member RAS oncogene family 2 2
MIRT489744 TACC3 transforming acidic coiled-coil containing protein 3 2 2
MIRT489960 GNB2 G protein subunit beta 2 2 2
MIRT490418 VPS51 VPS51, GARP complex subunit 2 4
MIRT490639 FEM1A fem-1 homolog A 2 2
MIRT491086 MSI1 musashi RNA binding protein 1 2 4
MIRT491298 VGF VGF nerve growth factor inducible 2 4
MIRT491366 SLC12A5 solute carrier family 12 member 5 2 2
MIRT492464 RASD1 ras related dexamethasone induced 1 2 4
MIRT492872 NFIX nuclear factor I X 2 2
MIRT492951 NEUROD2 neuronal differentiation 2 2 2
MIRT493704 H2AFX H2A histone family member X 2 2
MIRT493977 EIF1 eukaryotic translation initiation factor 1 2 4
MIRT500360 ZNF385A zinc finger protein 385A 2 2
MIRT501154 SLC10A7 solute carrier family 10 member 7 2 6
MIRT509625 RRP7A ribosomal RNA processing 7 homolog A 2 4
MIRT512232 ATG2A autophagy related 2A 2 8
MIRT529822 ARGFX arginine-fifty homeobox 2 4
MIRT531179 SIGLEC12 sialic acid binding Ig like lectin 12 (gene/pseudogene) 2 2
MIRT538971 BCL7A BCL tumor suppressor 7A 2 2
MIRT548357 ENTPD5 ectonucleoside triphosphate diphosphohydrolase 5 2 4
MIRT553634 TJAP1 tight junction associated protein 1 2 2
MIRT558050 EVI5L ecotropic viral integration site 5 like 2 2
MIRT562548 CCDC71L coiled-coil domain containing 71 like 2 4
MIRT568941 RUNX3 runt related transcription factor 3 2 2
MIRT569114 ONECUT3 one cut homeobox 3 2 2
MIRT573591 CERS1 ceramide synthase 1 2 2
MIRT619317 ARHGAP18 Rho GTPase activating protein 18 2 2
MIRT621202 ARPC1B actin related protein 2/3 complex subunit 1B 2 2
MIRT628844 FAM151B family with sequence similarity 151 member B 2 2
MIRT670497 LYRM4 LYR motif containing 4 2 2
MIRT670545 SHISA2 shisa family member 2 2 2
MIRT671026 PCDHB2 protocadherin beta 2 2 2
MIRT688989 ATP6AP1 ATPase H+ transporting accessory protein 1 2 2
MIRT709275 MAPK8IP2 mitogen-activated protein kinase 8 interacting protein 2 2 2
MIRT715084 ELOF1 elongation factor 1 homolog 2 2
MIRT718348 NPBWR1 neuropeptides B and W receptor 1 2 2
MIRT737406 MMP7 matrix metallopeptidase 7 2 0
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4697 Ceritinib 57379345 NSC776422 approved sensitive cell line (H3122)
hsa-miR-4697-5p Fulvestrant 17756771 NSC719276 approved resistant High Breast Cancer cell line (MCF-7)
hsa-miR-4697-5p Paclitaxel 36314 NSC125973 approved resistant High Breast Cancer cell line (Bads-200, Bats-72, BCap37)
hsa-miR-4697-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (CAL-27) (total RNA)
hsa-miR-4697-5p Osimertinib 71496458 NSC779217 approved resistant cell line (H1975)
hsa-miR-4697-5p Cisplatin 5460033 NSC119875 approved resistant cell line (MGC-803)
hsa-miR-4697-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A2780)
hsa-miR-4697-5p Neoadjuvant chemotherapy resistant tissue (breast cancer)
hsa-miR-4697-5p Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (100 ng/ml)
hsa-miR-4697-5p Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)

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