miRTarBase - #MIRT487987


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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 RXRB   
Synonyms DAUDI6, H-2RIIBP, NR2B2, RCoR-1
Description retinoid X receptor beta
Transcript NM_021976   
Expression
Putative miRNA Targets on RXRB
3'UTR of RXRB
(miRNA target sites are highlighted)		 
>RXRB|NM_021976|3'UTR
   1 GCTCAGACCCAGACGTGGTGCTTCTCACACTGGAGGAGCACACATCCAAGAGGGACTCCAAGCCCTGGGGCAGGGTGGGG
  81 GGCCATGTTCCCAGAACCTTGATGGGGTGAGAAGTACAGGGCAGAACCAAGAACATAAACCCTCCAAGGGATCTGCTTGA
 161 TATCCCAAGTTGGAAGGGACCCCAGATACCTGTGAGGACTGGTTGTCTCTCTTCGGTGGCCTTGAGTCTCTGAATTTGTC
 241 GGGTTCTCCCATGATTTGGGGTGATTTCTCACCCTCTGTCCTTCCCCCAGCACAAAGCACTGGCCTTGCCTCCAGGACCT
 321 TGCTTCCTTCTCATCTTGCCTCATTTTGCTTCCCATCTGAAGAGTGGAAATGGGGAACTCCCCCAGAGGTGGATACTGGG
 401 GGGCAGGCCTCCCAAGCTGATGGACATGAGAGTAGGGCCCTGACAGGCCTTCCTCCTCTCAAACCTGGCAGATGGGGGCC
 481 TCTCTGGAAGAGGGAGGGGCCCTGTCACTGTCCAGAGTCTCTTTTTACACTTCACCTCCTTCTGCAGTCAGACTGAAATA
 561 TAAAAAAGGTGGTGGTGGTGGTGAAGGGGCTGGTGGAGATGTAGGAACCGATCTGCTATTTTTAATTTCCTGTGAGGATA
 641 GAGACTTGCAGTTAGACTCAAAGAAGTACTGTACTTTCCCAGGTTGACTAAGAAATGCCAGTGGTGGAGGTGGGTGTTTG
 721 GGAAAGGCAGGGCCCTGAAATGGCCTGTCCCTAGGGCTCTCCAAGCACTAGCCTTCCCAGCTTCCCGCCGCCCCCCCTAT
 801 CTCTTCCTGTCTAACTTGGGGAAGGGGCCTGGGCTGTGAGGACAGGGCCCCCACAGGGGATGGTTTCACGAGTGTAGTCC
 881 CGGAGGCCTTCCCTTTACAGCTCTCCTCCAGCCCTGGGCACATAGCATAGGCTGGGGACACAGGATCCTGGCCTGAGAAT
 961 TGAGGGGAGGTGGCCAGCCCGCAGAGGTGGGGTGCTGGGGCTGCATGATTTTTGCCCTGCGTCCCTTCTCTTTGGGGCTC
1041 CTTTCCCCTCTCATACATAAAATCGCTTTCAAATTAAAATCGCTGTTTTCTGGACTG
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' gugcaGUC-ACUGAC-GCGGGGGa 5'
               ||| |  | | ||||||| 
Target 5' cttccCAGCTTCCCGCCGCCCCCc 3'
 773 - 796 145.00 -15.84
2 
miRNA  3' guGCAGUCACUGACGCGGGGGa 5'
            :|| || ||| | |||||| 
Target 5' gcTGTGAG-GACAGGGCCCCCa 3'
 833 - 853 135.00 -22.10
3 
miRNA  3' gugcaGUCACUGACGCGGGGGa 5'
               || ||:|  :|||:|| 
Target 5' caaagCACTGGCCTTGCCTCCa 3'
 293 - 314 125.00 -16.10
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN32110759 6 COSMIC
COSN30182286 12 COSMIC
COSN30477403 33 COSMIC
COSN30455702 50 COSMIC
COSN31510506 61 COSMIC
COSN27208802 798 COSMIC
COSN16144626 799 COSMIC
COSN23553429 881 COSMIC
COSN15668442 965 COSMIC
COSN25695545 1044 COSMIC
rs1050673 798 GWAS
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs781073340 1 dbSNP
rs1306061706 4 dbSNP
rs553683366 8 dbSNP
rs186981565 9 dbSNP
rs1429777509 11 dbSNP
rs777260045 12 dbSNP
rs201936341 14 dbSNP
rs748632306 15 dbSNP
rs748311732 21 dbSNP
rs1244866974 22 dbSNP
rs779324199 24 dbSNP
rs755536974 27 dbSNP
rs754099153 41 dbSNP
rs1199243810 44 dbSNP
rs377652976 45 dbSNP
rs756340454 49 dbSNP
rs900220325 56 dbSNP
rs1248962506 59 dbSNP
rs1017371918 62 dbSNP
rs1212329201 63 dbSNP
rs368402162 68 dbSNP
rs376632337 69 dbSNP
rs1370621349 70 dbSNP
rs35013264 72 dbSNP
rs879101029 72 dbSNP
rs1261859537 75 dbSNP
rs945013828 77 dbSNP
rs548082423 80 dbSNP
rs1241541663 83 dbSNP
rs1431648849 87 dbSNP
rs1315520996 88 dbSNP
rs542913956 104 dbSNP
rs1306279477 105 dbSNP
rs1395606675 107 dbSNP
rs748988941 111 dbSNP
rs1396607032 117 dbSNP
rs1335926975 124 dbSNP
rs1000491541 144 dbSNP
rs1235389126 149 dbSNP
rs533394360 150 dbSNP
rs1297826087 152 dbSNP
rs892079344 191 dbSNP
rs1053348488 192 dbSNP
rs1343871225 193 dbSNP
rs777543496 196 dbSNP
rs1225460739 200 dbSNP
rs1324026728 207 dbSNP
rs138424316 213 dbSNP
rs903520094 214 dbSNP
rs938910945 215 dbSNP
rs2982281 219 dbSNP
rs1042112337 220 dbSNP
rs5030979 231 dbSNP
rs150883479 240 dbSNP
rs948835033 241 dbSNP
rs2744537 244 dbSNP
rs1372638606 245 dbSNP
rs1173871350 251 dbSNP
rs938206844 254 dbSNP
rs1400022328 256 dbSNP
rs1469058361 261 dbSNP
rs182110328 267 dbSNP
rs781553184 272 dbSNP
rs950700934 273 dbSNP
rs1392696175 276 dbSNP
rs1026249257 278 dbSNP
rs1294206363 284 dbSNP
rs749331898 286 dbSNP
rs941482555 288 dbSNP
rs1234817553 289 dbSNP
rs1258232632 292 dbSNP
rs1192419485 293 dbSNP
rs1322047437 302 dbSNP
rs1203363464 315 dbSNP
rs976037283 319 dbSNP
rs576587393 326 dbSNP
rs1185054448 332 dbSNP
rs1261091453 335 dbSNP
rs1207470470 340 dbSNP
rs554818490 342 dbSNP
rs1017438026 343 dbSNP
rs950668491 347 dbSNP
rs1285808684 350 dbSNP
rs1211844047 356 dbSNP
rs1159610531 370 dbSNP
rs755455091 371 dbSNP
rs1350267380 374 dbSNP
rs2072915 377 dbSNP
rs566279728 380 dbSNP
rs1287881293 381 dbSNP
rs1391028332 384 dbSNP
rs554485393 398 dbSNP
rs903636226 399 dbSNP
rs1223506691 402 dbSNP
rs964576267 404 dbSNP
rs538661409 409 dbSNP
rs370103934 414 dbSNP
rs1022042516 416 dbSNP
rs1327114455 433 dbSNP
rs1260314341 437 dbSNP
rs1488938405 453 dbSNP
rs1009262380 455 dbSNP
rs1000612226 459 dbSNP
rs1297616508 466 dbSNP
rs1480056203 473 dbSNP
rs1380523654 474 dbSNP
rs903636009 479 dbSNP
rs1414128347 482 dbSNP
rs1313311825 484 dbSNP
rs571229669 498 dbSNP
rs1158117615 507 dbSNP
rs1373172858 513 dbSNP
rs2735326 515 dbSNP
rs2744538 517 dbSNP
rs1009254879 521 dbSNP
rs1172640829 528 dbSNP
rs1300734195 529 dbSNP
rs896702443 533 dbSNP
rs1404848725 535 dbSNP
rs1309126229 536 dbSNP
rs1352890063 538 dbSNP
rs1056725950 543 dbSNP
rs1306743063 546 dbSNP
rs1374363799 547 dbSNP
rs1195920201 549 dbSNP
rs1289643164 558 dbSNP
rs1490194419 559 dbSNP
rs549914578 561 dbSNP
rs532472178 568 dbSNP
rs938139160 568 dbSNP
rs376187890 569 dbSNP
rs111775605 570 dbSNP
rs1414337253 571 dbSNP
rs1003135587 572 dbSNP
rs1425168252 584 dbSNP
rs941430387 584 dbSNP
rs750696270 589 dbSNP
rs1278388657 590 dbSNP
rs567348600 590 dbSNP
rs781392035 596 dbSNP
rs1356720871 599 dbSNP
rs908651025 601 dbSNP
rs1044607905 609 dbSNP
rs370257361 613 dbSNP
rs1340147777 623 dbSNP
rs1359009782 632 dbSNP
rs1229145438 645 dbSNP
rs909324735 647 dbSNP
rs56381258 650 dbSNP
rs1225124804 658 dbSNP
rs775157330 659 dbSNP
rs560042135 661 dbSNP
rs1237811205 669 dbSNP
rs1484091648 670 dbSNP
rs910377049 678 dbSNP
rs1416333561 681 dbSNP
rs929363710 691 dbSNP
rs1333093565 695 dbSNP
rs979285433 702 dbSNP
rs1189938179 719 dbSNP
rs141536489 725 dbSNP
rs1408678974 727 dbSNP
rs1170311399 731 dbSNP
rs1397986854 734 dbSNP
rs1360267567 737 dbSNP
rs976448585 743 dbSNP
rs967768126 747 dbSNP
rs1335142854 753 dbSNP
rs1382301899 761 dbSNP
rs55678527 769 dbSNP
rs1271983547 771 dbSNP
rs1360009867 779 dbSNP
rs910450636 786 dbSNP
rs986013184 787 dbSNP
rs1313895964 789 dbSNP
rs960406806 790 dbSNP
rs529347210 792 dbSNP
rs967857887 792 dbSNP
rs1005687293 793 dbSNP
rs56058451 793 dbSNP
rs1174709948 794 dbSNP
rs201032946 794 dbSNP
rs1405875210 795 dbSNP
rs1009334362 796 dbSNP
rs1343676006 797 dbSNP
rs1050673 798 dbSNP
rs1355655904 798 dbSNP
rs3833487 798 dbSNP
rs1034695571 799 dbSNP
rs576307070 799 dbSNP
rs879178497 799 dbSNP
rs1282360595 800 dbSNP
rs1040140671 801 dbSNP
rs1210377196 819 dbSNP
rs1281629402 827 dbSNP
rs1446070433 828 dbSNP
rs759457467 830 dbSNP
rs1438654901 843 dbSNP
rs1248007715 848 dbSNP
rs1490978178 848 dbSNP
rs1197940190 854 dbSNP
rs1429241350 863 dbSNP
rs1003618541 866 dbSNP
rs1160672016 867 dbSNP
rs770612532 869 dbSNP
rs1324271594 870 dbSNP
rs910491968 872 dbSNP
rs576501041 881 dbSNP
rs369829068 889 dbSNP
rs1273723837 899 dbSNP
rs979231583 901 dbSNP
rs1013097970 905 dbSNP
rs1208337081 907 dbSNP
rs1351044584 914 dbSNP
rs1240839514 918 dbSNP
rs967882451 920 dbSNP
rs561418438 921 dbSNP
rs1228578524 942 dbSNP
rs1293285751 943 dbSNP
rs913614926 948 dbSNP
rs1235134313 964 dbSNP
rs1444322583 968 dbSNP
rs1332374348 976 dbSNP
rs1268729311 977 dbSNP
rs1483673203 978 dbSNP
rs1184427317 979 dbSNP
rs2975108 986 dbSNP
rs987906152 987 dbSNP
rs1283436048 997 dbSNP
rs1442693671 1006 dbSNP
rs542881758 1013 dbSNP
rs929394752 1020 dbSNP
rs1422755533 1021 dbSNP
rs919331175 1022 dbSNP
rs1040407920 1024 dbSNP
rs1393123543 1032 dbSNP
rs1326580149 1036 dbSNP
rs1334993437 1045 dbSNP
rs1394650397 1049 dbSNP
rs1448525565 1053 dbSNP
rs1166276555 1057 dbSNP
rs572573427 1059 dbSNP
rs1356841387 1060 dbSNP
rs944688353 1064 dbSNP
rs1162986471 1072 dbSNP
rs1470734864 1076 dbSNP
rs1365698966 1085 dbSNP
rs1198133988 1089 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' -------uucccgcCGCCCCCc 3'
 		1 - 15
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 ENST00000374685.4 | 3UTR | UUCCCGCCGCCCCCCCUAUCUCUUCCUG
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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