miRTarBase - #MIRT467919


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pre-miRNA Information
pre-miRNA hsa-mir-506   
Genomic Coordinates chrX: 147230720 - 147230843
Synonyms MIRN506, hsa-mir-506, MIR506
Description Homo sapiens miR-506 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-506-5p
Sequence 35| UAUUCAGGAAGGUGUUACUUAA |56
Evidence Not_experimental
Experiments
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs782463365 2 dbSNP
rs781802841 18 dbSNP
rs782722056 21 dbSNP
rs782039395 22 dbSNP
Putative Targets

Gene Information
Gene Symbol SLC20A1   
Synonyms GLVR1, Glvr-1, PIT1, PiT-1
Description solute carrier family 20 member 1
Transcript NM_005415   
Expression
Putative miRNA Targets on SLC20A1
3'UTR of SLC20A1
(miRNA target sites are highlighted)		 
>SLC20A1|NM_005415|3'UTR
   1 AGCTGTTTGAGATTAAAATTTGTGTCAATGTTTGGGACCATCTTAGGTATTCCTGCTCCCCTGAAGAATGATTACAGTGT
  81 TAACAGAAGACTGACAAGAGTCTTTTTATTTGGGAGCCAGAGGAGGGAAGTGTTACTTGTGCTATAACTGCTTTTGTGCT
 161 AAATATGAATTGTCTCAAAATTAGCTGTGTAAAATAGCCCGGGTTCCACTGGCTCCTGCTGAGGTCCCCTTTCCTTCTGG
 241 GCTGTGAATTCCTGTACATATTTCTCTACTTTTTGTATCAGGCTTCAATTCCATTATGTTTTAATGTTGTCTCTGAAGAT
 321 GACTTGTGATTTTTTTTTCTTTTTTTTAAACCATGAAGAGCCGTTTGACAGAGCATGCTCTGCGTTGTTGGTTTCACCAG
 401 CTTCTGCCCTCACATGCACAGGGATTTAACAACAAAAATATAACTACAACTTCCCTTGTAGTCTCTTATATAAGTAGAGT
 481 CCTTGGTACTCTGCCCTCCTGTCAGTAGTGGCAGGATCTATTGGCATATTCGGGAGCTTCTTAGAGGGATGAGGTTCTTT
 561 GAACACAGTGAAAATTTAAATTAGTAACTTTTTTGCAAGCAGTTTATTGACTGTTATTGCTAAGAAGAAGTAAGAAAGAA
 641 AAAGCCTGTTGGCAATCTTGGTTATTTCTTTAAGATTTCTGGCAGTGTGGGATGGATGAATGAAGTGGAATGTGAACTTT
 721 GGGCAAGTTAAGTGGGACAGCCTTCCATGTTCATTTGTCTACCTCTTAACTGAATAAAAAAGCCTACAGTTTTTAGAAAA
 801 AAAAAAAAAAA
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' aaUUCAUUGUGGA--A--GGACUUau 5'
            |:|| |: |||  |  ||||||  
Target 5' ttAGGT-ATTCCTGCTCCCCTGAAga 3'
 43 - 67 131.00 -12.90
2 
miRNA  3' aauucAUUGUGGAAGGACUUAu 5'
               || | |:|  |||||| 
Target 5' ttgtcTACCTCTTAACTGAATa 3'
 755 - 776 125.00 -10.50
3 
miRNA  3' aauucAUUGUGG-AAGGACUUau 5'
               |||:::: | :|||||  
Target 5' tgtttTAATGTTGTCTCTGAAga 3'
 297 - 319 117.00 -6.90
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31549829 6 COSMIC
COSN30167399 12 COSMIC
COSN30487948 23 COSMIC
COSN24309076 37 COSMIC
COSN30170696 44 COSMIC
COSN30508149 44 COSMIC
COSN30479754 60 COSMIC
COSN30157393 64 COSMIC
COSN30151082 67 COSMIC
COSN30151038 71 COSMIC
COSN21343154 75 COSMIC
COSN26994964 87 COSMIC
COSN20074507 106 COSMIC
COSN30107477 107 COSMIC
COSN26958126 109 COSMIC
COSN19727969 118 COSMIC
COSN20744948 322 COSMIC
COSN8607029 356 COSMIC
COSN9855292 361 COSMIC
COSN31591160 374 COSMIC
COSN16491578 470 COSMIC
COSN30172979 505 COSMIC
COSN15947690 733 COSMIC
COSN31479716 760 COSMIC
COSN31521510 765 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1466935672 2 dbSNP
rs1252148913 6 dbSNP
rs1467457768 10 dbSNP
rs747240381 12 dbSNP
rs768802552 13 dbSNP
rs1323489685 19 dbSNP
rs369605241 21 dbSNP
rs775395202 21 dbSNP
rs1027268858 25 dbSNP
rs748412387 29 dbSNP
rs202182626 30 dbSNP
rs1466357283 31 dbSNP
rs760851519 32 dbSNP
rs769600392 37 dbSNP
rs376250620 40 dbSNP
rs982943873 41 dbSNP
rs774219046 42 dbSNP
rs370981643 43 dbSNP
rs1234692324 44 dbSNP
rs757160531 46 dbSNP
rs1280215018 48 dbSNP
rs376659839 49 dbSNP
rs1345548250 58 dbSNP
rs1170019624 74 dbSNP
rs767149735 74 dbSNP
rs575164445 75 dbSNP
rs1394235629 78 dbSNP
rs749854267 84 dbSNP
rs768720817 85 dbSNP
rs143019736 92 dbSNP
rs755543010 93 dbSNP
rs148384108 94 dbSNP
rs762832854 103 dbSNP
rs982433462 107 dbSNP
rs1207330863 111 dbSNP
rs1252839414 113 dbSNP
rs1480394583 124 dbSNP
rs771559508 128 dbSNP
rs765701839 130 dbSNP
rs775050316 143 dbSNP
rs200389756 145 dbSNP
rs1052961280 148 dbSNP
rs1345121875 152 dbSNP
rs369637380 154 dbSNP
rs763700351 157 dbSNP
rs1347519791 161 dbSNP
rs1199559131 164 dbSNP
rs191216821 165 dbSNP
rs1303659397 173 dbSNP
rs560336885 175 dbSNP
rs74335232 177 dbSNP
rs1227106531 181 dbSNP
rs1370801736 185 dbSNP
rs750327884 188 dbSNP
rs747231955 193 dbSNP
rs932479023 201 dbSNP
rs1050989639 202 dbSNP
rs549101583 208 dbSNP
rs1370570408 216 dbSNP
rs1171582437 219 dbSNP
rs1432472717 226 dbSNP
rs1394141912 232 dbSNP
rs1174006538 235 dbSNP
rs1434648185 236 dbSNP
rs1420007143 243 dbSNP
rs1405528596 248 dbSNP
rs899753117 249 dbSNP
rs147106078 258 dbSNP
rs781268542 259 dbSNP
rs531657919 260 dbSNP
rs1053089648 261 dbSNP
rs1281251151 297 dbSNP
rs893170225 318 dbSNP
rs1315430798 326 dbSNP
rs1011666280 328 dbSNP
rs1224810891 329 dbSNP
rs1044877034 330 dbSNP
rs1289645083 330 dbSNP
rs1412437705 334 dbSNP
rs1374344675 338 dbSNP
rs1303000197 340 dbSNP
rs886962019 340 dbSNP
rs905998545 340 dbSNP
rs1003940000 342 dbSNP
rs1003466542 348 dbSNP
rs1035418262 354 dbSNP
rs1414159922 355 dbSNP
rs1185745617 356 dbSNP
rs1296061376 361 dbSNP
rs550844331 364 dbSNP
rs769896902 375 dbSNP
rs1308983642 377 dbSNP
rs950952319 378 dbSNP
rs1485047465 384 dbSNP
rs1005122951 385 dbSNP
rs1217004232 387 dbSNP
rs570616869 397 dbSNP
rs973808003 406 dbSNP
rs1022644345 412 dbSNP
rs921020445 415 dbSNP
rs34871350 421 dbSNP
rs1215625245 423 dbSNP
rs796444083 431 dbSNP
rs980109954 436 dbSNP
rs1288050483 437 dbSNP
rs925444820 442 dbSNP
rs539726637 445 dbSNP
rs553173165 446 dbSNP
rs1435487622 448 dbSNP
rs957078928 450 dbSNP
rs1162616062 452 dbSNP
rs576253857 453 dbSNP
rs1369112800 459 dbSNP
rs953873122 470 dbSNP
rs1426928099 474 dbSNP
rs1422124722 475 dbSNP
rs766566366 476 dbSNP
rs138485201 477 dbSNP
rs1251538332 479 dbSNP
rs1427088377 483 dbSNP
rs749247677 486 dbSNP
rs1265486432 490 dbSNP
rs1167963297 495 dbSNP
rs1422452705 501 dbSNP
rs988292750 510 dbSNP
rs912644665 513 dbSNP
rs1323711524 514 dbSNP
rs535525736 521 dbSNP
rs1039646240 527 dbSNP
rs921267793 529 dbSNP
rs1391411079 532 dbSNP
rs143944949 533 dbSNP
rs1169400583 538 dbSNP
rs931223954 550 dbSNP
rs1193447673 555 dbSNP
rs1048804645 556 dbSNP
rs1044458311 561 dbSNP
rs1435697198 567 dbSNP
rs1289351604 573 dbSNP
rs1194623785 580 dbSNP
rs905963487 586 dbSNP
rs575173152 587 dbSNP
rs1212586586 589 dbSNP
rs10141 595 dbSNP
rs1277872475 598 dbSNP
rs768580340 603 dbSNP
rs1057480958 612 dbSNP
rs147285360 613 dbSNP
rs1233352606 614 dbSNP
rs183761600 618 dbSNP
rs1303266350 621 dbSNP
rs772249672 622 dbSNP
rs1395848061 634 dbSNP
rs1468051325 646 dbSNP
rs1217196444 656 dbSNP
rs1308784733 660 dbSNP
rs1431828866 669 dbSNP
rs534990838 677 dbSNP
rs35578179 679 dbSNP
rs898131248 681 dbSNP
rs1478539378 682 dbSNP
rs1379741177 685 dbSNP
rs1244329475 686 dbSNP
rs995592588 687 dbSNP
rs1028048759 690 dbSNP
rs1205300560 697 dbSNP
rs1483818812 700 dbSNP
rs774230078 701 dbSNP
rs1277688441 702 dbSNP
rs1012672672 709 dbSNP
rs139765267 717 dbSNP
rs11552051 721 dbSNP
rs968802151 726 dbSNP
rs999893094 727 dbSNP
rs767239592 728 dbSNP
rs6793 733 dbSNP
rs1353679861 741 dbSNP
rs760150312 742 dbSNP
rs1415274678 743 dbSNP
rs1404779657 747 dbSNP
rs765897785 748 dbSNP
rs1453631771 749 dbSNP
rs1404207712 754 dbSNP
rs1019750264 762 dbSNP
rs529473816 764 dbSNP
rs1465130986 772 dbSNP
rs753210846 775 dbSNP
rs914506580 776 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions TZM-bl
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 GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami BaL ...

- 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' aauucauuguGGAAGGacuuau 5'
                    ||||||      
Target 5' ----------CCUUCCauguuc 3'
 		1 - 12
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 GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000272542.3 | 3UTR | CCUUCCAUGUUCAUUUGUCUACCUCUUAACUG
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
76 hsa-miR-506-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT081146 LDLR low density lipoprotein receptor 2 2
MIRT083631 PRNP prion protein 2 2
MIRT157309 IKZF2 IKAROS family zinc finger 2 2 2
MIRT172369 LONRF1 LON peptidase N-terminal domain and ring finger 1 2 2
MIRT175463 ZBTB33 zinc finger and BTB domain containing 33 2 2
MIRT178171 EIF5AL1 eukaryotic translation initiation factor 5A-like 1 2 4
MIRT209107 TBL1XR1 transducin beta like 1 X-linked receptor 1 2 2
MIRT254771 XRCC6 X-ray repair cross complementing 6 2 6
MIRT264771 PAFAH1B2 platelet activating factor acetylhydrolase 1b catalytic subunit 2 2 4
MIRT309156 FGF2 fibroblast growth factor 2 2 6
MIRT334098 SFT2D2 SFT2 domain containing 2 2 2
MIRT386044 RORA RAR related orphan receptor A 2 2
MIRT453248 FTSJ3 FtsJ RNA methyltransferase homolog 3 2 2
MIRT455924 RAPGEF1 Rap guanine nucleotide exchange factor 1 2 2
MIRT456349 OLIG3 oligodendrocyte transcription factor 3 2 8
MIRT462877 ZXDB zinc finger, X-linked, duplicated B 2 2
MIRT465017 LINC00598 long intergenic non-protein coding RNA 598 2 2
MIRT466897 STMN1 stathmin 1 2 2
MIRT467919 SLC20A1 solute carrier family 20 member 1 2 2
MIRT467927 SLC16A7 solute carrier family 16 member 7 2 2
MIRT468172 SGPL1 sphingosine-1-phosphate lyase 1 2 4
MIRT483372 CYP4A22 cytochrome P450 family 4 subfamily A member 22 2 2
MIRT484061 CYP4A11 cytochrome P450 family 4 subfamily A member 11 2 2
MIRT492425 RGL2 ral guanine nucleotide dissociation stimulator like 2 2 2
MIRT495350 ATP5S ATP synthase, H+ transporting, mitochondrial Fo complex subunit s (factor B) 2 2
MIRT496983 DNAJC27 DnaJ heat shock protein family (Hsp40) member C27 2 2
MIRT503380 SOD2 superoxide dismutase 2 2 4
MIRT505598 SLC38A1 solute carrier family 38 member 1 2 6
MIRT507384 EN2 engrailed homeobox 2 2 6
MIRT508638 RPL23A ribosomal protein L23a 2 6
MIRT509813 SULT1B1 sulfotransferase family 1B member 1 2 4
MIRT509883 ENPP6 ectonucleotide pyrophosphatase/phosphodiesterase 6 2 4
MIRT512038 DNAJC10 DnaJ heat shock protein family (Hsp40) member C10 2 4
MIRT512513 BTBD19 BTB domain containing 19 2 2
MIRT513071 CHST6 carbohydrate sulfotransferase 6 2 2
MIRT514049 AGO2 argonaute 2, RISC catalytic component 2 6
MIRT516464 RAB32 RAB32, member RAS oncogene family 2 4
MIRT523441 GPR137C G protein-coupled receptor 137C 2 4
MIRT523957 DYNLT1 dynein light chain Tctex-type 1 2 4
MIRT524143 LDHD lactate dehydrogenase D 2 4
MIRT524632 C4orf32 family with sequence similarity 241 member A 2 4
MIRT531710 TFEC transcription factor EC 2 2
MIRT532813 MRPS10 mitochondrial ribosomal protein S10 2 2
MIRT534244 SLC16A1 solute carrier family 16 member 1 2 2
MIRT534328 SHISA6 shisa family member 6 2 2
MIRT543334 UTP14C UTP14C, small subunit processome component 2 2
MIRT545944 ZBTB18 zinc finger and BTB domain containing 18 2 4
MIRT549008 CCDC6 coiled-coil domain containing 6 2 2
MIRT549226 BAZ2B bromodomain adjacent to zinc finger domain 2B 2 2
MIRT550121 RPF2 ribosome production factor 2 homolog 2 2
MIRT551421 SERTM1 serine rich and transmembrane domain containing 1 2 2
MIRT556787 KLF13 Kruppel like factor 13 2 2
MIRT561372 UBXN2B UBX domain protein 2B 2 2
MIRT561849 NPTX1 neuronal pentraxin 1 2 2
MIRT563981 SLFN11 schlafen family member 11 2 2
MIRT565747 SERTAD3 SERTA domain containing 3 2 2
MIRT569130 TMC5 transmembrane channel like 5 2 4
MIRT572714 LHX6 LIM homeobox 6 2 2
MIRT624539 BROX BRO1 domain and CAAX motif containing 2 2
MIRT637034 SPTLC3 serine palmitoyltransferase long chain base subunit 3 2 2
MIRT643213 TYW3 tRNA-yW synthesizing protein 3 homolog 2 2
MIRT646884 PLSCR1 phospholipid scramblase 1 2 2
MIRT650183 LILRA2 leukocyte immunoglobulin like receptor A2 2 2
MIRT651561 WISP1 WNT1 inducible signaling pathway protein 1 2 2
MIRT665188 HAUS5 HAUS augmin like complex subunit 5 2 2
MIRT665466 WDR13 WD repeat domain 13 2 2
MIRT668763 DDR2 discoidin domain receptor tyrosine kinase 2 2 2
MIRT680605 ZNF611 zinc finger protein 611 2 2
MIRT688564 DCAF16 DDB1 and CUL4 associated factor 16 2 2
MIRT698121 TOPBP1 DNA topoisomerase II binding protein 1 2 2
MIRT699130 SMNDC1 survival motor neuron domain containing 1 2 2
MIRT712282 PPIP5K2 diphosphoinositol pentakisphosphate kinase 2 2 2
MIRT712561 CENPO centromere protein O 2 2
MIRT715358 VCAM1 vascular cell adhesion molecule 1 2 2
MIRT720209 KCNN1 potassium calcium-activated channel subfamily N member 1 2 2
MIRT732331 MTDH metadherin 2 1
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-506 Glucose NULL 5793 Microarray endothelial cells 24394957 2014 up-regulated
miR-506 17beta-estradiol (E2) approved 5757 Microarray MCF-7 breast cancer cells 19528081 2009 down-regulated
miR-506 17beta-estradiol (E2) approved 5757 Microarray MCF-7AKT breast cancer cells 19528081 2009 down-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-506 Dabrafenib 44462760 NSC764134 approved resistant cell line (A375)
hsa-mir-506 Cisplatin 5460033 NSC119875 approved resistant cell line (CP20)
hsa-miR-506-5p Cisplatin + Decitabine sensitive High Non-Small Cell Lung Cancer cell line (A549)
hsa-miR-506-5p Tripterygium wilfordii Hook F resistant tissue
hsa-miR-506-5p Leuprorelin/Goserelin + Bicalutamide resistant tissue (prostate cancer)

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