miRTarBase - #MIRT562785


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pre-miRNA Information
pre-miRNA hsa-mir-4259   
Genomic Coordinates chr1: 159899979 - 159900079
Description Homo sapiens miR-4259 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4259
Sequence 70| CAGUUGGGUCUAGGGGUCAGGA |91
Evidence Experimental
Experiments SOLiD
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1237551241 4 dbSNP
rs772339482 8 dbSNP
rs1314022637 15 dbSNP
rs1414601728 19 dbSNP
rs746067692 20 dbSNP
rs779101228 21 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol LIMA1   
Synonyms EPLIN, SREBP3
Description LIM domain and actin binding 1
Transcript NM_001113546   
Other Transcripts NM_001113547 , NM_016357   
Expression
Putative miRNA Targets on LIMA1
3'UTR of LIMA1
(miRNA target sites are highlighted)		 
>LIMA1|NM_001113546|3'UTR
   1 CAAATTGCAATGATGCTGGGCCTTAAATTCATGTTAGTGTTAGCGAGCCACTGCCCTTTGTCAAAATGTGATGCACATAA
  81 GCAGGTATCCCAGCATGAAATGTAATTTACTTGGAAGTAACTTTGGAAAAGAATTCCTTCTTAAAATCAAAAACAAAACA
 161 AAAAAACACAAAAAACACATTCTAAATACTAGAGATAACTTTACTTAAATTCTTCATTTTAGCAGTGATGATATGCATAA
 241 GTGCTGTAAGGCTTGTAACTGGGGAAATATTCCACCTGATAATAGCCCAGATTCTACTGTATTCCCAAAAGGCAATATTA
 321 AGGTAGACAGATGATTAGTAGTATATTGTTACACACTATTTTGGAATTAGAGAACATACAGAAGGAATTTAGGGGCTTAA
 401 ACATTACGACTGAATGCACTTTAGTATAAAGGGCACAGTTTGTATATTTTTAAATGAATACCAATTTAATTTTTTAGTAT
 481 TTACCTGTTAAGAGATTATTTAGTCTTTAAATTTTTTAGGTTAATTTTCTTGCTGTGATATATATGAGGAATTTACTACT
 561 TTATGTCCTGCTCTCTAAACTACATCCTGAACTCGACGTCCTGAGGTATAATACAACAGAGCACTTTTTGAGGCAATTGA
 641 AAAACCAACCTACACTCTTCGGTGCTTAGAGAGATCTGCTGTCTCCCAAATAAGCTTTTGTATCTGCCAGTGAATTTACT
 721 GTACTCCAAATGATTGCTTTCTTTTCTGGTGATATCTGTGCTTCTCATAATTACTGAAAGCTGCAATATTTTAGTAATAC
 801 CTTCGGGATCACTGTCCCCCATCTTCCGTGTTAGAGCAAAGTGAAGAGTTTAAAGGAGGAAGAAGAAAGAACTGTCTTAC
 881 ACCACTTGAGCTCAGACCTCTAAACCCTGTATTTCCCTTATGATGTCCCCTTTTTGAGACACTAATTTTTAAATACTTAC
 961 TAGCTCTGAAATATATTGATTTTTATCACAGTATTCTCAGGGTGAAATTAAACCAACTATAGGCCTTTTTCTTGGGATGA
1041 TTTTCTAGTCTTAAGGTTTGGGGACATTATAAACTTGAGTACATTTGTTGTACACAGTTGATATTCCAAATTGTATGGAT
1121 GGGAGGGAGAGGTGTCTTAAGCTGTAGGCTTTTCTTTGTACTGCATTTATAGAGATTTAGCTTTAATATTTTTTAGAGAT
1201 GTAAAACATTCTGCTTTCTTAGTCTTACCTAGTCTGAAACATTTTTATTCAATAAAGATTTTAATTAAAATTTGAACTTT
1281 TCAAAAAAAAA
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' aggacuggggaucugGGUUGAc 5'
                         |||||| 
Target 5' cagggtgaaattaaaCCAACTa 3'
 998 - 1019 120.00 -8.50
2 
miRNA  3' aggaCUGGGGAU-CUGGGUUGAc 5'
              ||:| ||:   |||| || 
Target 5' tcggGATCACTGTCCCCCATCTt 3'
 803 - 825 118.00 -12.00
3 
miRNA  3' agGACUGGGGAUCUGGGUUGAc 5'
            ||| : :||   ||||| | 
Target 5' atCTGCTGTCT---CCCAAATa 3'
 674 - 692 117.00 -11.62
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31549680 20 COSMIC
COSN30102968 23 COSMIC
COSN30127884 36 COSMIC
COSN30500174 43 COSMIC
COSN30519911 51 COSMIC
COSN31601621 108 COSMIC
COSN31599229 131 COSMIC
COSN31560721 142 COSMIC
COSN30144445 148 COSMIC
COSN18747104 159 COSMIC
COSN30519510 212 COSMIC
COSN1148926 352 COSMIC
COSN5945638 604 COSMIC
COSN6616205 720 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1336017651 3 dbSNP
rs1308811694 5 dbSNP
rs1192583220 7 dbSNP
rs748625422 10 dbSNP
rs1191637353 11 dbSNP
rs1364809928 16 dbSNP
rs373388466 18 dbSNP
rs1426535965 20 dbSNP
rs769840083 30 dbSNP
rs1158108643 32 dbSNP
rs746814149 33 dbSNP
rs777671959 36 dbSNP
rs758451635 37 dbSNP
rs752660777 39 dbSNP
rs778346637 41 dbSNP
rs754509271 42 dbSNP
rs766072431 44 dbSNP
rs760201311 45 dbSNP
rs750813076 49 dbSNP
rs1047273659 53 dbSNP
rs1276193305 65 dbSNP
rs926088915 67 dbSNP
rs1405956146 71 dbSNP
rs557763648 73 dbSNP
rs1347708030 75 dbSNP
rs1044544874 77 dbSNP
rs1332419506 84 dbSNP
rs948780857 94 dbSNP
rs901405534 95 dbSNP
rs1041722444 102 dbSNP
rs1485241253 104 dbSNP
rs917334186 108 dbSNP
rs534688027 125 dbSNP
rs1265956374 126 dbSNP
rs565878967 131 dbSNP
rs1187867044 142 dbSNP
rs919298748 148 dbSNP
rs989213964 167 dbSNP
rs1165729693 176 dbSNP
rs1330369203 176 dbSNP
rs936440673 178 dbSNP
rs201225828 180 dbSNP
rs1300183961 181 dbSNP
rs972612475 184 dbSNP
rs868167823 185 dbSNP
rs1400465117 203 dbSNP
rs1177013723 207 dbSNP
rs1292632538 207 dbSNP
rs962624512 216 dbSNP
rs1229859814 224 dbSNP
rs1312981242 225 dbSNP
rs977879209 226 dbSNP
rs1426863355 236 dbSNP
rs1044370 237 dbSNP
rs1488312255 238 dbSNP
rs187574228 241 dbSNP
rs1233635890 246 dbSNP
rs1256085814 251 dbSNP
rs917834834 253 dbSNP
rs991184380 259 dbSNP
rs1407518676 269 dbSNP
rs1417496334 278 dbSNP
rs1160687914 286 dbSNP
rs567468343 314 dbSNP
rs1434209240 316 dbSNP
rs1006743192 323 dbSNP
rs953890376 325 dbSNP
rs9364 328 dbSNP
rs1449937249 329 dbSNP
rs997983366 340 dbSNP
rs1303153358 343 dbSNP
rs1257992780 346 dbSNP
rs1372345551 347 dbSNP
rs891446069 348 dbSNP
rs1237451128 353 dbSNP
rs1031341128 355 dbSNP
rs1224585744 363 dbSNP
rs1326267525 372 dbSNP
rs1000364771 375 dbSNP
rs904802097 376 dbSNP
rs530856969 377 dbSNP
rs1218988169 379 dbSNP
rs1314529526 385 dbSNP
rs1044513388 397 dbSNP
rs952790795 399 dbSNP
rs1025756268 402 dbSNP
rs1479882078 403 dbSNP
rs948875304 407 dbSNP
rs1203720402 408 dbSNP
rs1171914689 410 dbSNP
rs1443968182 412 dbSNP
rs896025077 415 dbSNP
rs565164129 421 dbSNP
rs1057460798 431 dbSNP
rs3794312 433 dbSNP
rs1337317992 438 dbSNP
rs929416366 440 dbSNP
rs368726386 442 dbSNP
rs973421343 444 dbSNP
rs941232807 446 dbSNP
rs559041020 452 dbSNP
rs1377270611 454 dbSNP
rs779759933 462 dbSNP
rs867791743 464 dbSNP
rs529123679 481 dbSNP
rs1272519154 492 dbSNP
rs985396742 492 dbSNP
rs1175139974 496 dbSNP
rs1369108495 503 dbSNP
rs954008451 509 dbSNP
rs889432306 510 dbSNP
rs1053883371 520 dbSNP
rs755663697 541 dbSNP
rs1200988331 559 dbSNP
rs1468158095 561 dbSNP
rs1197028921 567 dbSNP
rs1409013740 568 dbSNP
rs1179107305 570 dbSNP
rs976872377 572 dbSNP
rs1248485148 573 dbSNP
rs1437906966 575 dbSNP
rs1478407596 583 dbSNP
rs955817583 589 dbSNP
rs183299967 592 dbSNP
rs1042154872 594 dbSNP
rs1400784066 595 dbSNP
rs138900845 597 dbSNP
rs1209900957 598 dbSNP
rs79474948 600 dbSNP
rs1201955140 614 dbSNP
rs1351066554 624 dbSNP
rs1436636095 628 dbSNP
rs1270122528 634 dbSNP
rs1339166828 635 dbSNP
rs780922616 636 dbSNP
rs1221017624 647 dbSNP
rs904225483 648 dbSNP
rs1334641762 650 dbSNP
rs1237423779 651 dbSNP
rs1292347431 654 dbSNP
rs557558296 660 dbSNP
rs1215243453 661 dbSNP
rs1262374337 672 dbSNP
rs1476769500 673 dbSNP
rs1195764168 678 dbSNP
rs959565092 680 dbSNP
rs1474770827 682 dbSNP
rs150238660 700 dbSNP
rs984102620 710 dbSNP
rs3184122 720 dbSNP
rs191777026 721 dbSNP
rs757992397 727 dbSNP
rs1358078447 729 dbSNP
rs1057304531 737 dbSNP
rs1402354805 739 dbSNP
rs1299361759 740 dbSNP
rs74090094 749 dbSNP
rs965533513 752 dbSNP
rs1286169929 753 dbSNP
rs1376925592 755 dbSNP
rs1357397171 761 dbSNP
rs1223445877 766 dbSNP
rs530327773 768 dbSNP
rs1489332399 769 dbSNP
rs1218640909 778 dbSNP
rs569845402 800 dbSNP
rs1441602051 801 dbSNP
rs762254077 802 dbSNP
rs535967653 804 dbSNP
rs749836957 805 dbSNP
rs941994121 808 dbSNP
rs549937271 817 dbSNP
rs570031362 819 dbSNP
rs1053996219 820 dbSNP
rs1377889918 821 dbSNP
rs910593455 827 dbSNP
rs1159745396 828 dbSNP
rs985364148 830 dbSNP
rs76020374 834 dbSNP
rs922388123 869 dbSNP
rs949166130 877 dbSNP
rs1341453942 881 dbSNP
rs1441704085 881 dbSNP
rs1307377174 886 dbSNP
rs976630045 887 dbSNP
rs137999054 912 dbSNP
rs1286650424 915 dbSNP
rs1344142932 918 dbSNP
rs1184337742 925 dbSNP
rs955952221 931 dbSNP
rs1446483443 934 dbSNP
rs917728741 935 dbSNP
rs1055386561 936 dbSNP
rs9588 942 dbSNP
rs113893061 947 dbSNP
rs369182029 947 dbSNP
rs1440991199 961 dbSNP
rs1181732839 962 dbSNP
rs571614970 974 dbSNP
rs1486401315 975 dbSNP
rs937882265 984 dbSNP
rs978504999 986 dbSNP
rs1352591409 987 dbSNP
rs968348332 999 dbSNP
rs1329526737 1002 dbSNP
rs1022595187 1004 dbSNP
rs1379481578 1006 dbSNP
rs1447595366 1007 dbSNP
rs765295577 1017 dbSNP
rs960338743 1020 dbSNP
rs1230913541 1021 dbSNP
rs931298620 1022 dbSNP
rs1036241180 1034 dbSNP
rs35296054 1037 dbSNP
rs755086115 1040 dbSNP
rs1319343301 1041 dbSNP
rs1458776724 1050 dbSNP
rs1178873301 1055 dbSNP
rs1266011301 1056 dbSNP
rs141231876 1057 dbSNP
rs1430977757 1063 dbSNP
rs993670786 1065 dbSNP
rs1311926743 1066 dbSNP
rs1382771518 1067 dbSNP
rs1363968638 1070 dbSNP
rs75806702 1085 dbSNP
rs1037784863 1096 dbSNP
rs1378760831 1100 dbSNP
rs528355882 1108 dbSNP
rs972777799 1109 dbSNP
rs965865956 1114 dbSNP
rs1169063733 1118 dbSNP
rs1006341913 1119 dbSNP
rs1019721791 1127 dbSNP
rs1223831670 1128 dbSNP
rs186892814 1131 dbSNP
rs548678598 1132 dbSNP
rs766641034 1139 dbSNP
rs535980292 1141 dbSNP
rs1050417714 1142 dbSNP
rs544943633 1143 dbSNP
rs563226421 1146 dbSNP
rs1032554808 1172 dbSNP
rs932536516 1174 dbSNP
rs543656209 1175 dbSNP
rs1275999765 1181 dbSNP
rs577815937 1182 dbSNP
rs1198836452 1189 dbSNP
rs1264547210 1192 dbSNP
rs1001076977 1200 dbSNP
rs1205350558 1201 dbSNP
rs1211188148 1208 dbSNP
rs1268652502 1211 dbSNP
rs922557121 1219 dbSNP
rs1477748887 1221 dbSNP
rs760760709 1228 dbSNP
rs934492025 1229 dbSNP
rs902154142 1232 dbSNP
rs1192004746 1238 dbSNP
rs924481708 1242 dbSNP
rs1164302663 1254 dbSNP
rs564297290 1257 dbSNP
rs1013312333 1262 dbSNP
rs773745504 1265 dbSNP
rs896206470 1270 dbSNP
rs1488139173 1274 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
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 GSM545216. RNA binding protein: AGO2. Condition:miR-124 transfection ...

- Hafner M; Landthaler M; Burger L; Khorshid et al., 2010, Cell.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' aggacuggggaucugGGUUGAc 5'
                         |||||| 
Target 5' -------aaauuaaaCCAACUa 3'
 		1 - 15
Article - Hafner M; Landthaler M; Burger L; Khorshid et al.
- Cell, 2010
RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.
LinkOut: [PMID: 20371350]
CLIP-seq Support 1 for dataset GSM545216
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-124 transfection
Location of target site ENST00000552491.1 | 3UTR | AAAUUAAACCAACUAUAGGCCUUUUUC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
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
40 hsa-miR-4259 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT074403 TNRC6A trinucleotide repeat containing 6A 2 2
MIRT082380 HNRNPUL1 heterogeneous nuclear ribonucleoprotein U like 1 2 6
MIRT224489 NDRG1 N-myc downstream regulated 1 2 2
MIRT227807 GTF3C4 general transcription factor IIIC subunit 4 2 2
MIRT293253 DR1 down-regulator of transcription 1 2 2
MIRT455060 MEN1 menin 1 2 2
MIRT459206 RCE1 Ras converting CAAX endopeptidase 1 2 2
MIRT464866 UBB ubiquitin B 2 8
MIRT464897 UBALD1 UBA like domain containing 1 2 2
MIRT467210 SPRY4 sprouty RTK signaling antagonist 4 2 2
MIRT467749 SLC36A1 solute carrier family 36 member 1 2 2
MIRT470565 POU2F1 POU class 2 homeobox 1 2 2
MIRT473523 MAX MYC associated factor X 2 2
MIRT474955 KCTD10 potassium channel tetramerization domain containing 10 2 4
MIRT478575 CTNND1 catenin delta 1 2 2
MIRT479952 CBX4 chromobox 4 2 6
MIRT486151 SIX5 SIX homeobox 5 2 6
MIRT488836 MRRF mitochondrial ribosome recycling factor 2 2
MIRT489466 MSC musculin 2 2
MIRT498922 SRCAP Snf2 related CREBBP activator protein 2 2
MIRT501166 SLC10A7 solute carrier family 10 member 7 2 6
MIRT504195 FAM127B retrotransposon Gag like 8A 2 2
MIRT507342 FAM168A family with sequence similarity 168 member A 2 2
MIRT512629 GPX1 glutathione peroxidase 1 2 4
MIRT514365 UBBP4 ubiquitin B pseudogene 4 2 6
MIRT523321 H3F3B H3 histone family member 3B 2 2
MIRT529793 AP4S1 adaptor related protein complex 4 sigma 1 subunit 2 2
MIRT544301 TSPYL1 TSPY like 1 2 2
MIRT552985 VAT1 vesicle amine transport 1 2 2
MIRT562785 LIMA1 LIM domain and actin binding 1 2 2
MIRT653090 SSR3 signal sequence receptor subunit 3 2 2
MIRT661985 DSN1 DSN1 homolog, MIS12 kinetochore complex component 2 4
MIRT666982 PHAX phosphorylated adaptor for RNA export 2 2
MIRT683255 WFDC6 WAP four-disulfide core domain 6 2 2
MIRT684051 FOLR1 folate receptor 1 2 2
MIRT686137 B4GALT7 beta-1,4-galactosyltransferase 7 2 2
MIRT688435 DNAL1 dynein axonemal light chain 1 2 2
MIRT698391 TMED2 transmembrane p24 trafficking protein 2 2 2
MIRT698819 STK38 serine/threonine kinase 38 2 2
MIRT715754 HSD11B1L hydroxysteroid 11-beta dehydrogenase 1 like 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-4 Dexamethasone approved 5743 Microarray primary rat thymocytes 20847043 2010 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-4259 Cisplatin 5460033 NSC119875 approved resistant High Pancreatic Cancer cell line (BxPC-3)
hsa-miR-4259 Fluorouracil 3385 NSC19893 approved sensitive High Pancreatic Cancer cell line (PATU8988)
hsa-miR-4259 Paclitaxel 36314 NSC125973 approved resistant High Non-Small Cell Lung Cancer cell line (A549)
hsa-miR-4259 Imatinib 5291 NSC743414 approved resistant High Chronic Myelogenous Leukemia cell line (K562)
hsa-miR-4259 Temozolomide 5394 NSC362856 approved resistant High Glioblastoma cell line (U251)
hsa-mir-4259 Cisplatin 5460033 NSC119875 approved resistant cell line (BxPC3)
hsa-miR-4259 Temozolomide 5394 NSC362856 approved sensitive cell line (U251)
hsa-miR-4259 Osimertinib 71496458 NSC779217 approved sensitive cell line (H1975)
hsa-miR-4259 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4259 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)
hsa-miR-4259 Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (100 ng/ml)
hsa-miR-4259 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-4259 Docetaxel+Cisplatin+5-Fluorouracil resistant tissue (hypopharyngeal squamous cell carcinoma)

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