miRTarBase - #MIRT538707


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pre-miRNA Information
pre-miRNA hsa-mir-4473   
Genomic Coordinates chr9: 20411148 - 20411238
Description Homo sapiens miR-4473 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4473
Sequence 57| CUAGUGCUCUCCGUUACAAGUA |78
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs987949614 1 dbSNP
rs1199578146 4 dbSNP
rs1261784605 4 dbSNP
rs950939079 6 dbSNP
rs573478506 9 dbSNP
rs182397728 12 dbSNP
rs963590806 17 dbSNP
rs1452942530 19 dbSNP
rs1016614368 20 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol CAPRIN2   
Synonyms C1QDC1, EEG-1, EEG1, RNG140
Description caprin family member 2
Transcript NM_032156   
Other Transcripts NM_023925 , NM_001002259   
Expression
Putative miRNA Targets on CAPRIN2
3'UTR of CAPRIN2
(miRNA target sites are highlighted)		 
>CAPRIN2|NM_032156|3'UTR
   1 GCAGCCCAGAAAGAGACAACGAAACCTTTAACAGTGGTGACTCTGGACAAGGAGACTCCCGTAGCATGACCCCTGTGGAT
  81 GTGCCAGTGACAAATCCAGCAGCCACCATACTGCCAGTACACGTCTACCCTCTGCCTCAGCAGATGCGAGTTGCCTTCTC
 161 AGCAGCCAGAACCTCTAATCTGGCCCCTGGAACTTTAGACCAACCTATTGTGTTTGATCTTCTTCTGAACAACTTAGGAG
 241 AAACTTTTGATCTTCAGCTTGGTAGATTTAATTGCCCAGTGAATGGCACTTACGTTTTCATTTTTCACATGCTAAAGCTG
 321 GCAGTGAATGTGCCACTGTATGTCAACCTCATGAAGAATGAAGAGGTCTTGGTATCAGCCTATGCCAATGATGGTGCTCC
 401 AGACCATGAAACTGCTAGCAATCATGCAATTCTTCAGCTCTTCCAGGGAGACCAGATATGGTTACGTCTGCACAGGGGAG
 481 CAATTTATGGAAGTAGCTGGAAATATTCTACGTTTTCAGGCTATCTTCTTTATCAAGATTGAAAGTCAGTACAGTATTGA
 561 CAATAAAAGGATGGTGTTCTAATTAGTGGGATTGAAGGAAAAGTAGTCTTTGCCCTCATGACTGATTGGTTTAGGAAAAT
 641 GTTTTTGTTCCTAGAGGGAGGAGGTCCTTACTTTTTTGTTTTCCTTCCTGAGGTGAAAAATCAAGCTGAATGACAATTAG
 721 CACTAATCTGGCACTTTATAAATTGTGATGTAGCCTCGCTAGTCAAGCTGTGAATGTATATTGTTTGCACTTAATCCTTA
 801 ACTGTATTAACGTTCAGCTTACTAAACTGACTGCCTCAAGTCCAGGCAAGTTACAATGCCTTGTTGTGCCTCAATAAAAA
 881 AGTTACATGCACAAAAAAAAAAAAAAAAAA
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' augaacAUUGCCUCUCGUGAUc 5'
                |:||    ||||||| 
Target 5' gctgaaTGACAATTAGCACTAa 3'
 705 - 726 144.00 -9.00
2 
miRNA  3' augAAC--AUUGCCUCUCGUGAuc 5'
             |||   |::| | :|||||  
Target 5' taaTTGCCCAGTGAATGGCACTta 3'
 269 - 292 117.00 -6.90
3 
miRNA  3' augaacAUUGCCUCUCG--UGAUc 5'
                |||||   |||  |||| 
Target 5' ctgtatTAACGTTCAGCTTACTAa 3'
 802 - 825 116.00 -5.60
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSM1660979 3 COSMIC
COSM5693351 8 COSMIC
COSM1361180 13 COSMIC
COSM938647 21 COSMIC
COSM3792517 36 COSMIC
COSM4777589 55 COSMIC
COSM7122598 60 COSMIC
COSM2205129 61 COSMIC
COSM6136828 62 COSMIC
COSM5346157 63 COSMIC
COSM6620007 63 COSMIC
COSM4926328 70 COSMIC
COSM3460085 73 COSMIC
COSM5580520 80 COSMIC
COSM7227440 96 COSMIC
COSM243477 97 COSMIC
COSM4849937 101 COSMIC
COSM4669197 102 COSMIC
COSM5949547 111 COSMIC
COSM5696414 113 COSMIC
COSM6620001 117 COSMIC
COSM9066392 122 COSMIC
COSM6619987 124 COSMIC
COSM5633827 138 COSMIC
COSM7598776 148 COSMIC
COSM2205128 150 COSMIC
COSM8412134 157 COSMIC
COSM4430152 168 COSMIC
COSM4041363 182 COSMIC
COSM1188461 183 COSMIC
COSM4622587 213 COSMIC
COSM8266468 228 COSMIC
COSM2205127 237 COSMIC
COSM2205126 238 COSMIC
COSM9466709 240 COSMIC
COSM9682514 255 COSMIC
COSM7464513 261 COSMIC
COSM4669196 268 COSMIC
COSM8550685 286 COSMIC
COSM8219450 294 COSMIC
COSM9014014 295 COSMIC
COSM5375014 299 COSMIC
COSM1676815 306 COSMIC
COSM3416782 316 COSMIC
COSM54384 317 COSMIC
COSM272458 365 COSMIC
COSM8342849 369 COSMIC
COSM5051540 382 COSMIC
COSM9617289 407 COSMIC
COSM938646 429 COSMIC
COSM1361179 440 COSMIC
COSM4669195 446 COSMIC
COSM9593529 457 COSMIC
COSM7789144 459 COSMIC
COSM3460084 461 COSMIC
COSM6619976 468 COSMIC
COSM938645 470 COSMIC
COSM4752045 475 COSMIC
COSM324919 480 COSMIC
COSM8617886 506 COSMIC
COSM938644 512 COSMIC
COSM4669194 513 COSMIC
COSM938643 518 COSMIC
COSM938642 519 COSMIC
COSM4895174 528 COSMIC
COSM3931617 541 COSMIC
COSN30743279 552 COSMIC
COSN31566830 556 COSMIC
COSN30155251 594 COSMIC
COSN30159637 617 COSMIC
COSN1147004 720 COSMIC
COSN30112699 758 COSMIC
COSN14492544 812 COSMIC
COSN14442204 843 COSMIC
COSN24609770 874 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs767335762 11 dbSNP
rs761381989 12 dbSNP
rs1266097235 13 dbSNP
rs1291109213 14 dbSNP
rs371328465 20 dbSNP
rs763676110 21 dbSNP
rs201095477 32 dbSNP
rs775373364 33 dbSNP
rs927003563 35 dbSNP
rs1290081279 36 dbSNP
rs769605672 38 dbSNP
rs1203703629 39 dbSNP
rs1329347533 49 dbSNP
rs759274017 51 dbSNP
rs1387482218 54 dbSNP
rs367800608 60 dbSNP
rs772253137 61 dbSNP
rs1184415727 63 dbSNP
rs79552778 65 dbSNP
rs778912498 66 dbSNP
rs1160761901 67 dbSNP
rs1163985928 68 dbSNP
rs1321887575 81 dbSNP
rs375234262 83 dbSNP
rs878879989 87 dbSNP
rs976348698 97 dbSNP
rs535610393 98 dbSNP
rs1245791745 100 dbSNP
rs780659467 104 dbSNP
rs1407267158 105 dbSNP
rs1465146378 106 dbSNP
rs372208056 107 dbSNP
rs140741615 108 dbSNP
rs965803693 113 dbSNP
rs202247225 116 dbSNP
rs756917174 119 dbSNP
rs111761506 122 dbSNP
rs150951809 123 dbSNP
rs200055967 127 dbSNP
rs142547870 129 dbSNP
rs752649925 133 dbSNP
rs1389763799 135 dbSNP
rs570016104 136 dbSNP
rs765096929 137 dbSNP
rs759470076 140 dbSNP
rs957278438 147 dbSNP
rs1402077640 148 dbSNP
rs1455389279 155 dbSNP
rs1173720763 165 dbSNP
rs35671069 171 dbSNP
rs776471356 171 dbSNP
rs766177185 182 dbSNP
rs1187468293 185 dbSNP
rs951655638 186 dbSNP
rs368158820 190 dbSNP
rs774594835 192 dbSNP
rs768642984 198 dbSNP
rs375715809 202 dbSNP
rs776145639 212 dbSNP
rs1202129537 215 dbSNP
rs1207870603 225 dbSNP
rs770489821 233 dbSNP
rs1350095728 241 dbSNP
rs746362702 243 dbSNP
rs781457861 248 dbSNP
rs1366190046 249 dbSNP
rs774768463 252 dbSNP
rs900613675 270 dbSNP
rs1272219121 278 dbSNP
rs1446242687 290 dbSNP
rs7137533 293 dbSNP
rs746668837 294 dbSNP
rs777431817 296 dbSNP
rs995767047 309 dbSNP
rs1390514377 314 dbSNP
rs1431552996 316 dbSNP
rs1368096477 323 dbSNP
rs757913295 326 dbSNP
rs752132555 329 dbSNP
rs764717286 333 dbSNP
rs1421162128 338 dbSNP
rs1479836389 342 dbSNP
rs1179806087 365 dbSNP
rs754960381 366 dbSNP
rs1171614009 374 dbSNP
rs905471781 377 dbSNP
rs1237875538 378 dbSNP
rs1400936699 386 dbSNP
rs753786665 393 dbSNP
rs766120931 401 dbSNP
rs1251067671 407 dbSNP
rs1414537553 411 dbSNP
rs1204523298 413 dbSNP
rs181542791 425 dbSNP
rs774451227 429 dbSNP
rs1226851672 442 dbSNP
rs1324302170 443 dbSNP
rs1200599835 445 dbSNP
rs764345990 446 dbSNP
rs763263714 454 dbSNP
rs1297370920 455 dbSNP
rs1417071317 458 dbSNP
rs763274346 459 dbSNP
rs769971620 465 dbSNP
rs868684130 466 dbSNP
rs1273569334 473 dbSNP
rs1052436238 475 dbSNP
rs1355797209 487 dbSNP
rs746415665 488 dbSNP
rs371420705 491 dbSNP
rs925282811 496 dbSNP
rs886569319 506 dbSNP
rs766398707 511 dbSNP
rs552563059 512 dbSNP
rs777291280 523 dbSNP
rs1463736781 532 dbSNP
rs771471072 532 dbSNP
rs747779716 536 dbSNP
rs1480975218 541 dbSNP
rs1208271621 547 dbSNP
rs778437920 553 dbSNP
rs754447478 557 dbSNP
rs555054269 559 dbSNP
rs1043740457 560 dbSNP
rs779984888 562 dbSNP
rs1208500830 563 dbSNP
rs189968218 571 dbSNP
rs750299811 579 dbSNP
rs767407050 581 dbSNP
rs931902951 584 dbSNP
rs763315430 587 dbSNP
rs1173844666 595 dbSNP
rs1440990923 596 dbSNP
rs1385761857 597 dbSNP
rs563741832 601 dbSNP
rs1320742969 602 dbSNP
rs1314167580 603 dbSNP
rs1389913985 609 dbSNP
rs1413491435 610 dbSNP
rs899395230 629 dbSNP
rs762896446 638 dbSNP
rs140573371 640 dbSNP
rs770022713 669 dbSNP
rs748225054 671 dbSNP
rs1406212855 678 dbSNP
rs1158278811 683 dbSNP
rs1473240971 684 dbSNP
rs1420130415 687 dbSNP
rs1228072858 701 dbSNP
rs776477965 702 dbSNP
rs1268999418 704 dbSNP
rs927036348 719 dbSNP
rs7032 725 dbSNP
rs1266354119 730 dbSNP
rs1256654078 731 dbSNP
rs1216376636 745 dbSNP
rs559739172 754 dbSNP
rs983199926 757 dbSNP
rs1448556832 758 dbSNP
rs566062111 767 dbSNP
rs1281884601 775 dbSNP
rs1221739563 777 dbSNP
rs1222913652 789 dbSNP
rs1327827846 790 dbSNP
rs1292177073 801 dbSNP
rs988648503 811 dbSNP
rs1387874429 812 dbSNP
rs957308872 815 dbSNP
rs1294605120 816 dbSNP
rs1348776395 834 dbSNP
rs951811668 842 dbSNP
rs1027312391 845 dbSNP
rs1355410272 851 dbSNP
rs964649590 856 dbSNP
rs1433467809 861 dbSNP
rs1264648548 864 dbSNP
rs1356721292 866 dbSNP
rs1211627808 877 dbSNP
rs1249526074 881 dbSNP
rs1482466779 885 dbSNP
rs746846269 886 dbSNP
rs1343860850 887 dbSNP
rs1182294203 889 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 65981.0
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 GSM714644. RNA binding protein: AGO2. Condition:completeT1 ...

- Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' augaacauugccucUCGUGAUc 5'
                        ||||||| 
Target 5' --------acaauuAGCACUAa 3'
 		1 - 14
Article - Kishore S; Jaskiewicz L; Burger L; Hausser et al.
- Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions hESCs (WA-09)
Disease 65981.0
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 SRR359787. RNA binding protein: AGO2. Condition:4-thiouridine ...

- Lipchina I; Elkabetz Y; Hafner M; Sheridan et al., 2011, Genes & development.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' augaacauugccucUCGUGAUc 5'
                        ||||||| 
Target 5' --------acaauuAGCACUAa 3'
 		1 - 14
Article - Lipchina I; Elkabetz Y; Hafner M; Sheridan et al.
- Genes & development, 2011
MicroRNAs are important regulators in many cellular processes, including stem cell self-renewal. Recent studies demonstrated their function as pluripotency factors with the capacity for somatic cell reprogramming. However, their role in human embryonic stem (ES) cells (hESCs) remains poorly understood, partially due to the lack of genome-wide strategies to identify their targets. Here, we performed comprehensive microRNA profiling in hESCs and in purified neural and mesenchymal derivatives. Using a combination of AGO cross-linking and microRNA perturbation experiments, together with computational prediction, we identified the targets of the miR-302/367 cluster, the most abundant microRNAs in hESCs. Functional studies identified novel roles of miR-302/367 in maintaining pluripotency and regulating hESC differentiation. We show that in addition to its role in TGF-beta signaling, miR-302/367 promotes bone morphogenetic protein (BMP) signaling by targeting BMP inhibitors TOB2, DAZAP2, and SLAIN1. This study broadens our understanding of microRNA function in hESCs and is a valuable resource for future studies in this area.
LinkOut: [PMID: 22012620]
CLIP-seq Support 1 for dataset GSM714644
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repA
Location of target site ENST00000395805.2 | 3UTR | ACAAUUAGCACUAAUCUGGCACUUUAUAAAUUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset SRR359787
Method / RBP PAR-CLIP / AGO2
Cell line / Condition hESCs (WA-09) / 4-thiouridine, RNase T1
Location of target site ENST00000395805.2 | 3UTR | ACAAUUAGCACUAAUCUGGCACUUUAUAAAUUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22012620 / SRX103431
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
53 hsa-miR-4473 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT193963 GLCE glucuronic acid epimerase 2 2
MIRT232832 NUPL1 nucleoporin 58 2 2
MIRT306237 ZMAT3 zinc finger matrin-type 3 2 4
MIRT441353 ZNF75A zinc finger protein 75a 2 2
MIRT443665 FLT1 fms related tyrosine kinase 1 2 2
MIRT448553 RAP1A RAP1A, member of RAS oncogene family 2 2
MIRT448625 OSBPL8 oxysterol binding protein like 8 2 2
MIRT449138 UQCRB ubiquinol-cytochrome c reductase binding protein 2 2
MIRT462942 ZNF800 zinc finger protein 800 2 12
MIRT463962 WIPF2 WAS/WASL interacting protein family member 2 2 2
MIRT466315 THRA thyroid hormone receptor, alpha 2 2
MIRT493504 IL6ST interleukin 6 signal transducer 2 2
MIRT502727 CLIP1 CAP-Gly domain containing linker protein 1 2 8
MIRT503464 ZNF154 zinc finger protein 154 2 6
MIRT506738 LMLN leishmanolysin like peptidase 2 4
MIRT507282 FEM1B fem-1 homolog B 2 2
MIRT510711 SPG20 spartin 2 6
MIRT524495 CEP170 centrosomal protein 170 2 4
MIRT529425 MALT1 MALT1 paracaspase 2 2
MIRT533482 TRIM71 tripartite motif containing 71 2 2
MIRT533715 TMEM30A transmembrane protein 30A 2 2
MIRT534115 SOCS3 suppressor of cytokine signaling 3 2 2
MIRT534473 SAR1B secretion associated Ras related GTPase 1B 2 2
MIRT536519 KCTD10 potassium channel tetramerization domain containing 10 2 2
MIRT537263 GALNT3 polypeptide N-acetylgalactosaminyltransferase 3 2 2
MIRT537597 ESRP2 epithelial splicing regulatory protein 2 2 2
MIRT537918 DSTYK dual serine/threonine and tyrosine protein kinase 2 2
MIRT538074 DIAPH2 diaphanous related formin 2 2 2
MIRT538707 CAPRIN2 caprin family member 2 2 4
MIRT546187 TPD52 tumor protein D52 2 4
MIRT546942 SFTPA1 surfactant protein A1 2 2
MIRT549590 TMEM101 transmembrane protein 101 2 2
MIRT551686 ASB16 ankyrin repeat and SOCS box containing 16 2 2
MIRT551948 RNF157 ring finger protein 157 2 2
MIRT553176 UBE2D2 ubiquitin conjugating enzyme E2 D2 2 2
MIRT555074 PURG purine rich element binding protein G 2 2
MIRT556214 MB21D2 Mab-21 domain containing 2 2 2
MIRT556476 LIPA lipase A, lysosomal acid type 2 2
MIRT556683 KLHL28 kelch like family member 28 2 2
MIRT556863 JMY junction mediating and regulatory protein, p53 cofactor 2 2
MIRT558402 DEPDC1 DEP domain containing 1 2 2
MIRT558716 CLCN3 chloride voltage-gated channel 3 2 2
MIRT559512 ARHGEF26 Rho guanine nucleotide exchange factor 26 2 2
MIRT566872 LRP12 LDL receptor related protein 12 2 2
MIRT567038 KCNB1 potassium voltage-gated channel subfamily B member 1 2 2
MIRT574515 PRC1 protein regulator of cytokinesis 1 2 2
MIRT642220 RABAC1 Rab acceptor 1 2 2
MIRT651915 UEVLD UEV and lactate/malate dehyrogenase domains 2 2
MIRT654128 RPL14 ribosomal protein L14 2 2
MIRT654344 RBM27 RNA binding motif protein 27 2 2
MIRT669250 C4orf36 chromosome 4 open reading frame 36 2 2
MIRT683176 UBL3 ubiquitin like 3 2 2
MIRT718768 ABHD15 abhydrolase domain containing 15 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-4473 Plx-4720 24180719 NSC757438 resistant High Thyroid Cancer cell line (8505c, BCPAP)
hsa-miR-4473 Ceritinib 57379345 NSC776422 approved sensitive High Non-Small Cell Lung Cancer cell line (H3122, H2228)
hsa-miR-4473 Vincristine 5978 approved sensitive High Colorectal Cancer cell line (HCT8)
hsa-miR-4473 Doxorubicin 31703 NSC123127 approved sensitive High Colorectal Cancer cell line (HCT8)
hsa-miR-4473 Etoposide 36462 NSC141540 approved sensitive High Colorectal Cancer cell line (HCT8)
hsa-miR-4473 Vinorelbine 44424639 approved sensitive High Colorectal Cancer cell line (HCT8)
hsa-miR-4473 Paclitaxel 36314 NSC125973 approved sensitive High Colorectal Cancer cell line (HCT8)
hsa-mir-4473 Paclitaxel 36314 NSC125973 approved sensitive cell line (A2780)
hsa-mir-4473 Ceritinib 57379345 NSC776422 approved sensitive cell line (H3122)
hsa-miR-4473 Gefitinib 123631 NSC715055 approved resistant cell line (PC9)
hsa-miR-4473 Prednisone/Azathioprine/Methotrexate/Cyclophosphamide/Mycophenolate mofetil resistant tissue (myasthenia gravis)

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