pre-miRNA Information
pre-miRNA hsa-mir-4742   
Genomic Coordinates chr1: 224398227 - 224398311
Description Homo sapiens miR-4742 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4742-5p
Sequence 1| UCAGGCAAAGGGAUAUUUACAGA |23
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1234293681 4 dbSNP
rs778464201 9 dbSNP
rs758952505 12 dbSNP
rs753463665 16 dbSNP
rs765920862 18 dbSNP
rs1205603801 20 dbSNP
rs756994761 21 dbSNP
Putative Targets

Gene Information
Gene Symbol LRRC40   
Synonyms dJ677H15.1
Description leucine rich repeat containing 40
Transcript NM_017768   
Expression
Putative miRNA Targets on LRRC40
3'UTR of LRRC40
(miRNA target sites are highlighted)
>LRRC40|NM_017768|3'UTR
   1 CATGGAGTTGCTTTATAACCCTTGTCATGTATTATTAACCCTGGTTAATTCTAAGGAGGATGTAACATTTGTTTTAGTAT
  81 CATCTTAAAAGGTGATTATTGTAATTGATCTTGTAGTTTCCCAGTATCACCTACCTGTTGGTATAATTAGCCTGGGCCAT
 161 ATTCACTGCCAGTAAATATTTTTACATTTTTATTTAAGATTTTTGTAAGGTGTTGTATACATTTGTAATGGTGATAACCA
 241 CAATGTGTTCATACATTTGTTCTAAATGTTTTGCTTATGATTTATCCTGCTAACTTTCATTTTCTTATAGCAAGCAGTTT
 321 TTTCAAAAATGAATTTTTATTTAATGTGGTTCAGTATTATAATAACAAAGCATTTTTGTAGAACTGGTTTTTTTTCTCAT
 401 TTATTTTTGTATTCCATACAATGTGACCAATTGACTTGAATATGACTAGCCAGTTTCTATGTTTTTGTTAGATATAAAAT
 481 TAAATCGAATTTTGTTGAATACTGTTCTTTGGCATTTAAAAAATAAGACCTTCTTATCTTGGGCCACATGTCAAAAGAAA
 561 AAGGAAACAAAAATATATTAAAAATAAGACTTTTCATTACCCATGATAGGACTTTTGTGATATGGCTAATCTCAGTACAC
 641 ATTTCAACTTAAAACCTTTTTATTTACAGCACCATAATTTTAAAATTTACTTGCAATCTTGGTAAGACTAAACTTGCAGT
 721 GTTTTTCTAAAAGGGAATTTGATAGGTAAACTTGATTTAATAAAAATTAAATATCATTTTTGTTTACACCAAAATTATCA
 801 GAAGTAGGTTGATTAGTCATTATAACACTTACCATATGATTCTATTAAGAAGTCAATTCAGTAGCATGTATATCAATTTA
 881 TATAGATAGGTAGATAGCTTTTGGATGATTGAGGCATGCTTATATTATGAAAAAAATTGCTAATAAAGATAAATACTACA
 961 TGTTCAGAATAAAAGTTACATTTTTCAAATATTGATTAAAAAAAAAAAAAA
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' agACAUUUAUAGGGAAACGGAcu 5'
            | |||||:|   |||||:|  
Target 5' gtTCTAAATGT---TTTGCTTat 3'
259 - 278 130.00 -5.50
2
miRNA  3' agACAUUUAUAGGGAAACGGACu 5'
            ||| ::|||   || ||||| 
Target 5' ccTGTTGGTAT-AATTAGCCTGg 3'
134 - 155 128.00 -15.00
3
miRNA  3' agacAUUUAUAG-GGAAACGGAcu 5'
              |||||||| ::||||::|  
Target 5' aaatTAAATATCATTTTTGTTTac 3'
764 - 787 127.00 -8.80
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30185316 21 COSMIC
COSN22278003 42 COSMIC
COSN30454458 58 COSMIC
COSN5743329 77 COSMIC
COSN30186964 91 COSMIC
COSN31602094 107 COSMIC
COSN31491914 152 COSMIC
COSN30536962 221 COSMIC
COSN6465986 275 COSMIC
COSN4751719 405 COSMIC
COSN5375509 716 COSMIC
COSN20094937 741 COSMIC
COSN17822890 772 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs369993141 7 dbSNP
rs754040008 10 dbSNP
rs1041921525 20 dbSNP
rs201647517 24 dbSNP
rs377219130 27 dbSNP
rs750545446 39 dbSNP
rs1376634355 43 dbSNP
rs1005113451 51 dbSNP
rs1297277480 52 dbSNP
rs1417532738 56 dbSNP
rs952338890 61 dbSNP
rs947279347 62 dbSNP
rs1346683564 63 dbSNP
rs1252995530 71 dbSNP
rs1177844506 75 dbSNP
rs1488198433 78 dbSNP
rs1271128600 92 dbSNP
rs1281739835 93 dbSNP
rs1215506712 101 dbSNP
rs1335438111 103 dbSNP
rs772970035 105 dbSNP
rs576227712 110 dbSNP
rs1012039308 113 dbSNP
rs1479664551 119 dbSNP
rs894895252 120 dbSNP
rs1318352134 123 dbSNP
rs1307268484 130 dbSNP
rs595662 136 dbSNP
rs1197244690 137 dbSNP
rs1003217938 144 dbSNP
rs1428936482 149 dbSNP
rs1169233265 158 dbSNP
rs902148559 166 dbSNP
rs1042721254 171 dbSNP
rs1459177583 171 dbSNP
rs1364457805 177 dbSNP
rs1301862943 196 dbSNP
rs1342694174 196 dbSNP
rs1404854321 196 dbSNP
rs1324423255 205 dbSNP
rs1443711168 212 dbSNP
rs952985062 213 dbSNP
rs1247304324 217 dbSNP
rs76255519 220 dbSNP
rs1358840817 227 dbSNP
rs113086890 228 dbSNP
rs1443991724 234 dbSNP
rs553853037 239 dbSNP
rs1486041270 243 dbSNP
rs1185704987 245 dbSNP
rs184637262 256 dbSNP
rs1425154807 259 dbSNP
rs1004787985 262 dbSNP
rs1384026967 271 dbSNP
rs676753 275 dbSNP
rs1347449763 279 dbSNP
rs1454823515 280 dbSNP
rs558881607 294 dbSNP
rs1251187739 296 dbSNP
rs922026108 313 dbSNP
rs1027161547 330 dbSNP
rs976107424 336 dbSNP
rs1468852333 343 dbSNP
rs1013127257 349 dbSNP
rs966457556 359 dbSNP
rs1243890890 372 dbSNP
rs1203089332 377 dbSNP
rs1486733788 378 dbSNP
rs1260898790 387 dbSNP
rs1232120785 391 dbSNP
rs1258716574 396 dbSNP
rs1484126248 396 dbSNP
rs907853706 407 dbSNP
rs1242159057 414 dbSNP
rs1442456796 416 dbSNP
rs1179967559 418 dbSNP
rs1408124222 421 dbSNP
rs1345344900 422 dbSNP
rs1420177924 428 dbSNP
rs1304961772 439 dbSNP
rs894451007 447 dbSNP
rs984140093 459 dbSNP
rs1337574647 473 dbSNP
rs192472835 476 dbSNP
rs1027866443 480 dbSNP
rs1012425013 482 dbSNP
rs1380824068 486 dbSNP
rs903261183 486 dbSNP
rs775047417 487 dbSNP
rs1041839450 493 dbSNP
rs947173342 494 dbSNP
rs959495196 497 dbSNP
rs775663284 498 dbSNP
rs569843170 504 dbSNP
rs1434319602 514 dbSNP
rs1232900654 521 dbSNP
rs1003275101 526 dbSNP
rs1480042599 529 dbSNP
rs902206091 552 dbSNP
rs1406446194 563 dbSNP
rs931899352 572 dbSNP
rs1177600597 574 dbSNP
rs1042047247 575 dbSNP
rs1468411969 582 dbSNP
rs879228158 595 dbSNP
rs1331155567 601 dbSNP
rs1355149967 607 dbSNP
rs923212910 616 dbSNP
rs1347314794 619 dbSNP
rs549934931 622 dbSNP
rs749414065 628 dbSNP
rs893724658 633 dbSNP
rs148058487 634 dbSNP
rs1273271775 640 dbSNP
rs76272036 641 dbSNP
rs1201811915 649 dbSNP
rs984567723 651 dbSNP
rs779944569 654 dbSNP
rs1040461748 656 dbSNP
rs944798009 662 dbSNP
rs907902406 674 dbSNP
rs991644487 681 dbSNP
rs983471075 687 dbSNP
rs958927568 699 dbSNP
rs930601029 701 dbSNP
rs1409673822 702 dbSNP
rs1168381011 703 dbSNP
rs1262131688 703 dbSNP
rs920855515 713 dbSNP
rs576477554 718 dbSNP
rs1035940966 719 dbSNP
rs1302502184 726 dbSNP
rs756369678 732 dbSNP
rs991041804 734 dbSNP
rs112396146 745 dbSNP
rs56291538 745 dbSNP
rs1432650147 755 dbSNP
rs1484477422 757 dbSNP
rs1270614167 771 dbSNP
rs1360834457 775 dbSNP
rs774525430 777 dbSNP
rs1293298719 778 dbSNP
rs959547386 799 dbSNP
rs1359561447 800 dbSNP
rs1282099913 801 dbSNP
rs1291700373 814 dbSNP
rs1003277055 815 dbSNP
rs1450177254 815 dbSNP
rs768753366 816 dbSNP
rs1243094326 822 dbSNP
rs1210892650 826 dbSNP
rs1475194970 829 dbSNP
rs1185020596 833 dbSNP
rs1387119783 839 dbSNP
rs1340855884 842 dbSNP
rs903191335 844 dbSNP
rs1363626396 853 dbSNP
rs1402447465 853 dbSNP
rs1270072860 858 dbSNP
rs1020748610 861 dbSNP
rs547041174 865 dbSNP
rs1011678920 867 dbSNP
rs1316756065 868 dbSNP
rs1382802610 870 dbSNP
rs892947468 877 dbSNP
rs1312361213 889 dbSNP
rs1035172253 896 dbSNP
rs1207460964 898 dbSNP
rs1225915444 898 dbSNP
rs982301974 904 dbSNP
rs1446814358 913 dbSNP
rs1296728052 914 dbSNP
rs1206984588 916 dbSNP
rs1424304684 919 dbSNP
rs1245210591 920 dbSNP
rs1414628285 929 dbSNP
rs901758900 931 dbSNP
rs1040327820 937 dbSNP
rs527271908 937 dbSNP
rs1315024723 942 dbSNP
rs1471109552 948 dbSNP
rs1383919400 950 dbSNP
rs746008301 950 dbSNP
rs1395903760 954 dbSNP
rs1166271572 958 dbSNP
rs1476337967 960 dbSNP
rs752211106 960 dbSNP
rs1373631128 969 dbSNP
rs1451512090 969 dbSNP
rs940318010 976 dbSNP
rs1337040077 980 dbSNP
rs148236608 986 dbSNP
rs1280649064 992 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HEK293S
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... HITS-CLIP data was present in GSM1084067. RNA binding protein: AGO2. Condition:CLIP_emetine_SantaCruzAb HITS-CLIP data was present in GSM1084082. RNA binding protein: AGO2. Condition:CLIP_nohippuristanol_rep2_SigmaAb ...

- Karginov FV; Hannon GJ, 2013, Genes & development.

Article - Karginov FV; Hannon GJ
- Genes & development, 2013
When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Argonaute 2 (Ago2)/microRNA (miRNA) machinery has been shown to participate in stress-induced translational up-regulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (UTR) and coding sequence (CDS) sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2-binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA sequencing (RNA-seq). Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian miRNAs in mediating the translational component of the stress response.
LinkOut: [PMID: 23824327]
CLIP-seq Support 1 for dataset GSM1084067
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_emetine_SantaCruzAb
Location of target site ENST00000370952.3 | 3UTR | GCAAAAAAAAAAAAAAUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1084082
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293S / CLIP_nohippuristanol_rep2_SigmaAb
Location of target site ENST00000370952.3 | 3UTR | AAAUGCAAAAAAAAAAAAAAU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23824327 / GSE44404
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
70 hsa-miR-4742-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT065632 CLIC4 chloride intracellular channel 4 2 4
MIRT068170 TXLNA taxilin alpha 2 2
MIRT119024 TSN translin 2 2
MIRT165212 GRAMD3 GRAM domain containing 2B 2 2
MIRT175254 PSAT1 phosphoserine aminotransferase 1 2 4
MIRT213228 REST RE1 silencing transcription factor 2 6
MIRT296337 PARD6B par-6 family cell polarity regulator beta 2 2
MIRT316776 FOXC1 forkhead box C1 2 2
MIRT453943 XRCC6 X-ray repair cross complementing 6 2 6
MIRT454599 RPL13A ribosomal protein L13a 2 2
MIRT458485 RMI1 RecQ mediated genome instability 1 2 6
MIRT458650 SGPP2 sphingosine-1-phosphate phosphatase 2 2 2
MIRT459240 ADRBK1 G protein-coupled receptor kinase 2 2 2
MIRT461008 SYT7 synaptotagmin 7 2 2
MIRT462026 RIF1 replication timing regulatory factor 1 2 2
MIRT462103 TMEM214 transmembrane protein 214 2 2
MIRT463255 ZIC5 Zic family member 5 2 4
MIRT465190 TRPS1 transcriptional repressor GATA binding 1 2 2
MIRT470507 PPP1R11 protein phosphatase 1 regulatory inhibitor subunit 11 2 2
MIRT472356 TSPAN1 tetraspanin 1 2 2
MIRT473260 MIDN midnolin 2 2
MIRT477527 EIF4G2 eukaryotic translation initiation factor 4 gamma 2 2 4
MIRT485182 PTP4A1 protein tyrosine phosphatase type IVA, member 1 2 4
MIRT486461 MDM2 MDM2 proto-oncogene 2 2
MIRT492760 PER1 period circadian clock 1 2 8
MIRT496703 TRIM39 tripartite motif containing 39 2 2
MIRT497227 MORC2 MORC family CW-type zinc finger 2 2 2
MIRT499582 INTU inturned planar cell polarity protein 2 4
MIRT504081 C9orf40 chromosome 9 open reading frame 40 2 6
MIRT505484 SRSF2 serine and arginine rich splicing factor 2 2 2
MIRT513255 FBXO17 F-box protein 17 2 2
MIRT525061 FRK fyn related Src family tyrosine kinase 2 2
MIRT528798 RAB32 RAB32, member RAS oncogene family 2 2
MIRT534357 SFT2D2 SFT2 domain containing 2 2 2
MIRT538731 CAPN1 calpain 1 2 2
MIRT550792 WARS2 tryptophanyl tRNA synthetase 2, mitochondrial 2 2
MIRT553994 SRPR SRP receptor alpha subunit 2 4
MIRT568102 CDKN1B cyclin dependent kinase inhibitor 1B 2 2
MIRT570107 SLC18B1 solute carrier family 18 member B1 2 2
MIRT570823 RPL7L1 ribosomal protein L7 like 1 2 2
MIRT572004 HMGB1 high mobility group box 1 2 2
MIRT572352 PCYT2 phosphate cytidylyltransferase 2, ethanolamine 2 2
MIRT609716 TMEM132C transmembrane protein 132C 2 2
MIRT613982 LRRC40 leucine rich repeat containing 40 2 2
MIRT620740 CCL16 C-C motif chemokine ligand 16 2 2
MIRT625074 C15orf41 chromosome 15 open reading frame 41 2 4
MIRT627941 NNT nicotinamide nucleotide transhydrogenase 2 2
MIRT629941 IGSF6 immunoglobulin superfamily member 6 2 2
MIRT633396 FBXW8 F-box and WD repeat domain containing 8 2 2
MIRT635846 ZNF264 zinc finger protein 264 2 2
MIRT638086 ZNF652 zinc finger protein 652 2 2
MIRT643996 TCHP trichoplein keratin filament binding 2 2
MIRT660020 C1GALT1 core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1 2 2
MIRT660161 BRCC3 BRCA1/BRCA2-containing complex subunit 3 2 2
MIRT668887 CSRP1 cysteine and glycine rich protein 1 2 2
MIRT676729 METTL14 methyltransferase like 14 2 2
MIRT677210 MURC caveolae associated protein 4 2 2
MIRT685949 PTGIS prostaglandin I2 synthase 2 2
MIRT687816 ITPRIPL2 inositol 1,4,5-trisphosphate receptor interacting protein like 2 2 2
MIRT689900 SOD2 superoxide dismutase 2 2 2
MIRT698214 TMEM248 transmembrane protein 248 2 2
MIRT698279 TMEM2 transmembrane protein 2 2 2
MIRT698758 STK4 serine/threonine kinase 4 2 2
MIRT698789 STK38 serine/threonine kinase 38 2 2
MIRT703152 GPR137C G protein-coupled receptor 137C 2 2
MIRT704408 CTPS1 CTP synthase 1 2 2
MIRT705067 C4orf32 family with sequence similarity 241 member A 2 2
MIRT710201 FLVCR1 feline leukemia virus subgroup C cellular receptor 1 2 2
MIRT714495 HSPA4 heat shock protein family A (Hsp70) member 4 2 2
MIRT720082 TNRC6B trinucleotide repeat containing 6B 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4742-5p Imatinib 5291 NSC743414 approved sensitive High Chronic Myelogenous Leukemia tissue
hsa-miR-4742-5p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-4742-5p Osimertinib 71496458 NSC779217 approved resistant cell line (HCC827)
hsa-miR-4742-5p Cisplatin 5460033 NSC119875 approved resistant cell line (A549)
hsa-miR-4742-5p Gefitinib 123631 NSC715055 approved resistant cell line (HCC827)
hsa-miR-4742-5p Paclitaxel 36314 NSC125973 approved resistant cell line (BAS)
hsa-miR-4742-5p Paclitaxel 36314 NSC125973 approved sensitive cell line (A2780)
hsa-miR-4742-5p Cisplatin 5460033 NSC119875 approved sensitive cell line (A2780)
hsa-miR-4742-5p Gemcitabine 60750 NSC613327 approved sensitive cell line (PANC-1) (1500 ng/ml)

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