pre-miRNA Information
pre-miRNA hsa-mir-4301   
Genomic Coordinates chr11: 113450023 - 113450088
Description Homo sapiens miR-4301 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4301
Sequence 11| UCCCACUACUUCACUUGUGA |30
Evidence Experimental
Experiments SOLiD
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs184176277 2 dbSNP
rs1191324913 13 dbSNP
rs1369198005 15 dbSNP
rs1036973189 16 dbSNP
rs944900541 18 dbSNP
Putative Targets

miRNA Expression profile
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol YRDC   
Synonyms DRIP3, IRIP, SUA5
Description yrdC N6-threonylcarbamoyltransferase domain containing
Transcript NM_024640   
Expression
Putative miRNA Targets on YRDC
3'UTR of YRDC
(miRNA target sites are highlighted)
>YRDC|NM_024640|3'UTR
   1 AACTCTGGGAAGCAGGAAGGCCCAAGACCTGGTGCTGGATACTATGTGTCTGTCCACTGACGACTGTCAAGGCCTCATTT
  81 GCAGAGGCCACCGGAGCTAGGGCACTAGCCTGACTTTTAAGGCAGTGTGTCTTTCTGAGCACTGTAGACCAAGCCCTTGG
 161 AGCTGCTGGTTTAGCCTTGCACCTGGGGAAAGGATGTATTTATTTGTATTTTCATATATCAGCCAAAAGCTGAATGGAAA
 241 AGTTAAGAACATTCCTAGGTGGCCTTATTCTAATAAGTTTCTTCTGTCTGTTTTGTTTTTCAATTGAAAAGTAATTAAAT
 321 AACAGATTTAGAATCTAGTGAGAGCCTCCTCTCTGGTGGGTGGTGGCATTTAAGGTTCAAACCAGCCAGAAGTGCTGGTG
 401 CTGTTTAAAAAGTCTCAGGTGGCTGCGTGTGGTGGCTCATGCCTGTAATCCCAACATTCTGGGAGGCCCAGGCGGGAGAA
 481 CTGCTTGAGCCCAGGAGTTCAGAATCAGCCTGGGCAACATAGCAATACTCCGTCTCATAAAAATTAATAAATAAAAAGTC
 561 TCAGGTGACCAAAGGCTCCTGAAGCTAGAACCAGGTTTGGATAAAGATTGAAGAGCCACAGGCCACTCTTCCCTCTGAGC
 641 CATTGGGCCTAGTGGTGTCATGTATTGTAATTGCTCGCAGGGAGAGCAGTCTTTTTGGTGTAATAGTGGGATGTCTGCTT
 721 AGTTGGCAGGGGTTCAGTCCAAATGGAAGAATATTGGGAAATAAACCTCCACTATCCTTTATAGCCAGGGACTTTTTTCT
 801 TATTTATTCATAAAATAAATTATAGTTAATTATACCCATAACACCTTTATTTAAATCCAGTGTTCTCCGCAGCCTTTTGT
 881 CTATTTATATGTGTACCAAGTGTTAAACATAATTATTATTGGGCATTTGAACTTTGTTTTTCTTTAAAGAAATGCTGCTA
 961 TTAAACATATTTGTAAATGGTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
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' aguguUCACUUCAUCACCCu 5'
               :||| | ||||||| 
Target 5' tttttGGTGTAATAGTGGGa 3'
692 - 711 155.00 -15.40
2
miRNA  3' aguGUUCACU-UC---------AUCACCCu 5'
             | ||||| ||         |:||||| 
Target 5' aatCTAGTGAGAGCCTCCTCTCTGGTGGGt 3'
332 - 361 129.00 -14.60
3
miRNA  3' aguGUUCA-CUUC--AUCACCCu 5'
             ||| | ||||  || |||| 
Target 5' gtcCAAATGGAAGAATATTGGGa 3'
737 - 759 127.00 -10.20
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30450073 15 COSMIC
COSN31587435 20 COSMIC
COSN30179598 38 COSMIC
COSN31492786 39 COSMIC
COSN19003373 61 COSMIC
COSN6035151 122 COSMIC
COSN15720035 138 COSMIC
COSN31522777 147 COSMIC
COSN31595149 186 COSMIC
COSN31959412 679 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1474327672 6 dbSNP
rs745626718 9 dbSNP
rs757033765 20 dbSNP
rs753760956 29 dbSNP
rs116663798 32 dbSNP
rs755668390 38 dbSNP
rs752319475 41 dbSNP
rs767044057 45 dbSNP
rs912033196 56 dbSNP
rs987524394 61 dbSNP
rs932029497 62 dbSNP
rs1452491664 76 dbSNP
rs921978285 92 dbSNP
rs1342600914 93 dbSNP
rs1225777171 102 dbSNP
rs1327602565 113 dbSNP
rs1269212139 116 dbSNP
rs979164835 118 dbSNP
rs752985444 120 dbSNP
rs543992314 127 dbSNP
rs1260660027 131 dbSNP
rs187139243 138 dbSNP
rs955625138 139 dbSNP
rs1220357565 140 dbSNP
rs1366966292 142 dbSNP
rs1273173319 148 dbSNP
rs1445055618 156 dbSNP
rs1192132716 169 dbSNP
rs1433101866 179 dbSNP
rs1389658069 180 dbSNP
rs1022617149 183 dbSNP
rs1427269850 184 dbSNP
rs988049650 185 dbSNP
rs1177776867 188 dbSNP
rs975238156 190 dbSNP
rs1381034763 212 dbSNP
rs956536187 213 dbSNP
rs1034816210 216 dbSNP
rs541641405 217 dbSNP
rs1022142099 221 dbSNP
rs1456496310 230 dbSNP
rs1281022370 234 dbSNP
rs1003294692 237 dbSNP
rs969123074 242 dbSNP
rs766213294 255 dbSNP
rs1223658805 256 dbSNP
rs1023332530 273 dbSNP
rs1178103379 281 dbSNP
rs1433725898 290 dbSNP
rs570641323 292 dbSNP
rs1196070959 294 dbSNP
rs1267114931 297 dbSNP
rs1199596033 299 dbSNP
rs1480141309 299 dbSNP
rs1379447902 303 dbSNP
rs1188958074 304 dbSNP
rs994897894 315 dbSNP
rs529826597 319 dbSNP
rs956661899 322 dbSNP
rs1421978976 323 dbSNP
rs1031058967 325 dbSNP
rs1300890004 325 dbSNP
rs1405185383 331 dbSNP
rs559251123 339 dbSNP
rs1302716036 343 dbSNP
rs182505472 344 dbSNP
rs577209437 347 dbSNP
rs1261287893 352 dbSNP
rs1355574215 353 dbSNP
rs1220047971 359 dbSNP
rs1290773577 398 dbSNP
rs899438037 403 dbSNP
rs745489469 406 dbSNP
rs1005057484 414 dbSNP
rs1417456634 416 dbSNP
rs190483363 425 dbSNP
rs890627651 426 dbSNP
rs1051877697 427 dbSNP
rs1442100798 429 dbSNP
rs932104720 431 dbSNP
rs1365381107 436 dbSNP
rs1023375528 445 dbSNP
rs1013036432 455 dbSNP
rs894608146 456 dbSNP
rs1038542575 459 dbSNP
rs1307598086 461 dbSNP
rs1378942155 471 dbSNP
rs941585311 472 dbSNP
rs887391056 473 dbSNP
rs543770485 474 dbSNP
rs1043088330 475 dbSNP
rs1222555444 479 dbSNP
rs947395098 484 dbSNP
rs913200636 489 dbSNP
rs1479691266 490 dbSNP
rs988468534 493 dbSNP
rs576474350 522 dbSNP
rs927820060 525 dbSNP
rs1459453861 530 dbSNP
rs758302036 531 dbSNP
rs1384981976 532 dbSNP
rs969154193 537 dbSNP
rs1433218159 539 dbSNP
rs776394949 546 dbSNP
rs770513640 547 dbSNP
rs1166473445 550 dbSNP
rs1362709203 550 dbSNP
rs1023786803 551 dbSNP
rs1371039276 554 dbSNP
rs1466426779 555 dbSNP
rs1461182059 556 dbSNP
rs774646946 556 dbSNP
rs558163376 557 dbSNP
rs1173942699 559 dbSNP
rs1431104382 562 dbSNP
rs975457672 562 dbSNP
rs1336059176 563 dbSNP
rs942771901 566 dbSNP
rs1167550458 569 dbSNP
rs1447304501 572 dbSNP
rs555085335 579 dbSNP
rs1182806562 584 dbSNP
rs1483174503 600 dbSNP
rs963382994 616 dbSNP
rs1208004357 619 dbSNP
rs765050575 627 dbSNP
rs1258736943 629 dbSNP
rs1320153041 631 dbSNP
rs1202293893 638 dbSNP
rs1243135705 641 dbSNP
rs75464904 642 dbSNP
rs530024611 643 dbSNP
rs1260094566 659 dbSNP
rs1226409493 660 dbSNP
rs572671331 661 dbSNP
rs890702140 663 dbSNP
rs989345311 667 dbSNP
rs956813819 668 dbSNP
rs1175614245 669 dbSNP
rs1359612910 674 dbSNP
rs1314540515 676 dbSNP
rs1396382336 677 dbSNP
rs1030943957 678 dbSNP
rs7686 679 dbSNP
rs1279122041 684 dbSNP
rs1320084961 685 dbSNP
rs1484731347 686 dbSNP
rs184228046 697 dbSNP
rs1313235170 698 dbSNP
rs1212902883 710 dbSNP
rs1411642799 711 dbSNP
rs181554343 718 dbSNP
rs1167447571 722 dbSNP
rs1479259550 725 dbSNP
rs900647268 730 dbSNP
rs1011917004 732 dbSNP
rs1416049528 736 dbSNP
rs1043545790 742 dbSNP
rs947458297 743 dbSNP
rs1420145933 754 dbSNP
rs12395 761 dbSNP
rs148951967 768 dbSNP
rs1342550508 771 dbSNP
rs1412130483 771 dbSNP
rs1053104251 775 dbSNP
rs935268935 776 dbSNP
rs1368428346 780 dbSNP
rs1184941443 789 dbSNP
rs375505058 790 dbSNP
rs1005748565 791 dbSNP
rs1316693889 792 dbSNP
rs1217880947 797 dbSNP
rs1047801 799 dbSNP
rs14614 800 dbSNP
rs981965300 801 dbSNP
rs1047804 802 dbSNP
rs778978467 802 dbSNP
rs1221308955 803 dbSNP
rs1203130679 806 dbSNP
rs969645725 807 dbSNP
rs1489540504 809 dbSNP
rs1175405296 819 dbSNP
rs540166672 823 dbSNP
rs916382666 833 dbSNP
rs1320870420 838 dbSNP
rs147311863 838 dbSNP
rs973564649 844 dbSNP
rs963158181 850 dbSNP
rs1230106332 865 dbSNP
rs1328289768 867 dbSNP
rs141678587 868 dbSNP
rs1350511868 869 dbSNP
rs942737484 872 dbSNP
rs1278281712 883 dbSNP
rs1306808326 889 dbSNP
rs983067968 889 dbSNP
rs796491658 892 dbSNP
rs954984167 897 dbSNP
rs1392338521 900 dbSNP
rs989704999 909 dbSNP
rs1227350467 913 dbSNP
rs1293720326 914 dbSNP
rs1271402911 917 dbSNP
rs1452816743 917 dbSNP
rs935211102 920 dbSNP
rs1231821738 921 dbSNP
rs1457136608 936 dbSNP
rs1458130199 936 dbSNP
rs529885137 937 dbSNP
rs1161832137 940 dbSNP
rs1473171954 941 dbSNP
rs10015 942 dbSNP
rs377551518 960 dbSNP
rs559113176 960 dbSNP
rs71671712 960 dbSNP
rs1407308303 963 dbSNP
rs916218412 973 dbSNP
rs1399673102 979 dbSNP
rs900673780 981 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 GSM545214. RNA binding protein: AGO3. Condition:Control ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' aguguUCACUUCAUCACCCu 5'
               :||| | ||||||| 
Target 5' uuuuuGGUGUAAUAGUGGGa 3'
6 - 25
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 GSM4903825
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / PID14_NS
Location of target site NM_024640 | 3UTR | AGUGGGAUGUCUGCUUAGUUGGCAGG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161237
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4903833
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_a
Location of target site NM_024640 | 3UTR | GUAAUAGUGGGAUGUCUGCUUAGUUGGCAGG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM4903838
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_c
Location of target site NM_024640 | 3UTR | UUUGGUGUAAUAGUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM545214
Method / RBP PAR-CLIP / AGO3
Cell line / Condition HEK293 / Control
Location of target site ENST00000373044.2 | 3UTR | CAGUCUUUUUGGUGUAAUAGUGGGAUG
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
83 hsa-miR-4301 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT081134 LDLR low density lipoprotein receptor 2 4
MIRT090911 ARHGEF26 Rho guanine nucleotide exchange factor 26 2 2
MIRT229436 MECP2 methyl-CpG binding protein 2 2 2
MIRT274717 CPSF6 cleavage and polyadenylation specific factor 6 2 2
MIRT350957 BACH1 BTB domain and CNC homolog 1 2 2
MIRT386722 NUFIP2 NUFIP2, FMR1 interacting protein 2 2 2
MIRT446022 PEX3 peroxisomal biogenesis factor 3 2 2
MIRT481303 ATP5G3 ATP synthase, H+ transporting, mitochondrial Fo complex subunit C3 (subunit 9) 2 14
MIRT483959 ZNF354B zinc finger protein 354B 2 6
MIRT495667 TUBAL3 tubulin alpha like 3 2 2
MIRT496554 TBX15 T-box 15 2 2
MIRT497702 ARL6IP6 ADP ribosylation factor like GTPase 6 interacting protein 6 2 2
MIRT498105 RMND5A required for meiotic nuclear division 5 homolog A 2 2
MIRT512535 SEMA4D semaphorin 4D 2 2
MIRT512556 MFN2 mitofusin 2 2 6
MIRT521465 RABGAP1 RAB GTPase activating protein 1 2 6
MIRT526236 C2orf15 chromosome 2 open reading frame 15 2 2
MIRT526743 HLA-DOB major histocompatibility complex, class II, DO beta 2 2
MIRT527578 BRD7 bromodomain containing 7 2 4
MIRT528038 WT1 Wilms tumor 1 2 2
MIRT528267 GPRIN2 G protein regulated inducer of neurite outgrowth 2 2 2
MIRT528505 HTR7 5-hydroxytryptamine receptor 7 2 4
MIRT528758 RPS27 ribosomal protein S27 2 6
MIRT528999 IPO9 importin 9 2 2
MIRT529701 MRPL30 mitochondrial ribosomal protein L30 2 2
MIRT529781 C17orf82 chromosome 17 open reading frame 82 2 2
MIRT533797 TMEM119 transmembrane protein 119 2 6
MIRT535308 PHF12 PHD finger protein 12 2 2
MIRT535917 MKL2 MKL1/myocardin like 2 2 2
MIRT544892 OSBPL1A oxysterol binding protein like 1A 2 2
MIRT555423 PPIC peptidylprolyl isomerase C 2 2
MIRT562068 KLHL15 kelch like family member 15 2 2
MIRT565623 SLC31A1 solute carrier family 31 member 1 2 2
MIRT565661 SIX1 SIX homeobox 1 2 2
MIRT570138 IL1RL2 interleukin 1 receptor like 2 2 2
MIRT571045 YRDC yrdC N6-threonylcarbamoyltransferase domain containing 2 2
MIRT621232 LMAN1 lectin, mannose binding 1 2 2
MIRT622272 SH3TC2 SH3 domain and tetratricopeptide repeats 2 2 2
MIRT623844 GAN gigaxonin 2 2
MIRT626158 NFYA nuclear transcription factor Y subunit alpha 2 2
MIRT626464 CMKLR1 chemerin chemokine-like receptor 1 2 2
MIRT632087 ALDH1A2 aldehyde dehydrogenase 1 family member A2 2 2
MIRT637243 FAM26E calcium homeostasis modulator family member 5 2 2
MIRT642710 FGFR1OP2 FGFR1 oncogene partner 2 2 2
MIRT643611 KANSL3 KAT8 regulatory NSL complex subunit 3 2 2
MIRT644270 PAFAH1B1 platelet activating factor acetylhydrolase 1b regulatory subunit 1 2 2
MIRT645470 SPIN3 spindlin family member 3 2 2
MIRT649193 DNPEP aspartyl aminopeptidase 2 2
MIRT650776 POP4 POP4 homolog, ribonuclease P/MRP subunit 2 2
MIRT651345 ZC2HC1C zinc finger C2HC-type containing 1C 2 2
MIRT652237 TRAPPC3L trafficking protein particle complex 3 like 2 2
MIRT652587 TIMM8A translocase of inner mitochondrial membrane 8A 2 2
MIRT654591 PURA purine rich element binding protein A 2 2
MIRT654649 PTAFR platelet activating factor receptor 2 2
MIRT656842 KLF7 Kruppel like factor 7 2 2
MIRT657209 IKZF2 IKAROS family zinc finger 2 2 2
MIRT658513 ETV3 ETS variant 3 2 2
MIRT659448 CNNM2 cyclin and CBS domain divalent metal cation transport mediator 2 2 2
MIRT668816 CYLD CYLD lysine 63 deubiquitinase 2 2
MIRT669067 CELSR3 cadherin EGF LAG seven-pass G-type receptor 3 2 2
MIRT677711 ELOF1 elongation factor 1 homolog 2 4
MIRT687146 PTPN12 protein tyrosine phosphatase, non-receptor type 12 2 2
MIRT698498 THOC2 THO complex 2 2 2
MIRT707930 PPP1R3D protein phosphatase 1 regulatory subunit 3D 4 2
MIRT708737 FAM71F2 family with sequence similarity 71 member F2 2 2
MIRT710031 POLL DNA polymerase lambda 2 2
MIRT712175 STK4 serine/threonine kinase 4 2 2
MIRT715297 MAPK1 mitogen-activated protein kinase 1 2 2
MIRT716892 AGPAT6 glycerol-3-phosphate acyltransferase 4 2 2
MIRT717378 RBM41 RNA binding motif protein 41 2 2
MIRT718082 CLIC5 chloride intracellular channel 5 2 2
MIRT718721 ANKRD18A ankyrin repeat domain 18A 2 2
MIRT719152 DPYSL5 dihydropyrimidinase like 5 2 2
MIRT719224 CAMK4 calcium/calmodulin dependent protein kinase IV 2 2
MIRT719528 SRCIN1 SRC kinase signaling inhibitor 1 2 2
MIRT719861 KLF2 Kruppel like factor 2 2 2
MIRT720326 CAMK2G calcium/calmodulin dependent protein kinase II gamma 2 2
MIRT721596 SREBF1 sterol regulatory element binding transcription factor 1 2 2
MIRT722020 NEBL nebulette 2 2
MIRT722484 QSOX1 quiescin sulfhydryl oxidase 1 2 2
MIRT722614 TEAD1 TEA domain transcription factor 1 2 2
MIRT723664 RPTN repetin 2 2
MIRT723939 SVOP SV2 related protein 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-4301 Cisplatin 5460033 NSC119875 approved sensitive High Hepatocellular Carcinoma cell line (Hep3B, 97L)
hsa-miR-4301 Imatinib 5291 NSC743414 approved resistant High Chronic Myelogenous Leukemia cell line (K562)
hsa-mir-4301 Paclitaxel 36314 NSC125973 approved resistant cell line (BAS)
hsa-mir-4301 Paclitaxel 36314 NSC125973 approved sensitive cell line (W1)
hsa-mir-4301 Doxorubicin 31703 NSC123127 approved sensitive cell line (W1)
hsa-mir-4301 Methotrexate 126941 NSC740 approved sensitive cell line (W1)
hsa-mir-4301 Topotecan 60699 NSC609699 approved sensitive cell line (W1)
hsa-miR-4301 Gefitinib 123631 NSC715055 approved resistant cell line (PC9)
hsa-miR-4301 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)

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