pre-miRNA Information
pre-miRNA hsa-mir-4464   
Genomic Coordinates chr6: 90312742 - 90312833
Description Homo sapiens miR-4464 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-4464
Sequence 12| AAGGUUUGGAUAGAUGCAAUA |32
Evidence Experimental
Experiments Illumina
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 12 6 + 90312764 29233923 MiREDiBase
A-to-I 14 6 + 90312766 29233923 MiREDiBase
A-to-I 19 6 + 90312771 29233923 MiREDiBase
A-to-I 21 6 + 90312773 29233923 MiREDiBase
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1240632245 2 dbSNP
rs34899210 2 dbSNP
rs1003034046 13 dbSNP
rs1475351324 14 dbSNP
rs1257582329 17 dbSNP
rs1193587810 20 dbSNP
Putative Targets

Gene Information
Gene Symbol NUDT7   
Synonyms -
Description nudix hydrolase 7
Transcript NM_001105663   
Expression
Putative miRNA Targets on NUDT7
3'UTR of NUDT7
(miRNA target sites are highlighted)
>NUDT7|NM_001105663|3'UTR
   1 TTTACTAGAGCAAGAGACAAAGAACTATTCACGAGGATTCTGTGTGTGCTTATTCGTAGAACAACAACAATGCCAGCTGT
  81 TGGAATTTGACAGGTGTGAATATTTTTTCTGCAGTATGTAGTTAGAATCCTTGCCTCTTTTCCAGTTGCCTTCTATTGTC
 161 TGAAAAAGTAAAAGCCATTCAAAAATGAAAACTATGTTCATAGTGTTGCATATTTTCACCCACAATATGTTAATAATATT
 241 TTTCTTACACATATAATAAAGAATATCTGGCACATACTAGGCCCTTAATAAAGATTTTTTGAATATATAA
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' auAACGUAG-AUAGGUU--UGGAa 5'
            |||| || | ||||:  :||| 
Target 5' ccTTGCCTCTTTTCCAGTTGCCTt 3'
129 - 152 99.00 -13.40
2
miRNA  3' auAACGUAGAUAGGUUUGGaa 5'
            | |||  || |:|::||  
Target 5' tcTGGCACATA-CTAGGCCct 3'
266 - 285 90.00 -8.40
3
miRNA  3' auaAC-GUAGAUAGGUUUGGAa 5'
             || || ||:|: :||::| 
Target 5' caaTGCCAGCTGTTGGAATTTg 3'
68 - 89 86.00 -7.90
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN1081726 23 COSMIC
COSN30523745 23 COSMIC
COSN28783253 33 COSMIC
COSN26537942 37 COSMIC
COSN30462006 56 COSMIC
COSN8865895 71 COSMIC
COSN17580306 90 COSMIC
COSN30155169 99 COSMIC
COSN31491541 187 COSMIC
COSN25087951 213 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs535467068 1 dbSNP
rs372695205 6 dbSNP
rs766762028 10 dbSNP
rs754087323 12 dbSNP
rs759733448 17 dbSNP
rs765443249 19 dbSNP
rs752776076 23 dbSNP
rs758846154 33 dbSNP
rs1397751035 34 dbSNP
rs1390426479 37 dbSNP
rs1051919072 39 dbSNP
rs778277632 41 dbSNP
rs1355923424 47 dbSNP
rs369736128 51 dbSNP
rs1007793995 54 dbSNP
rs386792391 56 dbSNP
rs115415384 57 dbSNP
rs375696182 58 dbSNP
rs1158034701 60 dbSNP
rs994526743 65 dbSNP
rs1133108 71 dbSNP
rs1055303592 74 dbSNP
rs1485651424 83 dbSNP
rs1262439873 86 dbSNP
rs529566174 89 dbSNP
rs1206987952 92 dbSNP
rs1484967543 95 dbSNP
rs1260361153 96 dbSNP
rs896265828 99 dbSNP
rs1013193944 101 dbSNP
rs1362883700 108 dbSNP
rs1294926557 110 dbSNP
rs1231337434 115 dbSNP
rs1162475038 119 dbSNP
rs1318337282 120 dbSNP
rs950499843 133 dbSNP
rs1382224220 134 dbSNP
rs1319430264 139 dbSNP
rs112968844 144 dbSNP
rs1397093251 150 dbSNP
rs1163235842 151 dbSNP
rs962268113 153 dbSNP
rs578185329 154 dbSNP
rs1374128207 155 dbSNP
rs1294913263 157 dbSNP
rs565950879 158 dbSNP
rs1381135195 172 dbSNP
rs1295561472 176 dbSNP
rs1247544694 179 dbSNP
rs1214498095 181 dbSNP
rs376398647 192 dbSNP
rs1220882532 193 dbSNP
rs1274743026 195 dbSNP
rs1211600216 201 dbSNP
rs1355447897 204 dbSNP
rs1027789147 210 dbSNP
rs1133110 213 dbSNP
rs925870606 215 dbSNP
rs1334597240 217 dbSNP
rs1441106847 230 dbSNP
rs1372747273 232 dbSNP
rs1323549540 233 dbSNP
rs957479407 237 dbSNP
rs1397711855 239 dbSNP
rs1170127063 240 dbSNP
rs554934145 241 dbSNP
rs1460936780 248 dbSNP
rs1222671873 250 dbSNP
rs1160086519 252 dbSNP
rs1194344754 253 dbSNP
rs989497337 256 dbSNP
rs780033233 257 dbSNP
rs1251357686 262 dbSNP
rs913887399 263 dbSNP
rs1198501245 265 dbSNP
rs945514077 269 dbSNP
rs112937116 278 dbSNP
rs1204578831 284 dbSNP
rs966150763 290 dbSNP
rs976077323 300 dbSNP
rs1273215281 303 dbSNP
rs888525215 304 dbSNP
rs945276856 305 dbSNP
rs912084848 306 dbSNP
rs943558857 308 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HeLa
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 Chi_ControlA_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell Control A ...

- Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature.

Article - Chi SW; Zang JB; Mele A; Darnell RB
- Nature, 2009
MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
LinkOut: [PMID: 19536157]
CLIP-seq Support 1 for dataset Chi_ControlA_2A8_130_50
Method / RBP HITS-CLIP / AGO
Cell line / Condition HeLa / HeLa cell Control A
Location of target site ENST00000564085.1 | 3UTR | aagggaaugacggcaaa
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 19536157 / Chi_HITSCLIP
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
81 hsa-miR-4464 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT056004 ARL5B ADP ribosylation factor like GTPase 5B 2 2
MIRT061568 BTG2 BTG anti-proliferation factor 2 2 2
MIRT078651 ICT1 mitochondrial ribosomal protein L58 2 2
MIRT087551 YWHAH tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein eta 2 4
MIRT088139 SEPT2 septin 2 2 4
MIRT095089 SEC24A SEC24 homolog A, COPII coat complex component 2 4
MIRT099065 FOXC1 forkhead box C1 2 4
MIRT150194 MIDN midnolin 2 2
MIRT178173 EIF5AL1 eukaryotic translation initiation factor 5A-like 1 2 4
MIRT178942 C11ORF57 chromosome 11 open reading frame 57 2 2
MIRT188776 SESN2 sestrin 2 2 2
MIRT267026 EFHD2 EF-hand domain family member D2 2 2
MIRT307213 ACVR2B activin A receptor type 2B 2 2
MIRT324750 ACER2 alkaline ceramidase 2 2 2
MIRT442732 TEAD1 TEA domain transcription factor 1 2 2
MIRT444087 C12orf73 chromosome 12 open reading frame 73 2 2
MIRT445527 KLF9 Kruppel like factor 9 2 2
MIRT449604 INIP INTS3 and NABP interacting protein 2 2
MIRT451129 ZNF99 zinc finger protein 99 2 2
MIRT452271 RPL30 ribosomal protein L30 2 2
MIRT452486 DDX4 DEAD-box helicase 4 2 2
MIRT454868 DNAJC15 DnaJ heat shock protein family (Hsp40) member C15 2 6
MIRT455773 TSPAN6 tetraspanin 6 2 4
MIRT463844 WRN Werner syndrome RecQ like helicase 2 2
MIRT465036 TTC39C tetratricopeptide repeat domain 39C 2 2
MIRT465176 TRPV2 transient receptor potential cation channel subfamily V member 2 2 4
MIRT465294 TRIB3 tribbles pseudokinase 3 2 4
MIRT467931 SLC16A7 solute carrier family 16 member 7 2 2
MIRT471906 NUAK2 NUAK family kinase 2 2 2
MIRT472724 MTUS1 microtubule associated scaffold protein 1 2 6
MIRT479785 CCND1 cyclin D1 2 2
MIRT482446 ADM adrenomedullin 2 10
MIRT485365 MYLIP myosin regulatory light chain interacting protein 2 12
MIRT498399 KIF6 kinesin family member 6 2 2
MIRT503202 ACTB actin beta 2 6
MIRT503819 TMEM242 transmembrane protein 242 2 2
MIRT504706 ZNF117 zinc finger protein 117 2 2
MIRT507802 CDKN1B cyclin dependent kinase inhibitor 1B 2 2
MIRT509968 KANSL1L KAT8 regulatory NSL complex subunit 1 like 2 4
MIRT517306 ELF4 E74 like ETS transcription factor 4 2 6
MIRT523900 ENPP6 ectonucleotide pyrophosphatase/phosphodiesterase 6 2 6
MIRT532018 NOX5 NADPH oxidase 5 2 2
MIRT535334 PHACTR2 phosphatase and actin regulator 2 2 2
MIRT536944 HCN4 hyperpolarization activated cyclic nucleotide gated potassium channel 4 2 4
MIRT539322 AHSA2 activator of HSP90 ATPase homolog 2 2 2
MIRT540189 GSTM4 glutathione S-transferase mu 4 2 2
MIRT545015 ZNF439 zinc finger protein 439 2 2
MIRT545265 TRIM36 tripartite motif containing 36 2 4
MIRT547230 PAG1 phosphoprotein membrane anchor with glycosphingolipid microdomains 1 2 4
MIRT548425 ELOVL5 ELOVL fatty acid elongase 5 2 2
MIRT549910 ADH4 alcohol dehydrogenase 4 (class II), pi polypeptide 2 2
MIRT550185 TMEM106C transmembrane protein 106C 2 2
MIRT550775 ENOX2 ecto-NOX disulfide-thiol exchanger 2 2 4
MIRT552401 ZNF487P zinc finger protein 487 1 1
MIRT554782 RHEBP1 RHEB pseudogene 1 2 4
MIRT557311 HIF1A hypoxia inducible factor 1 alpha subunit 2 2
MIRT558635 CNNM2 cyclin and CBS domain divalent metal cation transport mediator 2 2 2
MIRT563168 RPS14 ribosomal protein S14 2 2
MIRT564886 YWHAE tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon 2 2
MIRT565778 SEPHS1 selenophosphate synthetase 1 2 2
MIRT566480 PDCD4 programmed cell death 4 2 2
MIRT567206 IGFBP5 insulin like growth factor binding protein 5 2 2
MIRT568931 SMCR8 Smith-Magenis syndrome chromosome region, candidate 8 2 2
MIRT570698 FBXO41 F-box protein 41 2 2
MIRT573474 MTRNR2L9 MT-RNR2-like 9 2 2
MIRT576170 Hmox1 heme oxygenase 1 2 2
MIRT607555 GLI2 GLI family zinc finger 2 2 2
MIRT608203 ERBB2 erb-b2 receptor tyrosine kinase 2 2 2
MIRT609779 VWC2L von Willebrand factor C domain containing protein 2 like 2 4
MIRT616312 CELF2 CUGBP Elav-like family member 2 2 2
MIRT617190 CDH13 cadherin 13 2 2
MIRT626842 RPLP1 ribosomal protein lateral stalk subunit P1 2 2
MIRT636438 MARCH1 membrane associated ring-CH-type finger 1 2 2
MIRT639101 GLIPR1L2 GLI pathogenesis related 1 like 2 2 2
MIRT691018 CRTC3 CREB regulated transcription coactivator 3 2 2
MIRT700008 RPS21 ribosomal protein S21 2 2
MIRT701144 PANK1 pantothenate kinase 1 2 2
MIRT712691 NUDT7 nudix hydrolase 7 2 2
MIRT715505 MAZ MYC associated zinc finger protein 2 2
MIRT722509 PTPRC protein tyrosine phosphatase, receptor type C 2 2
MIRT724982 TNS1 tensin 1 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
miR-4464 5-Fluorouracil approved 3385 Microarray CNE cells 22614822 2012 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-4464 Tamoxifen 2733525 NSC180973 approved sensitive cell line (LCC2)

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