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 MTRNR2L9   
Synonyms HN9
Description MT-RNR2-like 9
Transcript NM_001190706   
Expression
Putative miRNA Targets on MTRNR2L9
3'UTR of MTRNR2L9
(miRNA target sites are highlighted)
>MTRNR2L9|NM_001190706|3'UTR
   1 TACAACAAGACGAGAAGACCATATGGAGCTTCAATTTACCAATGCAAACAACACCCAATAAGCCCACAGGCTCTAACCTA
  81 CCAAACCTGCATTAAAAATTTCGGCTGGGGCGACCTCGGAGTATAACCCAACCTCCGAGCAACATATGCTGAGACTTCAC
 161 CAGTCAAAACGAGTTACCACGTACAATTGATCCAATAATTTGACTAACGGAACAAGTTACCCTAGGG
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' auaacgUAGAUAGGUUUGGAa 5'
                | ||| |||||||| 
Target 5' gctctaACCTA-CCAAACCTg 3'
70 - 89 154.00 -11.80
2
miRNA  3' auaaCGUAGAUAGGUUUGGAa 5'
              | :| || || ||||| 
Target 5' ctcgGAGTATAACCCAACCTc 3'
115 - 135 125.00 -8.10
3
miRNA  3' auaacgUAGAUAGGU--UUGGAa 5'
                ||: |||||  ||::| 
Target 5' cgtacaATTGATCCAATAATTTg 3'
180 - 202 91.00 -5.90
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs371547997 2 dbSNP
rs778392432 3 dbSNP
rs749716970 4 dbSNP
rs1396637303 5 dbSNP
rs376461808 6 dbSNP
rs1390308787 7 dbSNP
rs1326511515 9 dbSNP
rs1372646864 10 dbSNP
rs757646162 12 dbSNP
rs186670655 13 dbSNP
rs946006087 14 dbSNP
rs1041713185 15 dbSNP
rs752722159 16 dbSNP
rs1251816561 20 dbSNP
rs1338891755 21 dbSNP
rs369045855 22 dbSNP
rs570642703 23 dbSNP
rs1275290040 24 dbSNP
rs907255247 25 dbSNP
rs1193425682 26 dbSNP
rs1251571493 28 dbSNP
rs1430628669 29 dbSNP
rs1002896411 30 dbSNP
rs1372992623 31 dbSNP
rs373795183 33 dbSNP
rs768225696 37 dbSNP
rs796875222 39 dbSNP
rs376968047 40 dbSNP
rs369774975 41 dbSNP
rs1055817823 42 dbSNP
rs1461687768 43 dbSNP
rs1324769104 44 dbSNP
rs1338602345 44 dbSNP
rs143580489 50 dbSNP
rs6915000 50 dbSNP
rs373259496 52 dbSNP
rs375931079 53 dbSNP
rs370535160 57 dbSNP
rs553063430 59 dbSNP
rs374048246 60 dbSNP
rs376876053 63 dbSNP
rs184746760 64 dbSNP
rs769508963 66 dbSNP
rs535121440 70 dbSNP
rs556550465 71 dbSNP
rs796591256 71 dbSNP
rs370206382 72 dbSNP
rs369330366 73 dbSNP
rs368811224 78 dbSNP
rs994192821 90 dbSNP
rs1370942286 93 dbSNP
rs774567462 96 dbSNP
rs1430616268 97 dbSNP
rs1259920274 99 dbSNP
rs1475303441 101 dbSNP
rs1164662133 103 dbSNP
rs1025290262 104 dbSNP
rs75364207 106 dbSNP
rs1402018110 107 dbSNP
rs574864159 107 dbSNP
rs546489834 112 dbSNP
rs1423366479 118 dbSNP
rs111233494 119 dbSNP
rs1354197345 121 dbSNP
rs796998664 122 dbSNP
rs74445006 123 dbSNP
rs1385786254 124 dbSNP
rs75153205 125 dbSNP
rs1264739418 126 dbSNP
rs543119826 127 dbSNP
rs1383932227 128 dbSNP
rs1276068267 130 dbSNP
rs1399079103 132 dbSNP
rs986520542 137 dbSNP
rs1304475301 138 dbSNP
rs796170511 142 dbSNP
rs75985652 143 dbSNP
rs79068574 144 dbSNP
rs80353892 146 dbSNP
rs1384526960 149 dbSNP
rs746038012 151 dbSNP
rs78792057 152 dbSNP
rs1463975454 156 dbSNP
rs796920110 157 dbSNP
rs1170381075 161 dbSNP
rs372335471 170 dbSNP
rs370976679 171 dbSNP
rs575207323 172 dbSNP
rs796719337 173 dbSNP
rs375763379 174 dbSNP
rs368330109 175 dbSNP
rs1197385371 177 dbSNP
rs772071185 178 dbSNP
rs371939180 179 dbSNP
rs374113189 180 dbSNP
rs386701883 180 dbSNP
rs6915206 181 dbSNP
rs562203725 182 dbSNP
rs376807184 184 dbSNP
rs1266598441 185 dbSNP
rs137884290 198 dbSNP
rs74613494 200 dbSNP
rs6929218 206 dbSNP
rs1217756697 208 dbSNP
rs1323853567 209 dbSNP
rs149446146 210 dbSNP
rs1230456298 216 dbSNP
rs762284070 223 dbSNP
rs1393695187 225 dbSNP
rs1398696382 229 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 GSM545212. RNA binding protein: AGO1. 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' auaacguagAUAGGUUUGGAa 5'
                   || |||||||| 
Target 5' ---------UA-CCAAACCUg 3'
1 - 11
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 GSM545212
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / Control
Location of target site ENST00000544932.1 | 3UTR | UACCAAACCUGCAUUAAAAAUUUCGG
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
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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