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 ERBB2   
Synonyms CD340, HER-2, HER-2/neu, HER2, MLN 19, NEU, NGL, TKR1
Description erb-b2 receptor tyrosine kinase 2
Transcript NM_001005862   
Other Transcripts NM_004448   
Expression
Putative miRNA Targets on ERBB2
3'UTR of ERBB2
(miRNA target sites are highlighted)
>ERBB2|NM_001005862|3'UTR
   1 ACCAGAAGGCCAAGTCCGCAGAAGCCCTGATGTGTCCTCAGGGAGCAGGGAAGGCCTGACTTCTGCTGGCATCAAGAGGT
  81 GGGAGGGCCCTCCGACCACTTCCAGGGGAACCTGCCATGCCAGGAACCTGTCCTAAGGAACCTTCCTTCCTGCTTGAGTT
 161 CCCAGATGGCTGGAAGGGGTCCAGCCTCGTTGGAAGAGGAACAGCACTGGGGAGTCTTTGTGGATTCTGAGGCCCTGCCC
 241 AATGAGACTCTAGGGTCCAGTGGATGCCACAGCCCAGCTTGGCCCTTTCCTTCCAGATCCTGGGTACTGAAAGCCTTAGG
 321 GAAGCTGGCCTGAGAGGGGAAGCGGCCCTAAGGGAGTGTCTAAGAACAAAAGCGACCCATTCAGAGACTGTCCCTGAAAC
 401 CTAGTACTGCCCCCCATGAGGAAGGAACAGCAATGGTGTCAGTATCCAGGCTTTGTACAGAGTGCTTTTCTGTTTAGTTT
 481 TTACTTTTTTTGTTTTGTTTTTTTAAAGATGAAATAAAGACCCAGGGGGAGAATGGGTGTTGTATGGGGAGGCAAGTGTG
 561 GGGGGTCCTTCTCCACACCCACTTTGTCCATTTGCAAATATATTTTGGAAAACAGCTAAAAAAAAAAAAAAAAAA
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--AUAGGUUUGGAa 5'
            | |::||  ||||||::|:| 
Target 5' aaTGGTGTCAGTATCCAGGCTTt 3'
432 - 454 121.00 -12.90
2
miRNA  3' auaacguagauaggUUUGGAa 5'
                        |||||| 
Target 5' agagactgtccctgAAACCTa 3'
383 - 403 120.00 -11.90
3
miRNA  3' auaacguaGAUA-GGU--UUGGAa 5'
                  | || |||  ||||| 
Target 5' ggaacctgCCATGCCAGGAACCTg 3'
107 - 130 109.00 -8.66
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN26830687 16 COSMIC
COSN30498266 17 COSMIC
COSN26855769 18 COSMIC
COSN30156929 26 COSMIC
COSN31511550 30 COSMIC
COSN31482246 40 COSMIC
COSN30497784 56 COSMIC
COSN26710484 73 COSMIC
COSN17267928 224 COSMIC
COSN17119572 393 COSMIC
COSN32058051 465 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs2230700 6 dbSNP
rs376055107 7 dbSNP
rs759138887 8 dbSNP
rs1344351646 11 dbSNP
rs1188524654 15 dbSNP
rs1198824920 17 dbSNP
rs369214536 18 dbSNP
rs763698349 19 dbSNP
rs1228882020 21 dbSNP
rs764649330 24 dbSNP
rs777932453 26 dbSNP
rs926732255 27 dbSNP
rs751957841 33 dbSNP
rs1406963176 37 dbSNP
rs772864303 38 dbSNP
rs756233934 40 dbSNP
rs1413136280 42 dbSNP
rs562868556 49 dbSNP
rs1307667124 50 dbSNP
rs192237900 51 dbSNP
rs1428787486 55 dbSNP
rs545634588 57 dbSNP
rs560774319 58 dbSNP
rs936754943 61 dbSNP
rs4252658 67 dbSNP
rs4252659 74 dbSNP
rs537313073 74 dbSNP
rs796253650 74 dbSNP
rs913868767 86 dbSNP
rs945954741 91 dbSNP
rs993183266 94 dbSNP
rs1057251748 95 dbSNP
rs895581608 98 dbSNP
rs1482276330 108 dbSNP
rs1041610291 113 dbSNP
rs1013142758 116 dbSNP
rs1196868025 123 dbSNP
rs36042695 123 dbSNP
rs549594933 128 dbSNP
rs890965903 142 dbSNP
rs1344977597 151 dbSNP
rs1372832259 153 dbSNP
rs1225363800 154 dbSNP
rs943911488 155 dbSNP
rs35040721 161 dbSNP
rs1382782055 162 dbSNP
rs1039556529 169 dbSNP
rs1022829354 174 dbSNP
rs1456654613 183 dbSNP
rs567252769 185 dbSNP
rs1389509223 189 dbSNP
rs995223536 190 dbSNP
rs1481094866 191 dbSNP
rs1437306478 192 dbSNP
rs1310913502 194 dbSNP
rs756776172 197 dbSNP
rs189417058 202 dbSNP
rs956881536 203 dbSNP
rs1026654308 208 dbSNP
rs988167169 210 dbSNP
rs886754869 213 dbSNP
rs1182936429 217 dbSNP
rs1246076140 220 dbSNP
rs550418471 228 dbSNP
rs954834676 234 dbSNP
rs778498515 236 dbSNP
rs1267640239 241 dbSNP
rs986684752 243 dbSNP
rs1025255685 245 dbSNP
rs1327444565 251 dbSNP
rs139158322 258 dbSNP
rs1269270352 260 dbSNP
rs1470949365 261 dbSNP
rs1406149713 270 dbSNP
rs980944649 271 dbSNP
rs1398484964 274 dbSNP
rs942277891 279 dbSNP
rs1037954812 286 dbSNP
rs747455080 287 dbSNP
rs1185941998 294 dbSNP
rs1462186779 302 dbSNP
rs1247984284 305 dbSNP
rs958123686 306 dbSNP
rs539073563 322 dbSNP
rs755575307 326 dbSNP
rs1206846509 327 dbSNP
rs781648400 331 dbSNP
rs989481837 337 dbSNP
rs1198207759 342 dbSNP
rs748570170 344 dbSNP
rs928938765 345 dbSNP
rs1355361306 348 dbSNP
rs945366680 356 dbSNP
rs1454486756 358 dbSNP
rs987861222 361 dbSNP
rs912521534 374 dbSNP
rs943946890 375 dbSNP
rs895538378 376 dbSNP
rs762528320 377 dbSNP
rs1165818349 379 dbSNP
rs1159848036 383 dbSNP
rs1414068002 386 dbSNP
rs1455452389 387 dbSNP
rs1445638764 391 dbSNP
rs1039567949 396 dbSNP
rs1044243016 402 dbSNP
rs899629366 404 dbSNP
rs1301166513 408 dbSNP
rs931068610 411 dbSNP
rs1221082973 413 dbSNP
rs4252660 414 dbSNP
rs886845964 416 dbSNP
rs1336324783 419 dbSNP
rs1003905622 429 dbSNP
rs1349048633 435 dbSNP
rs377267613 437 dbSNP
rs1296772520 452 dbSNP
rs1031558199 455 dbSNP
rs770027275 460 dbSNP
rs530844735 465 dbSNP
rs1363274687 466 dbSNP
rs1033809080 473 dbSNP
rs1390021417 477 dbSNP
rs755980905 478 dbSNP
rs1030353447 485 dbSNP
rs1483253620 485 dbSNP
rs1420282176 488 dbSNP
rs958174498 488 dbSNP
rs1190649452 489 dbSNP
rs1479511802 493 dbSNP
rs1271249986 498 dbSNP
rs989535492 498 dbSNP
rs954943465 499 dbSNP
rs749371173 500 dbSNP
rs1250593564 502 dbSNP
rs1202313313 523 dbSNP
rs910715580 543 dbSNP
rs967195174 545 dbSNP
rs1218067435 546 dbSNP
rs973557451 549 dbSNP
rs1182600687 552 dbSNP
rs1370315296 556 dbSNP
rs1296850550 561 dbSNP
rs552475695 562 dbSNP
rs1468239559 566 dbSNP
rs1414182782 568 dbSNP
rs987524957 574 dbSNP
rs911849256 577 dbSNP
rs1431358428 579 dbSNP
rs919480778 580 dbSNP
rs1481499275 582 dbSNP
rs1302193886 590 dbSNP
rs4252661 592 dbSNP
rs992891740 601 dbSNP
rs774416904 602 dbSNP
rs1264511790 605 dbSNP
rs921111907 606 dbSNP
rs1175779427 609 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions BT474
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 GSM1395167. RNA binding protein: AGO. Condition:BT474 AGO HITS-CLIP Replicate 2 ...

- Pillai MM; Gillen AE; Yamamoto TM; Kline E; et al., 2014, Breast cancer research and treatment.

Article - Pillai MM; Gillen AE; Yamamoto TM; Kline E; et al.
- Breast cancer research and treatment, 2014
miRNAs regulate the expression of genes in both normal physiology and disease. While miRNAs have been demonstrated to play a pivotal role in aspects of cancer biology, these reports have generally focused on the regulation of single genes. Such single-gene approaches have significant limitations, relying on miRNA expression levels and heuristic predictions of mRNA-binding sites. This results in only circumstantial evidence of miRNA-target interaction and typically leads to large numbers of false positive predictions. Here, we used a genome-wide approach (high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation, HITS-CLIP) to define direct miRNA-mRNA interactions in three breast cancer subtypes (estrogen receptor positive, Her2 amplified, and triple negative). Focusing on steroid receptor signaling, we identified two novel regulators of the ER pathway (miR-9-5p and miR-193a/b-3p), which together target multiple genes involved in ER signaling. Moreover, this approach enabled the definition of miR-9-5p as a global regulator of steroid receptor signaling in breast cancer. We show that miRNA targets and networks defined by HITS-CLIP under physiologic conditions are predictive of patient outcomes and provide global insight into miRNA regulation in breast cancer.
LinkOut: [PMID: 24906430]
CLIP-seq Support 1 for dataset GSM4903835
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / CTL_TD_21_c
Location of target site NM_004448 | 3UTR | CCAUUCAGAGACUGUCCCUGAAACCUAGUACUGCCCCCCAUGAGGAAGGAACAGCAAUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4903836
Method / RBP HITS-CLIP / AGO
Cell line / Condition Dermal fibroblasts / 124_TD_21_a
Location of target site NM_004448 | 3UTR | ACAAAAGCGACCCAUUCAGAGACUGUCCCUGAAACCUAGUACUGCCCCCCAUGAGGAAGGAACAGCAAUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE161239
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM1395167
Method / RBP HITS-CLIP / AGO
Cell line / Condition BT474 / BT474 AGO HITS-CLIP Replicate 2
Location of target site ENST00000584450.1 | 3UTR | UGUCUAAGAACAAAAGCGACCCAUUCAGAGACUGUCCCUGAAACCUAGUACUGCCCCCCAUGAGGAAGGAACAGCAAUGGUGUCAGUAUC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 24906430 / GSE57855
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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