pre-miRNA Information | |
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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 | ||||||||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-4464 | |||||||||||||||||||||||||||||||||||
Sequence | 12| AAGGUUUGGAUAGAUGCAAUA |32 | |||||||||||||||||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||||||||||||||||
Experiments | Illumina | |||||||||||||||||||||||||||||||||||
Editing Events in miRNAs |
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SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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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
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miRNA-target interactions (Predicted by miRanda) |
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DRVs in gene 3'UTRs | |||||||||||||||||||||
SNPs in gene 3'UTRs |
Experimental Support 1 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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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]
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CLIP-seq Support 1 for dataset GSM4903835 | |
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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 | |
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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 | |
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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 | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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81 hsa-miR-4464 Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT056004 | ARL5B | ADP ribosylation factor like GTPase 5B | ![]() |
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2 | 2 | ||||||
MIRT061568 | BTG2 | BTG anti-proliferation factor 2 | ![]() |
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2 | 2 | ||||||
MIRT078651 | ICT1 | mitochondrial ribosomal protein L58 | ![]() |
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2 | 2 | ||||||
MIRT087551 | YWHAH | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein eta | ![]() |
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2 | 4 | ||||||
MIRT088139 | SEPT2 | septin 2 | ![]() |
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2 | 4 | ||||||
MIRT095089 | SEC24A | SEC24 homolog A, COPII coat complex component | ![]() |
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2 | 4 | ||||||
MIRT099065 | FOXC1 | forkhead box C1 | ![]() |
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2 | 4 | ||||||
MIRT150194 | MIDN | midnolin | ![]() |
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2 | 2 | ||||||
MIRT178173 | EIF5AL1 | eukaryotic translation initiation factor 5A-like 1 | ![]() |
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2 | 4 | ||||||
MIRT178942 | C11ORF57 | chromosome 11 open reading frame 57 | ![]() |
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2 | 2 | ||||||
MIRT188776 | SESN2 | sestrin 2 | ![]() |
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2 | 2 | ||||||
MIRT267026 | EFHD2 | EF-hand domain family member D2 | ![]() |
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2 | 2 | ||||||
MIRT307213 | ACVR2B | activin A receptor type 2B | ![]() |
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2 | 2 | ||||||
MIRT324750 | ACER2 | alkaline ceramidase 2 | ![]() |
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2 | 2 | ||||||
MIRT442732 | TEAD1 | TEA domain transcription factor 1 | ![]() |
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2 | 2 | ||||||
MIRT444087 | C12orf73 | chromosome 12 open reading frame 73 | ![]() |
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2 | 2 | ||||||
MIRT445527 | KLF9 | Kruppel like factor 9 | ![]() |
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2 | 2 | ||||||
MIRT449604 | INIP | INTS3 and NABP interacting protein | ![]() |
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2 | 2 | ||||||
MIRT451129 | ZNF99 | zinc finger protein 99 | ![]() |
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2 | 2 | ||||||
MIRT452271 | RPL30 | ribosomal protein L30 | ![]() |
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2 | 2 | ||||||
MIRT452486 | DDX4 | DEAD-box helicase 4 | ![]() |
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2 | 2 | ||||||
MIRT454868 | DNAJC15 | DnaJ heat shock protein family (Hsp40) member C15 | ![]() |
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2 | 6 | ||||||
MIRT455773 | TSPAN6 | tetraspanin 6 | ![]() |
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2 | 4 | ||||||
MIRT463844 | WRN | Werner syndrome RecQ like helicase | ![]() |
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2 | 2 | ||||||
MIRT465036 | TTC39C | tetratricopeptide repeat domain 39C | ![]() |
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2 | 2 | ||||||
MIRT465176 | TRPV2 | transient receptor potential cation channel subfamily V member 2 | ![]() |
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2 | 4 | ||||||
MIRT465294 | TRIB3 | tribbles pseudokinase 3 | ![]() |
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2 | 4 | ||||||
MIRT467931 | SLC16A7 | solute carrier family 16 member 7 | ![]() |
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2 | 2 | ||||||
MIRT471906 | NUAK2 | NUAK family kinase 2 | ![]() |
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2 | 2 | ||||||
MIRT472724 | MTUS1 | microtubule associated scaffold protein 1 | ![]() |
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2 | 6 | ||||||
MIRT479785 | CCND1 | cyclin D1 | ![]() |
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2 | 2 | ||||||
MIRT482446 | ADM | adrenomedullin | ![]() |
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2 | 10 | ||||||
MIRT485365 | MYLIP | myosin regulatory light chain interacting protein | ![]() |
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2 | 12 | ||||||
MIRT498399 | KIF6 | kinesin family member 6 | ![]() |
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2 | 2 | ||||||
MIRT503202 | ACTB | actin beta | ![]() |
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2 | 6 | ||||||
MIRT503819 | TMEM242 | transmembrane protein 242 | ![]() |
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2 | 2 | ||||||
MIRT504706 | ZNF117 | zinc finger protein 117 | ![]() |
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2 | 2 | ||||||
MIRT507802 | CDKN1B | cyclin dependent kinase inhibitor 1B | ![]() |
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2 | 2 | ||||||
MIRT509968 | KANSL1L | KAT8 regulatory NSL complex subunit 1 like | ![]() |
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2 | 4 | ||||||
MIRT517306 | ELF4 | E74 like ETS transcription factor 4 | ![]() |
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2 | 6 | ||||||
MIRT523900 | ENPP6 | ectonucleotide pyrophosphatase/phosphodiesterase 6 | ![]() |
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2 | 6 | ||||||
MIRT532018 | NOX5 | NADPH oxidase 5 | ![]() |
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2 | 2 | ||||||
MIRT535334 | PHACTR2 | phosphatase and actin regulator 2 | ![]() |
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2 | 2 | ||||||
MIRT536944 | HCN4 | hyperpolarization activated cyclic nucleotide gated potassium channel 4 | ![]() |
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2 | 4 | ||||||
MIRT539322 | AHSA2 | activator of HSP90 ATPase homolog 2 | ![]() |
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2 | 2 | ||||||
MIRT540189 | GSTM4 | glutathione S-transferase mu 4 | ![]() |
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2 | 2 | ||||||
MIRT545015 | ZNF439 | zinc finger protein 439 | ![]() |
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2 | 2 | ||||||
MIRT545265 | TRIM36 | tripartite motif containing 36 | ![]() |
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2 | 4 | ||||||
MIRT547230 | PAG1 | phosphoprotein membrane anchor with glycosphingolipid microdomains 1 | ![]() |
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2 | 4 | ||||||
MIRT548425 | ELOVL5 | ELOVL fatty acid elongase 5 | ![]() |
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2 | 2 | ||||||
MIRT549910 | ADH4 | alcohol dehydrogenase 4 (class II), pi polypeptide | ![]() |
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2 | 2 | ||||||
MIRT550185 | TMEM106C | transmembrane protein 106C | ![]() |
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2 | 2 | ||||||
MIRT550775 | ENOX2 | ecto-NOX disulfide-thiol exchanger 2 | ![]() |
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2 | 4 | ||||||
MIRT552401 | ZNF487P | zinc finger protein 487 | ![]() |
1 | 1 | |||||||
MIRT554782 | RHEBP1 | RHEB pseudogene 1 | ![]() |
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2 | 4 | ||||||
MIRT557311 | HIF1A | hypoxia inducible factor 1 alpha subunit | ![]() |
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2 | 2 | ||||||
MIRT558635 | CNNM2 | cyclin and CBS domain divalent metal cation transport mediator 2 | ![]() |
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2 | 2 | ||||||
MIRT563168 | RPS14 | ribosomal protein S14 | ![]() |
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2 | 2 | ||||||
MIRT564886 | YWHAE | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon | ![]() |
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2 | 2 | ||||||
MIRT565778 | SEPHS1 | selenophosphate synthetase 1 | ![]() |
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2 | 2 | ||||||
MIRT566480 | PDCD4 | programmed cell death 4 | ![]() |
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2 | 2 | ||||||
MIRT567206 | IGFBP5 | insulin like growth factor binding protein 5 | ![]() |
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2 | 2 | ||||||
MIRT568931 | SMCR8 | Smith-Magenis syndrome chromosome region, candidate 8 | ![]() |
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2 | 2 | ||||||
MIRT570698 | FBXO41 | F-box protein 41 | ![]() |
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2 | 2 | ||||||
MIRT573474 | MTRNR2L9 | MT-RNR2-like 9 | ![]() |
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2 | 2 | ||||||
MIRT576170 | Hmox1 | heme oxygenase 1 | ![]() |
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2 | 2 | ||||||
MIRT607555 | GLI2 | GLI family zinc finger 2 | ![]() |
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2 | 2 | ||||||
MIRT608203 | ERBB2 | erb-b2 receptor tyrosine kinase 2 | ![]() |
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2 | 2 | ||||||
MIRT609779 | VWC2L | von Willebrand factor C domain containing protein 2 like | ![]() |
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2 | 4 | ||||||
MIRT616312 | CELF2 | CUGBP Elav-like family member 2 | ![]() |
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2 | 2 | ||||||
MIRT617190 | CDH13 | cadherin 13 | ![]() |
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2 | 2 | ||||||
MIRT626842 | RPLP1 | ribosomal protein lateral stalk subunit P1 | ![]() |
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2 | 2 | ||||||
MIRT636438 | MARCH1 | membrane associated ring-CH-type finger 1 | ![]() |
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2 | 2 | ||||||
MIRT639101 | GLIPR1L2 | GLI pathogenesis related 1 like 2 | ![]() |
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2 | 2 | ||||||
MIRT691018 | CRTC3 | CREB regulated transcription coactivator 3 | ![]() |
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2 | 2 | ||||||
MIRT700008 | RPS21 | ribosomal protein S21 | ![]() |
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2 | 2 | ||||||
MIRT701144 | PANK1 | pantothenate kinase 1 | ![]() |
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2 | 2 | ||||||
MIRT712691 | NUDT7 | nudix hydrolase 7 | ![]() |
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2 | 2 | ||||||
MIRT715505 | MAZ | MYC associated zinc finger protein | ![]() |
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2 | 2 | ||||||
MIRT722509 | PTPRC | protein tyrosine phosphatase, receptor type C | ![]() |
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2 | 2 | ||||||
MIRT724982 | TNS1 | tensin 1 | ![]() |
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2 | 2 |
miRNA-Drug Associations | |||||||||||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||
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