Accession ID: MIRT003549 [miRNA, hsa-miR-489-3p :: PTPN11, target gene]
pre-miRNA Information
pre-miRNA ID hsa-mir-489LinkOut: [miRBase ]
Synonyms MIRN489, hsa-mir-489, MIR489
Description Homo sapiens miR-489 stem-loop
Comment The mature sequence shown here represents the most commonly cloned form from large-scale cloning studies . The 5' end of the miRNA may be offset with respect to previous annotations.
2nd Structure of pre-miRNA
Disease
Mature miRNA Information
Mature miRNA hsa-miR-489-3p
Mature Sequence 52| GUGACAUCACAUAUACGGCAGC |73
Evidence Experimental
Experiments Array-cloned
Putative hsa-miR-489-3p Targets LinkOut: [ TargetScanS 5.1 | MicroCosm | microRNA.org | miRecords | miRDB | miRo | miRNAMap 2.0 ]
Gene Information
Gene Symbol PTPN11 LinkOut: [ Entrez Gene | BioGPS | Wikipedia | iHop ]
Synonyms BPTP3, CFC, NS1, PTP-1D, PTP2C, SH-PTP2, SH-PTP3, SHP2
Description protein tyrosine phosphatase, non-receptor type 11
Transcript NM_002834    LinkOut: [ RefSeq ]
Expression LinkOut: [ BioGPS ]
Putative miRNA Targets on PTPN11 LinkOut: [ TargetScan 5.1 | MicroCosm | miRNAMap 2.0 ]
3'UTR of PTPN11
(miRNA target sites are highlighted)
>PTPN11|NM_002834|3'UTR
   1 GAAAACCTGCCAAAACTTCAGCACAGAAATAGATGTGGACTTTCACCCTCTCCCTAAAAAGATCAAGAACAGACGCAAGA
  81 AAGTTTATGTGAAGACAGAATTTGGATTTGGAAGGCTTGCAATGTGGTTGACTACCTTTTGATAAGCAAAATTTGAAACC
 161 ATTTAAAGACCACTGTATTTTAACTCAACAATACCTGCTTCCCAATTACTCATTTCCTCAGATAAGAAGAAATCATCTCT
 241 ACAATGTAGACAACATTATATTTTATAGAATTTGTTTGAAATTGAGGAAGCAGTTAAATTGTGCGCTGTATTTTGCAGAT
 321 TATGGGGATTCAAATTCTAGTAATAGGCTTTTTTATTTTTATTTTTATACCCTTAACCAGTTTAATTTTTTTTTTCCTCA
 401 TTGTTGGGGATGATGAGAAGAAATGATTTGGGAAAATTAAGTAACAACGACCTAGAAAAGTGAGAACAATCTCATTTACC
 481 ATCATGTATCCAGTAGTGGATAATTCATTTTGATGGCTTCTATTTTTGGCCAAATGAGAATTAAGCCAGTGCCTGAGACT
 561 GTCAGAAGTTGACCTTTGCACTGGCATTAAAGAGTCATAGAAAAAGAATCATGGATATTTATGAATTAAGGTAAGAGGTG
 641 TGGCTTTTTTTTTTTTCTTTTTTCCAGCCGTTGACCAATTATAGTTCGGCTGTTGACTGAGAAGTTTGTGGTGGGAAAAC
 721 GTTTGCCATATTTTCTTTGCATTTGAATAATTGTCTTGTACTTAGAAAAAAGGCGTCTATGAATGACCAGTGTTTTTGGT
 801 CGCCAAATGTTGCTGACAAACTTATCCCAAAACTTTAGTGGCTTAAAAAAACCTGCCCCCAACTGTTAGTCAATCTGAGC
 881 TGGGCTCAGCTGGGCTGTTCTTCTGCCAGCCTGCAGGTGGCCACTCATGTGGTCAGCAGGTCGGCGGAGAGACTGGGATG
 961 GCTGGGCTTCTCTCTCTGCCTGCAGTCCTGAGTCTCTCCTTCTTCGTGTAGTCTCTTTCAGTGGCCTGGCTGGCAGGGTA
1041 GCTAGACCTCTCACATGCAGCTCAGAGCTCCCAAGAGCTCAAAAGCAGAAATGGCCAGGCCTTCTGAAAACTTAAGTCCA
1121 GAATTGTCACAGTGTCCCTTCTACTTCCCTCTATTGATGATGATGATGATGATGATGATGATGATGATGATGATGATGAT
1201 GGTTTTTTCTAATCAGAAGAAAGCTGGGGTATGCCCTCTACTTACTAAACAAGTCACAAGCCCAGCTCAGATTCAAGAAA
1281 AGGGTGTGAAGTAGAGGTGCAGTTAAGTGGGGGGCCACTAGTCTAACAGACGGTCACAACCAGTGCCATGGAAAACCAAG
1361 GATATTAGCAAAAGCAGAAGTTGCTAGTGACCTTGGGAAGCCGAAGCTGCTTACAGTAGCTGGGACAAGCTGAAAGTCAG
1441 ACTAAGAAATAAAGAGAGGGCCTTCAAGAAGCTTCCTGAATGATTTCTGCTAGCCCTGAGCCTATTTTTGGAACCAGCAC
1521 TTGGGGAAACTGATCTTGTGAGGATGGATGTGTTTAGGGACACAGGGCTTTTGAGAGCAGCACCACCCCACTGGGGCATC
1601 CCCAGACTTGGGAAACGTGACTCTTTCTTAATGCCACTGGGTTTTAGTCAGGCCACAGTGAGAAGGAACAGCCCTAACAG
1681 GCCTCCAGCCAGGTTGAATGAGCTCATTTTTGTTGTAGCCAACCAGTAAGATTTGCTAATGTTCTACATTAAGTGCCTTC
1761 TCCAAAGACATCCCTCTTTGCCTCATATGTTGAATCATCCAGTGCGGATATTTCAATGAAAATATCATTGGTTGACTTTT
1841 GTGATGGTAATAATGCTATGGCATCTTTGCCATGAAGTTGTGGCCTCCTTGGATTCTTCTGACTTTGGCTTCTGAAAGGA
1921 AGGCCTAGATCCAGCCCTGGTGGTAGTTCCTTTCTGAGGTCTCTCAGTCCCTTGAGACTTTGGGGTAGTTTGGCTGCCAT
2001 TCTCACTGACAAAATGTATATCAGCCCCCACCTCCACCCCCCAATATTCCTTGAACTTTGAATTGCTTCAGAACACAGGT
2081 GTGGCCTGAAGGTATTCCCTTATTAGGGAAGTGTCACTGCTGTCTTCTAGTCAAACTTGTAAAGAAAAAGATTCCAGTTC
2161 AGTATTTGCAGCAAGAAGCTTGAATGCTGTTCTTTTTATCGCATTGTTACATCGACTCATTCTCCATTTTGCTTTGGTTT
2241 TGTCTTGACTTGACTTGACTTTGGGGGTAAAGTCTTTCACCAGCACACAAGAGTTTGATTGTACAAATATATCTTCTGCA
2321 TTAACATCTCTGCCTGTTGCTTAAGATCAGTTGCTTTTATACTCAGAATGGAAATACCTGATCTTGGCTAGTTTTGTTAT
2401 AAGATATTGATTTCATTTAGATTTCCCTCCACGAGGTCAGCAAACTATCATGTTCTTATGTAAACTTAGGCCAAGGCCAG
2481 AGTTATCATAGTCCCTAGGTTGCTACGGCTTATCATGTGCTTGGTAAAAGGTGATCGCAGGTTCTCAGACGAGTTTACTT
2561 TACATGAGATGGAATCAGGCAGAGAGGCTGGGATGATGGAGAAAGCTCGAGGTGAAGTTTTAAAAAAAAAGTTGTGGAAA
2641 GGAAAGTTCCAAAGAGGTGGTTTCTGAGGAAGTCAGAGCGCCCAGGGCCAGAGCAGTCAGTAATGGGTGAATGAGGTTGT
2721 TTGGAAAGTCGGTGTGACAGACACATGGATGCCATCTACTTCTAGGTTGCTGGTGGGTATTAAATATGCACAATATTCCA
2801 TAGCTCACTGAGGATTTTAAAATTATAAGCATAGGATTTTATATTTTGGGGTGAAAGAATTATCTGGCACATTAGGTATT
2881 GGAGTTTAAAAAAAAAGCCAAATTTCACAGTCTTAATAACTTTTTTTAAAAAAAACTAAAAGGCGCTTCATGTCCAGTGT
2961 GTGGCCCTTCTGAAACTTATGGTCATCTCTCCCACTGAAACCAAGGTCTTTTCAAATGTGGCTAAATGGGGATGAGGAGA
3041 CACGGGTAGGACTTTCTTGGTGTGTGTGCATTCTTTAAAGAGCCAAGTTGCTTCGGGGAAACAGCCAGGAAAATGGTCAA
3121 GATTATTTTTAGAGGTTATTTTATTGGGGATTTTAAGAACTAATAACATCTTGAGTTATTTTTAATTCAGGGGGATGTGG
3201 AAAGGTTTGCAATTGTCAAGTGTTTTGTTGTAGCTTAGTATCCATAAGGGAAACTTAGACTATAGACATAACTACAAAGC
3281 CAGTGCAGCTTTTGTTTTCTGTATGTTGTTGGGGGATCAACTTTCACACATAGCAAGCACATGGCCTCCCTGATGTCAGG
3361 ATGCCTTTGTTAGGATCTGTATTTGCCCTTAATTTTGTTGAAATCTTTTTTCCTTCTTCCTCTTGAAAAGTTCCAAAATA
3441 TAGTTTATTGTATCTTTCATCACTAAAAATTTGTTCCTTTTTCACTATGGGCAGTTCACACAAGGCAAAAACTATTGAAC
3521 AGTTGGTTTTAGTGTGTTGTATAACTTTGCTGTATATCAAACTAATTTTGACAAGTTTTCATCCTAAGCCTCAAATCATG
3601 TAATTAATAATTTGCCTGTTTATTTATGACCTAATTGTGATTCTTTTATTAATAAAAGCTAATGGGAAAAGGATCCCTGA
3681 TTAAGCTGATGACTAGACCTACAATTAATTTTCCTGCAGTATATGAAGTATTGTACCAGAGTATTAAAAGATATGTAATA
3761 TTTTATTGATAAATCTATCCTTTAAAAGGAATACGTTTTAGGATGTCATCATTTTGATGTGAATCATGTAAATGTTGATA
3841 ATATGCTGTTTATTATACATTTAGTGTTTCAAGAGATTCACTTAATTGCCTTTTTGCCCACGTATATTATGTAGTCTATT
3921 TGCAACTGTTCTTAAAAAAATGACATTAAAAGAATAGTTTATGTAGAGAAACATTAGTGGATGTTAATTGTCTCCCCACC
4001 TATATTTATGGGTGTTAGCGCAACTGCTTTGCTAGTTGCAAAGCTGTATTATCAGAGTAAAAGTGTATTTGTAAACTGTA
4081 TGGGAACTAAAAATTAGGAATAAAACCATTTTCTTATATGA
Target sites Provided by authors  Predicted by miRanda
miRNA-target interactions (Predicted by miRanda)
IDDuplex structurePositionScoreMFE
1
miRNA  3' cgacgGCAUAUACACUACAGUg 5'
               ||| | |  ||||||| 
Target 5' gaataCGT-TTTAGGATGTCAt 3'
3789 - 3809 148.00 -12.60
2
miRNA  3' cgacggcauauacACUACAGUg 5'
                       |||||||| 
Target 5' cacatggcctcccTGATGTCAg 3'
3338 - 3359 145.00 -11.20
3
miRNA  3' cgacggcaUAUACA-CUACAGUg 5'
                  ||  || |||||:| 
Target 5' agagaaacATTAGTGGATGTTAa 3'
3965 - 3987 130.00 -8.00
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target hsa-miR-489-3p :: PTPN11    [ Functional MTI ]
Validation Method Luciferase reporter assay , Western blot ,
Location of target site 3'UTR
Tools used in this research TargetScan
Original Description (Extracted from the article) ... miR-489 negatively regulates PTPN11 expression.//This study is to identify tumour-suppressive miRNAs based on clinical HSCC miRNA expression signature. We have specifically identified a tumour-suppressive miRNA (miR-489) and found its direct target (PTPN11). Disruption of this interaction may lead to the deregulation of miR-489-PTPN11 signalling in HSCC.//Luminescence intensity was significantly decreased for the vectors carrying the 3'UTR and the deletion at position 3353a3359, but not in the vector with the deletion at position 3803a3809 (Figure 3), indicating that the region between positions 3803a3809 contains the miR-489 target site. ...

- Kikkawa, N. Hanazawa, T. Fujimura, L. et al., 2010, Br J Cancer.

Article - Kikkawa, N. Hanazawa, T. Fujimura, L. et al.
- Br J Cancer, 2010
Background:Hypopharyngeal squamous cell carcinoma (HSCC) is an aggressive malignancy with one of the worst prognoses among all head and neck cancers. Greater understanding of the pertinent molecular oncogenic pathways could help improve diagnosis, therapy, and prevention of this disease. The aim of this study was to identify tumour-suppressive microRNAs (miRNAs), based on miRNA expression signatures from clinical HSCC specimens, and to predict their biological target genes.Methods:Expression levels of 365 human mature miRNAs from 10 HSCC clinical samples were screened using stem-loop real-time quantitative PCR. Downregulated miRNAs were used in cell proliferation assays to identify a tumour-suppressive miRNA. Genome-wide gene expression analyses were then performed to identify the target genes of the tumour-suppressive miRNA.Results:Expression analysis identified 11 upregulated and 31 downregulated miRNAs. Gain-of-function analysis of the downregulated miRNAs revealed that miR-489 inhibited cell growth in all head and neck cancer cell lines examined. The gene PTPN11 coding for a cytoplasmic protein tyrosine phosphatase containing two Src Homology 2 domains was identified as a miR-489-targeted gene. Knockdown of PTPN11 resulted in the inhibition of cell proliferation in head and neck SCC cells.Conclusion:Identification of the tumour-suppressive miRNA miR-489 and its target, PTPN11, might provide new insights into the underlying molecular mechanisms of HSCC.British Journal of Cancer advance online publication, 10 August 2010; doi:10.1038/sj.bjc.6605811 www.bjcancer.com.
LinkOut: [PMID: 20700123]
MiRNA-Target Expression Profile:

 
MiRNA-Target Expression Profile(TCGA):

 
MiRNA-Target Interaction Network:
Strong evidence (reporter assay, western blot, qRT-PCR or qPCR)
Other evidence
63 hsa-miR-489-3p Target Genes:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT003549 PTPN11 protein tyrosine phosphatase, non-receptor type 11 3 1
MIRT016614 PEX7 peroxisomal biogenesis factor 7 1 1
MIRT016615 GCA grancalcin, EF-hand calcium binding protein 1 1
MIRT309170 SPATA5 spermatogenesis associated 5 1 2
MIRT332417 LDHA lactate dehydrogenase A 1 1
MIRT366485 KLHL15 kelch-like 15 (Drosophila) 1 1
MIRT441438 C4orf50 chromosome 4 open reading frame 50 1 1
MIRT442466 IQCG IQ motif containing G 1 1
MIRT445019 KLHL28 kelch-like 28 (Drosophila) 1 1
MIRT445484 KLF5 Kruppel-like factor 5 (intestinal) 1 1
MIRT447919 PAIP2B poly(A) binding protein interacting protein 2B 1 1
MIRT448137 CMTM6 CKLF-like MARVEL transmembrane domain containing 6 1 1
MIRT448870 FAM117B family with sequence similarity 117, member B 1 1
MIRT449204 RPL7L1 ribosomal protein L7-like 1 1 1
MIRT449807 TRIM38 tripartite motif containing 38 1 1
MIRT450230 ZNF25 zinc finger protein 25 1 1
MIRT450442 GLP2R glucagon-like peptide 2 receptor 1 1
MIRT450516 ZBED3 zinc finger, BED-type containing 3 1 1
MIRT450593 AADAC arylacetamide deacetylase 1 1
MIRT470567 POU2F1 POU class 2 homeobox 1 1 1
MIRT476279 GNAL guanine nucleotide binding protein (G protein), alpha activating activity polypeptide, olfactory type 1 3
MIRT477818 DYRK3 dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3 1 1
MIRT497360 SF1 splicing factor 1 1 1
MIRT497520 FUT4 fucosyltransferase 4 (alpha (1,3) fucosyltransferase, myeloid-specific) 1 1
MIRT500604 UBE2D1 ubiquitin-conjugating enzyme E2D 1 1 3
MIRT504389 PPIL4 peptidylprolyl isomerase (cyclophilin)-like 4 1 2
MIRT505537 SOX4 SRY (sex determining region Y)-box 4 1 1
MIRT527923 FRY furry homolog (Drosophila) 1 1
MIRT528584 PTGER3 prostaglandin E receptor 3 (subtype EP3) 1 1
MIRT531698 ADAM28 ADAM metallopeptidase domain 28 1 1
MIRT532530 NDFIP2 Nedd4 family interacting protein 2 1 1
MIRT533300 USP46 ubiquitin specific peptidase 46 1 1
MIRT534189 SLC7A11 solute carrier family 7 (anionic amino acid transporter light chain, xc- system), member 11 1 1
MIRT534917 PTPN4 protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte) 1 1
MIRT536896 HEPHL1 hephaestin-like 1 1 1
MIRT538134 DDI2 DNA-damage inducible 1 homolog 2 (S. cerevisiae) 1 1
MIRT545576 SNRPA1 small nuclear ribonucleoprotein polypeptide A' 1 1
MIRT548199 FNIP1 folliculin interacting protein 1 1 1
MIRT550704 TP53RK TP53 regulating kinase 1 2
MIRT555946 NUFIP2 nuclear fragile X mental retardation protein interacting protein 2 1 1
MIRT557897 FEM1B fem-1 homolog b (C. elegans) 1 2
MIRT558719 CITED2 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2 1 1
MIRT563542 GTF3C4 general transcription factor IIIC, polypeptide 4, 90kDa 1 1
MIRT572458 ZNF516 zinc finger protein 516 1 1
MIRT575860 Rab1 RAB1, member RAS oncogene family 1 1
MIRT615435 ZFP82 zinc finger protein 82 homolog (mouse) 1 1
MIRT616999 CADM2 cell adhesion molecule 2 1 1
MIRT632303 TMEM65 transmembrane protein 65 1 1
MIRT639159 LAMTOR3 late endosomal/lysosomal adaptor, MAPK and MTOR activator 3 1 1
MIRT639871 STC1 stanniocalcin 1 1 1
MIRT646642 COA4 cytochrome c oxidase assembly factor 4 homolog (S. cerevisiae) 1 1
MIRT651580 WDR26 WD repeat domain 26 1 1
MIRT655623 ONECUT1 one cut homeobox 1 1 1
MIRT666988 PDPN podoplanin 1 1
MIRT668408 FAM26E family with sequence similarity 26, member E 1 1
MIRT697182 QPCTL glutaminyl-peptide cyclotransferase-like 1 1
MIRT702497 KIAA0040 KIAA0040 1 1
MIRT702666 IRS2 insulin receptor substrate 2 1 1
MIRT706169 ZNF716 zinc finger protein 716 1 1
MIRT708346 CT62 cancer/testis antigen 62 1 1
MIRT710048 FAM46A family with sequence similarity 46, member A 1 1
MIRT719173 KCNS2 potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2 1 1
MIRT723595 FKRP fukutin related protein 1 1
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