pre-miRNA Information
pre-miRNA mmu-mir-129-1   
Genomic Coordinates chr6: 29022619 - 29022691
Description Mus musculus miR-129-1 stem-loop
Comment The mature sequence shown here represents the most commonly cloned form from large-scale cloning studies .
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-129-1-3p
Sequence 49| AAGCCCUUACCCCAAAAAGUAU |70
Evidence Experimental
Experiments Illumina
Putative Targets

Gene Information
Gene Symbol Il11   
Synonyms IL-11
Description interleukin 11
Transcript NM_008350   
Expression
Putative miRNA Targets on Il11
3'UTR of Il11
(miRNA target sites are highlighted)
>Il11|NM_008350|3'UTR
   1 CTCGGGACTGAAAACCACCATCGATACCGCCCTTTAAAACCAGATCTTATTTATTTATTTATTTTGGTACTTGGAGGGGG
  81 GCATGATGATCAGGGGCATGCCACACCCCAAACAACCGCCCCACACCCAGCTAGACAGTCTTTCCAGTAGACCTGGGTGA
 161 GGGGGATCACCTGTGGCTTATTTATACTTATTTATTTAAACAATTGGGGGGTGGGTGGGTGCATCTGAGACCCTGAAGAG
 241 CAGGGAACTGAGATCCTGGGTTCTGGGGTCTCTATGAAATCTGTTCACAGTGTCTTCCTCACTTCCTACATTATTTATTA
 321 AACGATTACTTTTTATATTAAGAGGAGGAAGGAGGGAAGCCGGGCGTGGTGGCGCATGCCTTTAATCCCAGCACTCGGGA
 401 GGCAGAGGCAGGCAGATTTCTGAGTTCGAGGCCAGCCTGGTCTAAGAGTGAGTTCGTGAGTTCCAGGACAGCCAGGGCTA
 481 CACAGAGAAACCCTGTCTCGAAAAACCAAAAAAAAAAAAAAAAAAAAAGAGGAGGAAGGAGGGGGAAAAAGGAAGCCTGG
 561 GGTTTTATACCAAAATGTGAGTTTTTTTTTGTGAGTCAGAGAAGTGAGAGGATTTAAATACATATCTATTTAGAGGTTAT
 641 TAGCAGGAGTATGCCGAAAGGATCGGAGTCTAAACTGGTACCCTAGCATTTCAAAGGTCCTCAACAGATACTTAACAAAA
 721 AGTTCCAGAGCATCACCTTATAACTAATAGCACCTGTATGGTACAGAGCTGTAAGGTACAAGGTTTTTTGTTTCAGCAAA
 801 ATTCACGATGACCAATGGGAAACAATCTAGGCTTTCTGGGGGGCGGGCAGGGGATGGATGAATAAAGCTAGGGATACATC
 881 CGCATGATGAAGTTCTAGCTCGCCAACCATAAAAAGGCAAGTTCCAGGCGAAGACTGCTTTAGATATTGAACGTCTCTGC
 961 GACCCAGGAGCAGCAGATGGTAGAACTACTCTCCCTATACATGAGTATGGACTGTTTGGTTTTTCAAAATGGAAACACCA
1041 TGATGTTGACGATAGCTGCCTCAGGGCTGAAAACAAGCAATGGCACAGTGGGTGACTGTTACTGTTTGTGTTTGCATTTT
1121 CCAGAGTTTTCACCATGACTGTATTTTGCAGGACACATTTATAAACATTAATAAACACTATTTTTAGAAAAAAA
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' uaugaaaaaccccauUCCCGAa 5'
                         |||||| 
Target 5' agttccaggacagccAGGGCTa 3'
459 - 480 120.00 -8.40
2
miRNA  3' uaugaaaaaccccauUCCCGAa 5'
                         |||||| 
Target 5' gacgatagctgcctcAGGGCTg 3'
1048 - 1069 120.00 -7.90
3
miRNA  3' uaUGAAAAAC------CCCAUUCCCGAa 5'
            :|||| ||      ||| |:||| | 
Target 5' agGCTTTCTGGGGGGCGGGCAGGGGATg 3'
829 - 856 114.00 -18.73
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions mESCs
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 GSM622570. RNA binding protein: AGO2. Condition:WT1A HITS-CLIP data was present in GSM622573. RNA binding protein: AGO2. Condition:KO1 HITS-CLIP data was present in GSM622574. RNA binding protein: AGO2. Condition:KO2 ...

- Leung AK; Young AG; Bhutkar A; Zheng GX; et al., 2011, Nature structural & molecular biology.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' uaugaaaaaccccauUCCCGAa 5'
                         |||||| 
Target 5' ---------------AGGGCUa 3'
1 - 7
Article - Leung AK; Young AG; Bhutkar A; Zheng GX; et al.
- Nature structural & molecular biology, 2011
MicroRNAs (miRNAs) are 19-22-nucleotide noncoding RNAs that post-transcriptionally regulate mRNA targets. We have identified endogenous miRNA binding sites in mouse embryonic stem cells (mESCs), by performing photo-cross-linking immunoprecipitation using antibodies to Argonaute (Ago2) followed by deep sequencing of RNAs (CLIP-seq). We also performed CLIP-seq in Dicer(-)/(-) mESCs that lack mature miRNAs, allowing us to define whether the association of Ago2 with the identified sites was miRNA dependent. A significantly enriched motif, GCACUU, was identified only in wild-type mESCs in 3' untranslated and coding regions. This motif matches the seed of a miRNA family that constitutes ~68% of the mESC miRNA population. Unexpectedly, a G-rich motif was enriched in sequences cross-linked to Ago2 in both the presence and absence of miRNAs. Expression analysis and reporter assays confirmed that the seed-related motif confers miRNA-directed regulation on host mRNAs and that the G-rich motif can modulate this regulation.
LinkOut: [PMID: 21258322]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions C2C12
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 GSM1385342. RNA binding protein: 聽AGO2. Condition:C2C12_GM_Ago2_CLIP-Seq_myoblast HITS-CLIP data was present in GSM1385343. RNA binding protein: 聽AGO2. Condition:C2C12_DM_Ago2_CLIP-Seq_myotubes ...

- Zhang X; Zuo X; Yang B; Li Z; Xue Y; Zhou et al., 2014, Cell.

Article - Zhang X; Zuo X; Yang B; Li Z; Xue Y; Zhou et al.
- Cell, 2014
MicroRNAs are well known to mediate translational repression and mRNA degradation in the cytoplasm. Various microRNAs have also been detected in membrane-compartmentalized organelles, but the functional significance has remained elusive. Here, we report that miR-1, a microRNA specifically induced during myogenesis, efficiently enters the mitochondria where it unexpectedly stimulates, rather than represses, the translation of specific mitochondrial genome-encoded transcripts. We show that this positive effect requires specific miR:mRNA base-pairing and Ago2, but not its functional partner GW182, which is excluded from the mitochondria. We provide evidence for the direct action of Ago2 in mitochondrial translation by crosslinking immunoprecipitation coupled with deep sequencing (CLIP-seq), functional rescue with mitochondria-targeted Ago2, and selective inhibition of the microRNA machinery in the cytoplasm. These findings unveil a positive function of microRNA in mitochondrial translation and suggest a highly coordinated myogenic program via miR-1-mediated translational stimulation in the mitochondria and repression in the cytoplasm.
LinkOut: [PMID: 25083871]
CLIP-seq Support 1 for dataset GSM4751756
Method / RBP HITS-CLIP / AGO
Cell line / Condition adipose tissue / RNA sequencing of iBAT 1
Location of target site NM_008350 | 3UTR | AGGACAGCCAGGGCUACACAGAGAAACCCUGUCUCGAAAAACCAAAAAAAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE142677
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM4751757
Method / RBP HITS-CLIP / AGO
Cell line / Condition adipose tissue / RNA sequencing of iBAT 2
Location of target site NM_008350 | 3UTR | CCAGGACAGCCAGGGCUACACAGAGAAACCCUGUCUCGAAAAACCAAAAAAAAAAAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE142677
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM4751759
Method / RBP HITS-CLIP / AGO
Cell line / Condition adipose tissue / RNA sequencing of iBAT 4
Location of target site NM_008350 | 3UTR | CAGGACAGCCAGGGCUACACAGAGAAACCCUGUCUCGAAAAACCAAAAAAAAAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE142677
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM622570
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / WT1A
Location of target site NM_008350 | 3UTR | AGGGCUACACAGAGAAACCCUGUCUCGAAAAAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM622573
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / KO1
Location of target site NM_008350 | 3UTR | ACACAGAGAAACCCUGUCUCGAAAAAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM622574
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / KO2
Location of target site NM_008350 | 3UTR | AGGGCUACACAGAGAAACCCUGUCUCGAAAAACC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
CLIP-seq Support 7 for dataset GSM1385342
Method / RBP HITS-CLIP /  AGO2
Cell line / Condition C2C12 / C2C12_GM_Ago2_CLIP-Seq_myoblast
Location of target site NM_008350 | 3UTR | AGUUCGUGAGUUCCAGGACAGCCAGGGCUACACAGAGAAACCCUGUCUCGAAAAACCAAAAAAAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 25083871 / GSE57596
CLIP-seq Viewer Link
CLIP-seq Support 8 for dataset GSM1385343
Method / RBP HITS-CLIP /  AGO2
Cell line / Condition C2C12 / C2C12_DM_Ago2_CLIP-Seq_myotubes
Location of target site NM_008350 | 3UTR | AGUUCGUGAGUUCCAGGACAGCCAGGGCUACACAGAGAAACCCUGUCUCGAAAAACCA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 25083871 / GSE57596
CLIP-seq Viewer Link
154 mmu-miR-129-1-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT577374 Ybey ybeY metallopeptidase 2 4
MIRT577528 Tirap toll-interleukin 1 receptor (TIR) domain-containing adaptor protein 2 4
MIRT577536 Timm17b translocase of inner mitochondrial membrane 17b 2 4
MIRT577611 Stxbp4 syntaxin binding protein 4 2 2
MIRT577653 Smyd4 SET and MYND domain containing 4 2 4
MIRT577661 Slc6a2 solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2 2 4
MIRT578366 Lrrc14b leucine rich repeat containing 14B 2 4
MIRT579042 Csf3r colony stimulating factor 3 receptor (granulocyte) 2 2
MIRT579177 Cd3eap CD3E antigen, epsilon polypeptide associated protein 2 4
MIRT579526 9230110C19Rik RIKEN cDNA 9230110C19 gene 2 2
MIRT579583 Uvssa UV stimulated scaffold protein A 1 1
MIRT579590 4930579G24Rik RIKEN cDNA 4930579G24 gene 2 4
MIRT579674 Inip INTS3 and NABP interacting protein 1 2
MIRT579681 Ccdc167 coiled-coil domain containing 167 1 1
MIRT579809 Zfp148 zinc finger protein 148 2 4
MIRT580341 Tmod1 tropomodulin 1 2 2
MIRT580436 Tmed5 transmembrane p24 trafficking protein 5 2 2
MIRT580518 Tet1 tet methylcytosine dioxygenase 1 2 2
MIRT581179 Scn8a sodium channel, voltage-gated, type VIII, alpha 2 4
MIRT581283 Rp2h retinitis pigmentosa 2 homolog 2 4
MIRT582042 Otud7b OTU domain containing 7B 2 4
MIRT582293 Nav2 neuron navigator 2 2 2
MIRT582403 Mprip myosin phosphatase Rho interacting protein 2 2
MIRT582579 Lypla1 lysophospholipase 1 2 2
MIRT582607 Lrrc3 leucine rich repeat containing 3 2 4
MIRT582823 Iws1 IWS1, SUPT6 interacting protein 2 4
MIRT582933 Il11 interleukin 11 2 4
MIRT583276 Gm6531 CDC28 protein kinase 1b, retrogene 2 4
MIRT583359 Gad2 glutamic acid decarboxylase 2 2 4
MIRT584153 Creb1 cAMP responsive element binding protein 1 2 2
MIRT584172 Cpox coproporphyrinogen oxidase 2 2
MIRT584306 Chic1 cysteine-rich hydrophobic domain 1 2 4
MIRT584544 Btaf1 B-TFIID TATA-box binding protein associated factor 1 2 2
MIRT584612 BC030476 glutamate rich 5 2 4
MIRT584770 Asap3 ArfGAP with SH3 domain, ankyrin repeat and PH domain 3 2 2
MIRT584946 Adarb1 adenosine deaminase, RNA-specific, B1 2 4
MIRT585126 Zfp933 zinc finger protein 933 2 4
MIRT585139 Zfp882 zinc finger protein 882 2 4
MIRT585209 Zfp553 zinc finger protein 553 2 4
MIRT585374 Xcr1 chemokine (C motif) receptor 1 2 2
MIRT585439 Veph1 ventricular zone expressed PH domain-containing 1 2 4
MIRT585463 Ube2c ubiquitin-conjugating enzyme E2C 2 4
MIRT585561 Tprkb Tp53rk binding protein 2 2
MIRT585676 Tfcp2l1 transcription factor CP2-like 1 1 1
MIRT585779 Spc24 SPC24, NDC80 kinetochore complex component, homolog (S. cerevisiae) 2 2
MIRT585868 Slc23a1 solute carrier family 23 (nucleobase transporters), member 1 2 2
MIRT585899 Slc17a8 solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8 2 4
MIRT585972 Sgpp2 sphingosine-1-phosphate phosphotase 2 2 4
MIRT585990 Sfxn2 sideroflexin 2 2 2
MIRT586068 Rhobtb1 Rho-related BTB domain containing 1 2 2
MIRT586089 Rft1 RFT1 homolog 2 2
MIRT586161 Pus7 pseudouridylate synthase 7 2 2
MIRT586201 Ptpn7 protein tyrosine phosphatase, non-receptor type 7 2 2
MIRT586228 Psmd9 proteasome (prosome, macropain) 26S subunit, non-ATPase, 9 2 2
MIRT586240 Psmb11 proteasome (prosome, macropain) subunit, beta type, 11 2 2
MIRT586256 Prss43 protease, serine 43 2 4
MIRT586361 Pdk1 pyruvate dehydrogenase kinase, isoenzyme 1 2 4
MIRT586433 Nwd1 NACHT and WD repeat domain containing 1 2 2
MIRT586522 Ndor1 NADPH dependent diflavin oxidoreductase 1 2 2
MIRT586601 Mob3c MOB kinase activator 3C 1 1
MIRT586637 Mettl2 methyltransferase like 2 2 4
MIRT586649 Med16 mediator complex subunit 16 2 4
MIRT586712 Lmbrd1 LMBR1 domain containing 1 2 2
MIRT586754 Kif1c kinesin family member 1C 2 4
MIRT586876 Hyal1 hyaluronoglucosaminidase 1 2 2
MIRT586894 Hsbp1l1 heat shock factor binding protein 1-like 1 2 4
MIRT586970 Gprc5c G protein-coupled receptor, family C, group 5, member C 2 2
MIRT587001 Gpi1 glucose phosphate isomerase 1 2 2
MIRT587030 Gmip Gem-interacting protein 2 4
MIRT587078 Glt28d2 glycosyltransferase 28 domain containing 2 2 2
MIRT587084 Glrx2 glutaredoxin 2 (thioltransferase) 2 2
MIRT587110 Gga2 golgi associated, gamma adaptin ear containing, ARF binding protein 2 2 4
MIRT587136 Gemin8 gem nuclear organelle associated protein 8 2 4
MIRT587209 Fbxo22 F-box protein 22 2 2
MIRT587288 F10 coagulation factor X 2 2
MIRT587366 E130311K13Rik RIKEN cDNA E130311K13 gene 2 4
MIRT587685 Cdh1 cadherin 1 2 4
MIRT587831 Casp8 caspase 8 2 2
MIRT587890 BC026590 family with sequence similarity 206, member A 2 2
MIRT587914 Bambi BMP and activin membrane-bound inhibitor 2 2
MIRT587925 B4galnt2 beta-1,4-N-acetyl-galactosaminyl transferase 2 2 4
MIRT587936 Atpbd4 diphthamine biosynthesis 6 2 4
MIRT587999 Alox12 arachidonate 12-lipoxygenase 2 4
MIRT588045 Aida axin interactor, dorsalization associated 2 4
MIRT588085 Agtrap angiotensin II, type I receptor-associated protein 2 2
MIRT588096 Afg3l1 AFG3-like AAA ATPase 1 2 4
MIRT588129 Abcd4 ATP-binding cassette, sub-family D (ALD), member 4 2 2
MIRT588170 Rmi2 RecQ mediated genome instability 2 1 1
MIRT588242 Ndufaf7 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex assembly factor 7 1 1
MIRT588327 Zfyve27 zinc finger, FYVE domain containing 27 2 4
MIRT588352 Zfp568 zinc finger protein 568 2 2
MIRT588404 Zdhhc20 zinc finger, DHHC domain containing 20 2 2
MIRT588707 Tecpr2 tectonin beta-propeller repeat containing 2 2 2
MIRT589367 Ogdh oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) 2 4
MIRT589444 Ncl nucleolin 2 4
MIRT589531 Mob4 MOB family member 4, phocein 1 1
MIRT589565 Mau2 MAU2 sister chromatid cohesion factor 2 2
MIRT589582 Magt1 magnesium transporter 1 2 4
MIRT589727 Kif11 kinesin family member 11 2 2
MIRT590244 Diap2 diaphanous related formin 2 2 4
MIRT590282 Dcp2 decapping mRNA 2 2 2
MIRT590303 Cxcl11 chemokine (C-X-C motif) ligand 11 2 2
MIRT590350 Cntn2 contactin 2 2 4
MIRT590451 Car5b carbonic anhydrase 5b, mitochondrial 2 2
MIRT590775 5730455P16Rik RIKEN cDNA 5730455P16 gene 2 2
MIRT590785 Epg5 ectopic P-granules autophagy protein 5 homolog (C. elegans) 1 1
MIRT596490 Zfp959 zinc finger protein 959 2 2
MIRT596696 Zbtb8b zinc finger and BTB domain containing 8b 2 2
MIRT596734 Wdfy1 WD repeat and FYVE domain containing 1 2 2
MIRT596782 Ubxn8 UBX domain protein 8 2 2
MIRT596943 Tmppe transmembrane protein with metallophosphoesterase domain 2 2
MIRT597221 Slc7a2 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 2 2
MIRT597371 Sap18 Sin3-associated polypeptide 18 2 2
MIRT597391 Rsad1 radical S-adenosyl methionine domain containing 1 2 2
MIRT597748 Pogk pogo transposable element with KRAB domain 2 2
MIRT597819 Pkd2 polycystic kidney disease 2 2 2
MIRT597872 Pdxdc1 pyridoxal-dependent decarboxylase domain containing 1 2 2
MIRT597993 Npy1r neuropeptide Y receptor Y1 2 2
MIRT598186 Mrpl19 mitochondrial ribosomal protein L19 2 2
MIRT598676 Hltf helicase-like transcription factor 2 2
MIRT598700 Haus2 HAUS augmin-like complex, subunit 2 2 2
MIRT598897 Gla galactosidase, alpha 2 2
MIRT599113 Ecd ecdysoneless homolog (Drosophila) 2 2
MIRT599289 Cxcr2 chemokine (C-X-C motif) receptor 2 2 2
MIRT599320 Comt catechol-O-methyltransferase 2 2
MIRT599376 Cml3 N-acetyltransferase 8 (GCN5-related) family member 3 2 2
MIRT599495 Ccdc78 coiled-coil domain containing 78 2 2
MIRT599730 Anapc16 anaphase promoting complex subunit 16 2 2
MIRT600302 Taf1 TATA-box binding protein associated factor 1 2 2
MIRT600940 Elk1 ELK1, member of ETS oncogene family 2 2
MIRT601239 Abl2 v-abl Abelson murine leukemia viral oncogene 2 (arg, Abelson-related gene) 2 2
MIRT601595 Slx1b SLX1 structure-specific endonuclease subunit homolog B (S. cerevisiae) 2 2
MIRT601758 Rapgef4 Rap guanine nucleotide exchange factor (GEF) 4 2 2
MIRT601823 Prpf31 pre-mRNA processing factor 31 2 2
MIRT601838 Polr3f polymerase (RNA) III (DNA directed) polypeptide F 2 2
MIRT601913 Opa3 optic atrophy 3 2 2
MIRT602113 Krr1 KRR1, small subunit (SSU) processome component, homolog (yeast) 2 2
MIRT602125 Klhl24 kelch-like 24 2 2
MIRT602173 Ifngr2 interferon gamma receptor 2 2 2
MIRT602382 Fam86 eukaryotic elongation factor 2 lysine methyltransferase 2 2
MIRT602466 Dnal1 dynein, axonemal, light chain 1 1 1
MIRT602570 Crtc3 CREB regulated transcription coactivator 3 2 2
MIRT603746 Mpv17 MpV17 mitochondrial inner membrane protein 2 2
MIRT604411 Adam28 a disintegrin and metallopeptidase domain 28 2 2
MIRT604653 Snx30 sorting nexin family member 30 2 2
MIRT605138 Clmn calmin 2 2
MIRT605173 Bri3bp Bri3 binding protein 2 2
MIRT605632 Mfsd11 major facilitator superfamily domain containing 11 2 2
MIRT605648 Mapre1 microtubule-associated protein, RP/EB family, member 1 2 2
MIRT605835 Cd300a CD300A molecule 2 2
MIRT605892 2010109I03Rik RIKEN cDNA 2010109I03 gene 2 2
MIRT605992 Lima1 LIM domain and actin binding 1 2 2
MIRT606568 Tstd3 thiosulfate sulfurtransferase (rhodanese)-like domain containing 3 1 1
MIRT606612 Sfn stratifin 2 2

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