pre-miRNA Information
pre-miRNA mmu-mir-344d-1   
Genomic Coordinates chr7: 61683124 - 61683192
Description Mus musculus miR-344d-1 stem-loop
Comment This sequence was identified as a miRNA candidate by Berezikov et al .
RNA Secondary Structure
pre-miRNA mmu-mir-344d-2   
Genomic Coordinates chr7: 61685272 - 61685351
Description Mus musculus miR-344d-2 stem-loop
Comment This sequence was identified as a miRNA candidate by Berezikov et al .
RNA Secondary Structure
pre-miRNA mmu-mir-344d-3   
Genomic Coordinates chr7: 61726249 - 61726328
Description Mus musculus miR-344d-3 stem-loop
Comment This sequence was identified as a miRNA candidate by Berezikov et al .
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-344d-3p
Sequence 45| GAUAUAACCACUGCCAGACUGA |66
Evidence Experimental
Experiments Illumina
Putative Targets

Gene Information
Gene Symbol Olr1   
Synonyms LOX-1, SR-EI, Scare1
Description oxidized low density lipoprotein (lectin-like) receptor 1
Transcript NM_138648   
Expression
Putative miRNA Targets on Olr1
3'UTR of Olr1
(miRNA target sites are highlighted)
>Olr1|NM_138648|3'UTR
   1 TGAATCTAAAGATTCTGGAGAAGACCATGAGAAGACTTTTGACTGTCGCTCTGAAATTTAAGCTATTCTTTATTACCTGC
  81 ATGTAAAGCATGTTGGCCTTGACATCTGTCAGTTACCTGATAGCTACAGTTCACCTCAACAAAGACAAGGACCAGAAGCA
 161 AATACTGGTGGATCCAGATGTTTGAAATCTTTGTATCAAAACGTGTGAGTTCAATTGTTTATCCATATACACTGGCCTTG
 241 CCCCTCCAAAGTCTCCCAACCAACCTGCAATCCTTCTTCCCCTTCGTGTTTTAAATGATGCTTCCTGCCTGACCTGGCCA
 321 TGCTTTGTACTCAGTCTCCTCTACCTCAGTATGCCTCCTGTTGCCGCATGAAAGACAGGATGTAGAAATCCTCCTCAAGT
 401 GCAGGCAGAGGGCTCAAAGGCAAAGCTCGTCCGAGAAATAACATGCAAAGAAACAGAACTGGAAAAACTACACTGCAAAC
 481 AGGAACTCATGATCTCTAAAAAGCCATGGCTTGATCTTTATGACAGGAGTCCATCTCCAGACTGCACTTTTACACACATA
 561 TTTTTTATTTTCCTTTTATTGTAAGTTTATGGATAGTTTGCCTACTTGAATTCTGTGTACCACATGAGTGCCTGGTGCCA
 641 CTGAAGATCAGAAGAGGACATCAGATTCTCTGGATCTGGAATTGCAGATGGTTGTAAGCTGCTATGTAGATGTGAAGAAT
 721 TGAATTCGTGTCCCCTGGAAGAACAGCCAGTACTCTTTGCCATGAGCTATCTCTCAAGCTCCTGTGATCAATTCTTGTAT
 801 CAGTTATGTCTCCATTTTTGCTCTACCAAAGAACAGTGTTATAACTTTAAAACAGTAAGTATTTTCATTATTCTAGGGGT
 881 ATTATAGCAGATATATAGATATAGATATAGATGATATAGATATAGATATAGATATAGATATAGATATAGATATAGATATA
 961 GATATAGATATAGATATAGATATAGATATAGATATAGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTCTAT
1041 GCTAGATACATCCTTGAGAAGATGAGACAGTTTTGTGTGAAATGAGTTTGTAATAATCCAAATTTAAAAATAAATTCGAT
1121 GATTACCTGTAGTGGTCATATTACCACAGCTAAGATGATGAACATACCTGTCACTTCTGCCCCTTTCCAAAGCCTCCCCC
1201 CTAAAACAAACACCAATCTGCTTTCAGTTCGCATTTTATAGAGCTTATCATTTTGTTTTTAAGACAGAATCTCATTATAT
1281 AGTTCTGGCTGGCCTGGAACTCACTACACAGAGCAGGCTGGCCTCCACCTTCTAGAGCTCCTCCTGCCAGACTCCCAAAC
1361 CTTAAGACTGAAGGAGTGCCCTGCCATGTGTGACTCAAACACCTTAATGTGAATGGAATAGCATAAGATGTCCAGGTTTT
1441 TTCAGTCCAGCTTCTTCCACTTGGTACAATTTTTAATTTTTGTGTTCATACATCTCCACCACAGTGTTTGTATCAGTTCA
1521 TCATTCTTTTCAAATGTTGAGCCTTCCCCTGTGGATCTATAGTGTCATTTGTTATCTGTGTATTTGTTGATGCGATTTGG
1601 GTTGTTTTTATTTGGGGTCACCTACAAATAAAGCTGCTATGGATGTCCATGGACAAGGCTAATATCTTAGGTAAGCACCT
1681 ACGAGTAAGATGCTTGGGTCATTCAGTGTGGGAATATATGGTTGGCTATTTTAACCATTCCTGTTTGAAAACATTAATTT
1761 TTTTATTTTTGAAATCAATTTTTTAAAAAATTAGTCTATTTTACATCTCAACCCCAGTTTCTCTTCCTCCTCTCCTCTCA
1841 ACCTTCTCCCACCTTCTCTCCCTGACCCCATCCACCCCTCCTCCCTTTCTCTCCAGAAGAGGGGAGGCCTCCCATGGATG
1921 CCAACCAGCCTCAGCATCTCAAGTTACAGTAAGAATAGGTTTGTCTTCTCTTGTGAAAATCTTAATTTTTAGATTTATCT
2001 ATTATATATGCAGTACTTTGCTTGCACATATGTATTGGTACCATGTACATGAATGGTACCAGAGAAAGTCAGAAGAGGCC
2081 ATTGTATTTTCTGGGACTGGAATTACAGACGGTTTTGAACAATCCTATAGACTCTGGGAACTGAACCCAGGTCCTCTGGA
2161 AAGGCAAGCAGTGCTCTTAACCCCTGAGCCATTTCTTCTGGCCTTTTAGCAATTTTTATTAATATATAACTGTGTATAAT
2241 TGCACTTTTAGCTCAAAGTTCTTAAGTGTCAAATAGTCTTGGATTTATTTTCATGTTATCACTGTCTGTACAATTTCTGT
2321 GATGAAATAACTGAGCATATATTTTGAGAATTTGGTTTTCTTAAATTTTAAATCTGAAGGATTTACATATTTGAGAATAA
2401 AAACCAGCCAGATATGAAAAAAAAAAAAAAA
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' agUCAGACCGUCACCAAUAUAg 5'
            | ||| |:|   |||||:| 
Target 5' caATTCTTGTATCAGTTATGTc 3'
789 - 810 140.00 -8.80
2
miRNA  3' agucaGACCGUCACCAAUAUAg 5'
               || |:|||||| |||| 
Target 5' attacCT-GTAGTGGTCATATt 3'
1122 - 1142 136.00 -13.80
3
miRNA  3' agucagaccGUCACCAAUAUag 5'
                   |||| ||||||  
Target 5' accaaagaaCAGT-GTTATAac 3'
825 - 845 132.00 -8.00
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 GSM622572. RNA binding protein: AGO2. Condition:WT2 ...

- 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' agucagaccgucacCAAUAUag 5'
                        ||| |:  
Target 5' -------------aGUUCUGgc 3'
1 - 9
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]
151 mmu-miR-344d-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT411457 Timp3 tissue inhibitor of metalloproteinase 3 1 1
MIRT429040 Nfib nuclear factor I/B 1 1
MIRT577364 Zbed6 zinc finger, BED type containing 6 1 1
MIRT577414 Ugt2b35 UDP glucuronosyltransferase 2 family, polypeptide B35 1 1
MIRT577446 Ttc17 tetratricopeptide repeat domain 17 1 1
MIRT577510 Tmem100 transmembrane protein 100 1 1
MIRT577584 Tcf21 transcription factor 21 1 1
MIRT577728 Slc12a8 solute carrier family 12 (potassium/chloride transporters), member 8 1 1
MIRT577751 Shh sonic hedgehog 1 1
MIRT577867 Rassf5 Ras association (RalGDS/AF-6) domain family member 5 1 1
MIRT577938 Ppp6r1 protein phosphatase 6, regulatory subunit 1 1 1
MIRT577948 Pou4f2 POU domain, class 4, transcription factor 2 1 1
MIRT577957 Pm20d2 peptidase M20 domain containing 2 1 1
MIRT578019 Pfkl phosphofructokinase, liver, B-type 1 2
MIRT578051 Pcdhb17 protocadherin beta 17 1 1
MIRT578198 Nadsyn1 NAD synthetase 1 1 1
MIRT578516 Igfbp3 insulin-like growth factor binding protein 3 1 1
MIRT578556 Hopx HOP homeobox 1 1
MIRT578585 Hist1h1d histone cluster 1, H1d 1 1
MIRT578725 Gm8369 predicted gene 8369 1 1
MIRT578807 Folh1 folate hydrolase 1 1 1
MIRT578869 Fam151b family with sequence similarity 151, member B 1 1
MIRT579021 Ctxn3 cortexin 3 1 1
MIRT579051 Crp C-reactive protein, pentraxin-related 1 1
MIRT579404 Akna AT-hook transcription factor 1 1
MIRT579629 Mettl20 electron transfer flavoprotein beta subunit lysine methyltransferase 1 1
MIRT579672 1200011I18Rik GPALPP motifs containing 1 1 1
MIRT579704 Zmynd8 zinc finger, MYND-type containing 8 1 1
MIRT579747 Zfp644 zinc finger protein 644 1 1
MIRT579787 Zfp384 zinc finger protein 384 1 1
MIRT579806 Zfp148 zinc finger protein 148 1 1
MIRT579835 Zfand5 zinc finger, AN1-type domain 5 1 1
MIRT579837 Zer1 zyg-11 related, cell cycle regulator 1 1
MIRT579859 Zc3hav1l zinc finger CCCH-type, antiviral 1-like 1 1
MIRT579994 Wnt3 wingless-type MMTV integration site family, member 3 1 1
MIRT580000 Wnt11 wingless-type MMTV integration site family, member 11 1 1
MIRT580022 Whsc1l1 nuclear receptor binding SET domain protein 3 1 1
MIRT580091 Usp6nl USP6 N-terminal like 1 1
MIRT580213 Ttc39b tetratricopeptide repeat domain 39B 1 1
MIRT580238 Trps1 transcriptional repressor GATA binding 1 1 1
MIRT580242 Trpc7 transient receptor potential cation channel, subfamily C, member 7 1 1
MIRT580413 Tmem161b transmembrane protein 161B 1 1
MIRT580507 Tfam transcription factor A, mitochondrial 1 1
MIRT580532 Tead3 TEA domain family member 3 1 1
MIRT580553 Tcf7l2 transcription factor 7 like 2, T cell specific, HMG box 1 1
MIRT580566 Tbx4 T-box 4 1 1
MIRT580614 Syp synaptophysin 1 1
MIRT580667 Strbp spermatid perinuclear RNA binding protein 1 1
MIRT580795 Snx27 sorting nexin family member 27 1 1
MIRT580821 Smurf2 SMAD specific E3 ubiquitin protein ligase 2 1 1
MIRT580866 Slc8a1 solute carrier family 8 (sodium/calcium exchanger), member 1 1 1
MIRT580881 Slc7a11 solute carrier family 7 (cationic amino acid transporter, y+ system), member 11 1 1
MIRT580921 Slc35a1 solute carrier family 35 (CMP-sialic acid transporter), member 1 1 1
MIRT581143 Senp3 SUMO/sentrin specific peptidase 3 1 1
MIRT581246 Rufy2 RUN and FYVE domain-containing 2 1 1
MIRT581262 Rragb Ras-related GTP binding B 1 1
MIRT581294 Rnf166 ring finger protein 166 1 1
MIRT581353 Ret ret proto-oncogene 1 1
MIRT581391 Rbms3 RNA binding motif, single stranded interacting protein 1 1
MIRT581423 Rasal2 RAS protein activator like 2 1 1
MIRT581454 Ranbp10 RAN binding protein 10 1 1
MIRT581540 Pten phosphatase and tensin homolog 1 1
MIRT581574 Prrx1 paired related homeobox 1 1 1
MIRT581588 Lzts3 leucine zipper, putative tumor suppressor family member 3 1 1
MIRT581664 Ppp4r2 protein phosphatase 4, regulatory subunit 2 1 1
MIRT581739 Plxnc1 plexin C1 1 1
MIRT581792 Plaur plasminogen activator, urokinase receptor 1 1
MIRT581821 Pkib protein kinase inhibitor beta, cAMP dependent, testis specific 1 1
MIRT581895 Phf17 jade family PHD finger 1 1 1
MIRT581983 Pcsk5 proprotein convertase subtilisin/kexin type 5 1 1
MIRT582001 Pcdh20 protocadherin 20 1 1
MIRT582053 Osbp oxysterol binding protein 1 1
MIRT582101 Nupl2 nucleoporin like 2 1 1
MIRT582147 Nol7 nucleolar protein 7 1 1
MIRT582158 Nln neurolysin (metallopeptidase M3 family) 1 1
MIRT582255 Nckap5l NCK-associated protein 5-like 1 1
MIRT582371 Map1a microtubule-associated protein 1 A 1 1
MIRT582409 Mpped2 metallophosphoesterase domain containing 2 1 1
MIRT582441 Mgea5 meningioma expressed antigen 5 (hyaluronidase) 1 1
MIRT582585 Lrrtm2 leucine rich repeat transmembrane neuronal 2 1 1
MIRT582669 Lin54 lin-54 homolog (C. elegans) 1 1
MIRT582720 Larp1 La ribonucleoprotein domain family, member 1 1 1
MIRT582726 L3mbtl4 l(3)mbt-like 4 (Drosophila) 1 2
MIRT582762 Klf12 Kruppel-like factor 12 1 1
MIRT582856 Ism1 isthmin 1, angiogenesis inhibitor 1 1
MIRT582942 Ikzf5 IKAROS family zinc finger 5 1 1
MIRT583000 Id2 inhibitor of DNA binding 2 1 1
MIRT583059 Hoxa11 homeobox A11 1 1
MIRT583102 Hiat1 major facilitator superfamily domain containing 14A 1 1
MIRT583107 Hexim1 hexamethylene bis-acetamide inducible 1 1 1
MIRT583134 Has2 hyaluronan synthase 2 1 1
MIRT583188 Grhl3 grainyhead-like 3 (Drosophila) 1 1
MIRT583230 Gpc6 glypican 6 1 1
MIRT583393 Fzd5 frizzled class receptor 5 1 1
MIRT583412 Fzd1 frizzled class receptor 1 1 1
MIRT583426 Fsd1l fibronectin type III and SPRY domain containing 1-like 1 1
MIRT583526 Fgf16 fibroblast growth factor 16 1 1
MIRT583545 Fbxl20 F-box and leucine-rich repeat protein 20 1 1
MIRT583612 Fam46a family with sequence similarity 46, member A 1 1
MIRT583737 Erc1 ELKS/RAB6-interacting/CAST family member 1 1 3
MIRT583769 Ep300 E1A binding protein p300 1 1
MIRT583795 Elavl4 ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D) 1 1
MIRT583816 Eif2s1 eukaryotic translation initiation factor 2, subunit 1 alpha 1 1
MIRT583954 Dlx3 distal-less homeobox 3 1 1
MIRT584137 Crebzf CREB/ATF bZIP transcription factor 1 1
MIRT584209 Cops7b COP9 signalosome subunit 7B 1 1
MIRT584434 Ccdc90b coiled-coil domain containing 90B 1 1
MIRT584452 Cbx3 chromobox 3 1 1
MIRT584465 Casc4 cancer susceptibility candidate 4 1 1
MIRT584507 Calm1 calmodulin 1 1 1
MIRT584733 Atp2b2 ATPase, Ca++ transporting, plasma membrane 2 1 1
MIRT584808 Arl15 ADP-ribosylation factor-like 15 1 1
MIRT584848 Arhgap11a Rho GTPase activating protein 11A 1 1
MIRT584999 Ndnf neuron-derived neurotrophic factor 1 1
MIRT585043 Lrrc71 leucine rich repeat containing 71 1 1
MIRT585731 Synpr synaptoporin 1 1
MIRT585763 Sri sorcin 1 1
MIRT586098 Reep5 receptor accessory protein 5 1 1
MIRT586122 Rccd1 RCC1 domain containing 1 1 1
MIRT587443 Dimt1 DIM1 dimethyladenosine transferase 1-like (S. cerevisiae) 1 1
MIRT587532 Cxxc5 CXXC finger 5 1 1
MIRT588361 Zfp518b zinc finger protein 518B 1 1
MIRT588471 Wwtr1 WW domain containing transcription regulator 1 1 1
MIRT588621 Trak2 trafficking protein, kinesin binding 2 1 1
MIRT588694 Tet2 tet methylcytosine dioxygenase 2 1 1
MIRT588845 Sort1 sortilin 1 1 1
MIRT588975 Runx1t1 runt-related transcription factor 1; translocated to, 1 (cyclin D-related) 1 1
MIRT589265 Plau plasminogen activator, urokinase 1 1
MIRT589380 Ntrk3 neurotrophic tyrosine kinase, receptor, type 3 1 1
MIRT589448 Nck2 non-catalytic region of tyrosine kinase adaptor protein 2 1 1
MIRT589537 Mllt3 myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3 1 1
MIRT590501 Cacnb2 calcium channel, voltage-dependent, beta 2 subunit 1 1
MIRT590675 Anln anillin, actin binding protein 1 3
MIRT590760 Acbd5 acyl-Coenzyme A binding domain containing 5 1 1
MIRT590793 4921524J17Rik RIKEN cDNA 4921524J17 gene 1 1
MIRT593049 Nf2 neurofibromin 2 1 1
MIRT594247 Sox11 SRY (sex determining region Y)-box 11 1 1
MIRT594397 Ints6 integrator complex subunit 6 1 1
MIRT594713 Zwint ZW10 interactor 1 1
MIRT594773 Tex12 testis expressed gene 12 1 1
MIRT594789 Slitrk2 SLIT and NTRK-like family, member 2 1 1
MIRT595121 Mex3b mex3 RNA binding family member B 1 1
MIRT595540 Etv3 ets variant 3 1 1
MIRT595680 Rnf6 ring finger protein (C3H2C3 type) 6 1 1
MIRT595834 Tmem56 transmembrane protein 56 1 1
MIRT595895 Cd69 CD69 antigen 1 1
MIRT595961 Znrf1 zinc and ring finger 1 1 1
MIRT595980 Ocrl OCRL, inositol polyphosphate-5-phosphatase 1 1
MIRT596011 Ceacam1 carcinoembryonic antigen-related cell adhesion molecule 1 1 1
MIRT596189 Lrig2 leucine-rich repeats and immunoglobulin-like domains 2 1 1
MIRT603672 Olr1 oxidized low density lipoprotein (lectin-like) receptor 1 1 1

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