miRTarBase - #MIRT581641


—
pre-miRNA Information
pre-miRNA mmu-mir-449c   
Genomic Coordinates chr13: 113035983 - 113036091
Description Mus musculus miR-449c stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-449c-5p
Sequence 26| AGGCAGUGCAUUGCUAGCUGG |46
Evidence Experimental
Experiments MPSS
Putative Targets

Gene Information
Gene Symbol Prex2   
Synonyms 6230420N16Rik, AI316880, AI553603, C030045D06Rik, D430013K02, Depdc2, P-Rex2
Description phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2
Transcript NM_001033636   
Other Transcripts NM_029525   
Expression
Putative miRNA Targets on Prex2
3'UTR of Prex2
(miRNA target sites are highlighted)		 
>Prex2|NM_001033636|3'UTR
   1 GCATTCCACGTGCCATGGGACAGATGCTTCCAGATGCTGCCCAAATTAACATTCTCCACCGAAGACAAAGAGATGCAAAT
  81 TAAAGATTTAAAGTTTTCCCATGATGTAAATAACTGATGTTTGGTTTGGACATTTATGCTGGAACTAGAAGTTCCTTCAG
 161 ACAGTTCAGCCTTACACTCTATACATTAAGAATACAGATTCACATTAGGGCAAAATTCACTTCTCGTATTTGTAGAAAAA
 241 TATACAGAGATAAAAGATTAACTATTTTGGTTCCTTTCTCATTCATTAATTATATTGTATTTGTGTTTAGCTTCCCCAAT
 321 GGACAGATATTATACTTGATAGTTTTTCTTGAAGAAGTCTGTCCTAAAAATGATGACCACACTCTGGAAACAATCATACA
 401 GAAACGTTAAGGACAGTGTAGATGAGGAGTTACAGGTGTCCCATATACCACTTGAGTCACCAAGAAAGGCGCATATGAGA
 481 GGTAGGGAAGTACCTGCCTCCCTTTCTTCTTGGGCTTCCTGGTAACAAAGAGAGCTCAGAGGTTCTGGCAAGACTTTTTC
 561 CCTTTTGTTATGTCTAGTCTCTGGTCTTGTAAACACTCCAGTAGGCAGGTGCTTTTCTTGATCTTTCCAATGAGCCATGA
 641 GTGCTGCGTGATGGACCACTGATGGCGGTGGGTAGGAAGTTGCTAGGTTGGAGAGAGAGGAGTGAATGAGGATGGAAAAT
 721 AATACATGTATTGACCACTCACCCCTTGCCAGAGAAAGATAAATTCTTAATTATATGAAGTCTTACTATGAAATGTCAGA
 801 CTGTTAAAATAACACACCTTCCTGAGAATTTTTCTATCAAGTTATATGTGTAAGATATGAAAATAGATTTATTTGTTGTA
 881 CTTCAAAAGGTCATTAGAGAAAAACTTTGATAATTTATGGAACCAAGGTATAGACTGTATTCATTCTAAAGTATATGCAA
 961 TATTTATCACTTCTGTGTTAATATACTAAAATTATTTTAGCACATAAATATATTAATATTGGTTTTAAATATATATCTTT
1041 ACAAATAATTAAAACAGCATCACTGTGATTATGATAGTTGTGCTTTGTTTAATGACAGGAATAAATTGTGCCTTTAGGTG
1121 ATATTATCATCGTATAAATGTCATGGGGTGTACTTACACAAGCTGAGATGACTGTGGCCTCAGACACTATGACCTATGGA
1201 ACCACTTCCTATAGGCTGTGCATCACTGGCCCAAAGACCTCTAACAGCACAGAACTGTGTGTGGATATGGGCTAAGCACA
1281 TGAATTCCTTACTTTAACTACAGGTTTGGCAAACCATTATTCAGCTTTACTTTATAAATCTCATAATGAATTTCAGACTA
1361 TCATTAAAAGCTATCATTACTGCCAGTGATATATTGAATTTAAAAGTGTGCTTCAAAGGTATGGGATACATATATCCTAC
1441 AAGTTAAGAGTGAAAATTATTCATCACAGAGTACATAAGATTTTTCAGTAAATCTATTTGTGACTAATCATAGAGAAACC
1521 AACATTAGTTTCTAAAAAAAAGCCTTAGCATTTTGAATTTAATAAAGATATGACCTACGTTTGCATATATGTGACATACA
1601 TCCATAACTTTCAGGATTAATATTTTTGCTATCATCAGCATATAAGTGTGAAGCTCTGGTAGTTCAGGCTGCCTTCTCTG
1681 AAAGTCTTGAGCGTAAGGAGAGCTGATTGCCCGACTAGGCAGACCCTTCACACTGCTTTACTCTTCTGTGTTCACCAGCC
1761 TCACTAAGTCTCCATAGAGGAACAGAAGGGCTACGAAGCAAGCTTATTTTATTTTTTCTCATTAAACTTGTTTTAATGGT
1841 CTCAAAATTCTGTGACAGATTTTTGGTCAAGTTGTTTCCATTAAAAAAATACTGATTTTGAAAACTAATAACTTAAAACT
1921 GCCATACACACACACACACACACACACACACACACACACACACACACACACACACACAAATGGTCCACAAAACATTCTTT
2001 CCTTCTGAAGGTTTTATGATTATATTGCCTGGGCATATTATCTGCTTTTTCAGTATTTATAAATTAGTGTATTTTAAGGA
2081 TCCAGTCTATATAACAGAATGTGGTTAATGTTATCATTTTTGTTAAACATATTATTTGTGTACACAGCACTTACAAACTA
2161 TAAAGCTTGCTAGTGTTTTATAGTAACGTCTATCACTGTCATATTTTTTCATAGTAAAATCATAGCTGACATGGTTTAGT
2241 GTATTCTAAATGGCACCTTTAATTACCTAGCCCACGTTTTGATATTCCTCCTTCACATAGCCTTGTAGCAGGGATGAAAG
2321 CTGACCTTGTCTTATTACCTGTACTTCACAGTTCTGCTAAGCAAATACTAACCCAGTGACTTGCACAAGTCCACTTGATG
2401 AACATGGGGGAGTCCGAAGTTAATGGTTAAAACCTGTCTTAAGGATTGCACTGCCTTTATCTGTTGTATGAGTACCATTA
2481 TAATATTAATAATTATTTTCTGACTAAAGTTGGAGTTTTATGACATGTATTGTCATTTAATTTATATGGAAGATGTTGCA
2561 AAGTCCAGTGGGAATATGCAGAATGCCTTTAAAGTGCAAGAACTATTTTCTTGGCATTTTCCATTCATAACTGAAGAGGA
2641 TCCACATGTATTGCAAGCCAGGAGTAGGACATTATATAAAATTTGACTATAATTTTAAAAGTGTTAACACTTAAAAACCT
2721 TTGATAGATGAGTAATCATTTTCAATACCATAATATACACATTCTTTTGACATTGGAATTTTACAGGCCTTGGGAGTTTA
2801 GAACTTTAATGTTGCACTATCCTCTGCAACTGGGGATTATTGATAAGCTAAGGAAAACACTGCTTACTGTTCTTACAACT
2881 TCTATATGTGGACATAGATTCCTGTCTACCCATTGAGAGATTTCAGATCTTATGGGGACAGAATCATATTTACTATCTTA
2961 CAGATTTTCTCATTCGTTTTAAACATTACAAATTTAATTTTGTAAAAATATGAGAATTTAAGGGCTGAAAATATGAGAGA
3041 AAGACAGACAGAGGATGACAATTTCTGGTCCAGGTTTACTTGGCAGAATATGTAAATGCTGGGTTTCTACTGCATGCTCT
3121 CTCCTGGAAACCAGAATCCTCATCTTTAGGAGCATGCTACTTTCTTTCCTTTTAACAGAAGTTTTCTGATGTCTTCAATC
3201 CCCTGTGTATTCATTTGGCTCCTCTTCTTGCTACAAGATGTTCAATTAAACAGGAAGGTAGAGCTGGGAATGTGGCACAG
3281 TGGTTGAGTGCTTGCCTAGCACATGTGAAGCCATGTTAAAATATATTGGCTCTCCTTTAAACCAATGGTGGCTCACACCT
3361 GTAATCCCAGTACTTGGAGAGTCAGTAGGATTTTCAGGAGTTCAAGGGAAGCTTGAGATAAATATGAATGTGAGGCCAGT
3441 CTAAACTACAGTGGGAGACATGGCCCATGAAGGAAACAAAGATACTACAGTGTGTGTTACATGGGGTTGGTGCTATTTCT
3521 GGCTCTATTAATTTTAACTTTGAATAGCTCAATTCAGAAAGAAATGAAGTTGATCCTATGTTAACTTTAATGGTGAAGAA
3601 AATCAATGAGAAAGAAATTCAAGAGGAAGTATTAGCTAACTTAAGCAAAAAATATCCTGCAGTAAGCACATAGATTTTAT
3681 AGGCAAGGTTATTTAAAGCAAATAAGTTTCTATCTCAAGCTATCAAGTATTCTTACACAGTCCAAGCATCTGTAGTCATC
3761 ACATCTAAGCAGGTGTTTTCTCAGGCATTTGGATTTCTATAGAATCATAGTATTAAAATTTCAAAGTAATAACATTGCTT
3841 TTTAAGTTATTTGTCCTTTTAAAAAAATTTTGAAAGTAATTCTGGAAATATACCCTACTGGTATTCCAGTCAAACTACTA
3921 AAGCTTTGTATCTGACTGAACTGCTTCTAAATTTTAGGAACTTTCTTTTTTAAAGTCTGTTTTTATGTGAGTGTTCCTGT
4001 GAAACTGAGGTCTGATGACTCTTCCTTAAGCAATTACAACTTCATTAGCATACATAAGGTTCAATTAAATAAGAAACACT
4081 GTATATTTGTGTGTTTAAAGTCTTATAGGAGAGCCTCAGGAAAATCTTTATTCTGAAGAACTAGCAGGGTAAATGTAAGA
4161 GGCACCATTGCAAGAATGGCCTCAGCATAGTAGTTTTACAAAATGGCCACCATTTTACTAGGTGCTGCAATTCCATGTTG
4241 GTGATAGTGGTTAATACTTGGTTCCAGAATCATTGGATACTTTAATGATTTGCCATTGTCACTGTTGTTAACATTCCTGT
4321 TGCTGAGCACCCCTGGCATGTCTATTAAAGTACAGTTAGTCTGTGTGACTCTCAGTGGTGACCTAGTGAGAAATCTGACT
4401 CACTCAGAACAGTTTATTCTCTTAATGGGTTAGGTTCTGAAATCTGCTAAGTCTGCTAATGATATACAGATGTGAGTGTG
4481 TATGTGTGTGTATGTTCTCTTATAACATAAACCACTTTTTAGTTTTGTAAACATTAATAATAAACATTAGATTTTGGTTT
4561 CTTCATTGTATGGAAATATGAGACATGTATTTTATAGATGAACTATATGATGTCTGCTGTAAACAAAGGTGCTGCCTGTG
4641 TCATGGGTGGACTTGTTGGCTGTCCTTTGTTCACTGATGTTCATCTGTTATTTGTATGATCCAGTTTGGTTTCTGATTTG
4721 TCTTGTTTGTCATCACTGTGACAAATCATCTGAGATAATTAAGTTACAAAGACAAAAGGTTTATTTTGGCTCAAAGTGTT
4801 GGAGATTCTATTCCACAATCAACTGAAGTCTGTGGTTGGGCCTGTCATGAAGTAGCAAGTAGTGTCATGACAGAGGAAGA
4881 GAGCAGGACACAACTCCTTTGCTCATTAGCCACATCACAAAGTAAGAGACATTGGCCCCACAGTCTTTCAAAGGCAGCCT
4961 TCAACAGACACAGAACCACCCATTGGCCTCCATCTTTCAGATGCTTTACCACCTCCCAATAGCACTATTCTGGAGATCAA
5041 GCCCTTAATACAGGGACCTTTGGGAGACACACCAGGGTCCAAACTAAATCACTATCCAGTCAATCTCAAATCTGCTTTTC
5121 TGGTTTACCATTAAGAATTAGCTTACAGTGGACATAATTGCTGAATTTTTAAATGATTGTTACTAGAAATACTGGTAATA
5201 ACAGAAATAACAAAGATTGGGAAATTAATTTTAGGCACAGACAATGATAACTATTATCCATTCATATAATCAGCAAATGT
5281 TTTGAAATTCACTTAATAAGACTCAACCAGAATTGAGTATATTGGATAGATTTAAATAAAAAAGATTGTCATAGGGTCTC
5361 TGTATTCCTATATATACAAAGGTAACTTGTATCTTTTACTTAAAAATTATATTATTAACAAGGTAAATATATCCTAATAC
5441 TATGTGTTTATTATATACTATATAGTCAAGAATACTAAGTTGTAGAAATATTTAGAAAGCATACCTTTGAATTTAAGTAT
5521 CTAATGCCTCAAGCAAATCTGCTAGTTTCAGAAGAATATATATTTTTGTAACTGCAAGAATATGAGTAGATCATAGCTTT
5601 TGCTTAAAATATTTTTGTAAGCATTCATTTACACATACTCATTTTAATAGTAAAATATTAAACTGATTCTGTAAAAGAAC
5681 CTGTTTTGACTATGTCTATATTTAATATTATGTAATATCCAAAATTCAATAAATTTCATCTGAATGTATTATTAGCCTTT
5761 TTTTCCTTTGTAAAGTAGCCATGTTACATAGTTTCAATCATTCCATAGTTTGTGTATGGTTAAATTATCTAAAGTTCATT
5841 ATGTATTTTATGTCATTTGTTTTTCCCCACATAAAAGATTGTAAAAGATCTGATAAATGTCAATAATAATAAAGTGAATT
5921 ATAGAATGAAAA
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' ggucgaUCGUUACGUGACGGa 5'
                || | ||||||||| 
Target 5' gtcttaAGGATTGCACTGCCt 3'
 2436 - 2456 159.00 -18.10
2 
miRNA  3' ggUCGA-UCGUUACGUGACGGa 5'
            |||| || ||  ||||||: 
Target 5' taAGCTAAGGAAAACACTGCTt 3'
 2844 - 2865 147.00 -15.30
3 
miRNA  3' ggUCGAUCGUUACGUGACGGa 5'
            ||||| | || :|||||| 
Target 5' aaAGCTATC-AT-TACTGCCa 3'
 1367 - 1385 145.00 -15.00
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions Brain (Mouse neocortex)
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 Chi_BrainB_130_50. RNA binding protein: AGO. Condition:Brain B 2A8 P13 130 KD ...

- Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature.

Article - Chi SW; Zang JB; Mele A; Darnell RB
- Nature, 2009
MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
LinkOut: [PMID: 19536157]
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]
41 mmu-miR-449c-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT577806 Rnmtl1 mitochondrial rRNA methyltransferase 3 1 1
MIRT581641 Prex2 phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2 1 2
MIRT587396 Dnase2a deoxyribonuclease II alpha 1 1
MIRT588268 Smco1 single-pass membrane protein with coiled-coil domains 1 1 2
MIRT595436 9930013L23Rik cell migration inducing protein, hyaluronan binding 1 1
MIRT595972 Tbc1d2 TBC1 domain family, member 2 1 1
MIRT596032 Vps9d1 VPS9 domain containing 1 1 1
MIRT596042 Ubp1 upstream binding protein 1 1 1
MIRT596048 Shisa7 shisa family member 7 1 1
MIRT596070 Ywhag tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide 1 1
MIRT596093 St6galnac3 ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3 1 1
MIRT596128 Rgs17 regulator of G-protein signaling 17 1 1
MIRT596176 Med22 mediator complex subunit 22 1 1
MIRT596199 Fyco1 FYVE and coiled-coil domain containing 1 1 1
MIRT597335 Sema4b sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B 1 1
MIRT598319 Mbd4 methyl-CpG binding domain protein 4 1 1
MIRT599424 Cercam cerebral endothelial cell adhesion molecule 1 1
MIRT599598 Bloc1s3 biogenesis of lysosomal organelles complex-1, subunit 3 1 1
MIRT599659 B3galtl beta-3-glucosyltransferase 1 1
MIRT600185 Wipf2 WAS/WASL interacting protein family, member 2 1 1
MIRT600239 Trim36 tripartite motif-containing 36 1 1
MIRT600385 Slc35e2 solute carrier family 35, member E2 1 1
MIRT600677 Mapre1 microtubule-associated protein, RP/EB family, member 1 1 1
MIRT601685 Sco1 SCO1 cytochrome c oxidase assembly protein 1 1
MIRT601718 Rheb Ras homolog enriched in brain 1 1
MIRT601800 Rab11b RAB11B, member RAS oncogene family 1 1
MIRT601868 Pin1 protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1 1 1
MIRT602435 Epb4.2 erythrocyte membrane protein band 4.2 1 1
MIRT602459 Dusp11 dual specificity phosphatase 11 (RNA/RNP complex 1-interacting) 1 1
MIRT602620 Cenpl centromere protein L 1 1
MIRT602637 Cd93 CD93 antigen 1 1
MIRT602799 Ankrd28 ankyrin repeat domain 28 1 1
MIRT603072 Zfp446 zinc finger protein 446 1 1
MIRT603468 Trmt10a tRNA methyltransferase 10A 1 1
MIRT604685 Sgk3 serum/glucocorticoid regulated kinase 3 1 1
MIRT605120 Cnnm3 cyclin M3 1 1
MIRT605335 Zfp317 zinc finger protein 317 1 1
MIRT606441 Fam118a family with sequence similarity 118, member A 1 1
MIRT606475 Ctsa cathepsin A 1 1
MIRT606636 Phc3 polyhomeotic-like 3 (Drosophila) 1 1
MIRT736224 TUBB4B tubulin beta 4B class IVb 3 0

Error report submission