miRTarBase - #MIRT597335


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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 Sema4b   
Synonyms SemC, Semac, mKIAA1745
Description sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B
Transcript NM_013659   
Expression
Putative miRNA Targets on Sema4b
3'UTR of Sema4b
(miRNA target sites are highlighted)		 
>Sema4b|NM_013659|3'UTR
   1 GAGCTGACTTTAGATGTGGTCACCCTGACCTCAGGGGTTGTGAGTGTTCAGTGGAGGTCAGCTACCTCTGCTTCTCACAG
  81 AACACAGCCACGGTACCCTGACTGGAGGGCAGCTGGTACCACAGGCCCAACAGCCCAGCCAGCTGCTTCCAGTGTCTGGC
 161 CGAGAACTGGGCTGCCTCCAGGGGCCAGAGGGTCCTTGTCTGGGTGGCAGAACTCTGCTACTTAACTGAGCCCTTTGTTT
 241 AAAACTGCAAATGTGAAGCCAGAGAGGAAGGAGAAACAGACAAGGAAGACTACAACATAGCCACTCCAGTTCAGCCTGCT
 321 GGGCTCTTGGGGACTTCTCCAAAGTGGCTTTGTGAGCAAGCCGAAGTTGAGAATCCCTCCCCGACTGGACTATTCTACCT
 401 TCCGCCTTACTCTGCTGCTGAGGCTACCCTTTCTCACTGCAGAATCAGGGCCCTGCTCCAGCTTCAGCCAACCGAGGACA
 481 TATCTGTGACCGCTGACACCCTACCACCTCAGGGACCAGAGGGCTAGGCTGATTCTGCAGCCCTCCTCACCAGACCCTGG
 561 GCTCAGTCCCAGTTCCCGGACTTCTCCAGCCTGTATCAGGCTGTGGCCTCAAAAGCAAGGGAGTGACCCCCAAGGGGGGT
 641 TGTGACAGAAGACTTGCCTACTGTCCTTTTCCCAGTCAGAGAACTATGTCCCTACCCATCGACGTCTTTTTTTTTTTTTT
 721 TTTTTTTTTTTTTTGGTTTTTCGAGACAGGCTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCAGGC
 801 TGGTCTCGAACTTAGAAATCCGCCTGACTGCCTCCCAAGTGCTGGGATTAAAGGCGTGTGCCACCACTGCCCGGCCCCAC
 881 CCATCTTCTAATTCCTACACAGACTCCTGGATCCTCGTTCCTTGTCCTAGCTCACCGTGCCCGTCACTCTAAGGGATGCT
 961 GACACTGCCCATCACAAGGACCCTGAATTTACATGGGTTTTATATTTTTTTTTAATAAGATGCACTTTACTTTCTTTTTT
1041 AAATAAAATCCGACAAATTATAGTTATTTGTGGCCCACATTCCTGAAGGGCTTTGCTTTGTGTGTATGTGATATGAATAT
1121 ATGTATATGCGGAGACCAGAGGCTCTCCTTTGCTTTGTGTGTATGTGATAGGAATATATGTATATGCGG
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' ggucGA-UCGUUAC----GUGACGGa 5'
              || || :|||    ||||||| 
Target 5' cactCTAAGGGATGCTGACACTGCCc 3'
 945 - 970 151.00 -14.80
2 
miRNA  3' ggUCG-AU-CGUUACGUGACGGa 5'
            :|| |: || |  ||||||| 
Target 5' aaGGCGTGTGCCA-CCACTGCCc 3'
 851 - 872 142.00 -14.70
3 
miRNA  3' ggUCGAUCGUUA--CGUGACGga 5'
            :|||| |  |   ||||||  
Target 5' gaGGCTACCCTTTCTCACTGCag 3'
 420 - 442 129.00 -10.50
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 GSM622571. RNA binding protein: AGO2. Condition:WT1B HITS-CLIP data was present in GSM622572. RNA binding protein: AGO2. Condition:WT2 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.

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]
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

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