miRTarBase - #MIRT600385


—
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 Slc35e2   
Synonyms A530082C11Rik, AI957035
Description solute carrier family 35, member E2
Transcript NM_177186   
Expression
Putative miRNA Targets on Slc35e2
3'UTR of Slc35e2
(miRNA target sites are highlighted)		 
>Slc35e2|NM_177186|3'UTR
   1 TCACCTGATGCTGTGTAGATCCAGGCCTAGATGTTCCTTCTGTACTAGAGGGAAATGATGCAGGGCAGGTCTCTCGCTCC
  81 TTCCTGGAAATCAGATGGGGAATTTGGGACTCAGCTTCTGCCTGGCAGAGCACCACAGGACCAAATGATCTACAGCTTCC
 161 CTGGCTGCAAGTGAACCAGTGTCTCCGTGCCCAGCCTGCACTGTGGAATAAGCACAGGCTCCAGGATCAACCCGAGTTGC
 241 TGTCTGTTTGATGCCATCCAGGAGACCTAAACTTTTCTATCACCACCACCACCACCACCACCACCACCATGGAAGCCTCT
 321 TGGTTCTTGACAGTCTATGAAACAGACATTCCAGATGCCAATGACTCTAGCATGGAGCCATAAAACCCAGAGTAGCAGGC
 401 AGAAGAGACAAGTTTCTCCTGCCACGGAGAGACAGTGCTGTGTGAAGGAGAAGTGTCTCCTCCTTGGCCTGTGCTACATT
 481 GAACTACCCTGCTCCAGGGTTGTTGTCCCATGTTTCTGCTACCATTTTGTGATTGCCCATTCTGGGAAGTTGGCAGCAAA
 561 TCTCTAATTCAAGCAGATGGTCTGGAGTGCTTTTCCATTTTAAGTATGTGAATGTGAAGCGGGCGATTCTGAATGGCACA
 641 GTGGCTGCCCTATGAAGATTTCCCTTCAGGATGCTTGATAGGGACGTTCTGACGAGCATTTGAGTGTTTATAGGCTATGC
 721 TGTAGTTAAAGGGACACTTCTTTTTGATGTAGCAGGTGCCTGTCGAGGTTTCTCTGTGTCTCCATGTAAGGTACATCAAA
 801 GTGTACATGCACAACTAACTCTTCACCAGGGATCATATGATGACTGCCTGAGCCACCAGGTCTCCAGAGCTTAAGGTGGA
 881 GTGGAGGACAACAGTGGGCCTTGGGTTAACACGCTGAGGTTCTACATTATTCGGCATTTTGTGAGTTGTGTGTGGGGTGC
 961 AGTCTGTTGCTAGCCAGTCTCTAAGACTCCATTACTTACAAGCTGCAGCCACTGGCACTCCTTGTCCAGGTCTCACTGGT
1041 CCTCCCTGCTCTAAGTCTTTCGTGCACATGGTGGTTCAAAAAGATAATGGGGTGAAAAAGAGCAATAATTATGTCTACAT
1121 TTTATTTACTTGAAAAAGCCATCTGCCATGATGATGGATCAAAATGAGGCCTTTTAATCCATAAGCCAACTTTTAAAAGA
1201 AGCTGATGTGTGCTGGACATCAGCTAGGTGTATCTTTACTATGCTATGTAAAGATATTGTGAAGATGTTCTCTCATTTGA
1281 CTTTGCCCAGGTTTCTAGTTCCTTCCTCTTTGCTCTTCTCAAAATAAAGATCCAGTGGAGGACAGATGGCAGACGTTGGA
1361 TTAATCTGTGTAGACCTGTCTGCTCAAGATCTGGCTGTGGAGCTGCTGACACCGAAGAGCACGTGCTTGTGGGTATTGGT
1441 TGGCAGAGCTCTTCTGGCCTTCCCGCAGACCTGTCTAAGTATGCTCAGAGCTCTACATGCCTGGCTTCTTACTATTATTT
1521 GGAATTTCTGCCTGTGTCCTATGTTTAATTAGGAAATGACCTATTGTGACTTGCTCTGGCCATCCCTCCCCCATGTCACA
1601 AGACTCAGCTTGTTTTGATTTTCTTAAGGTTTGGGCTAGAAACAAAAACAAAGATTTTTCTTAAAGCAATTTTCTCTAAA
1681 GCTGCTTTGAGACTTTTCCTCATAGGTGGAAAGATCATGGAATCAGCTGCTTCCTTCAGGTCTTCCAGGACAGGGCTGGG
1761 TTGAGAATCGTGGAACGGCCCTGCTTGACCATTTGTTATGACTATACCATAACAATACATTTTTAATTGACTTTGTTAGT
1841 ACTTTCATAGAATACTATGTTCTTCATGAATTGTTACTGATGTAAATGTACAAATATTGACACCACGTGTCATTCCTTGT
1921 CCTGGATAATTCCTCCTGAGTTTATGTCATTGTCTGGTCTGTTGTAAACAGAACACTGGATTGACCTTCTGAGCCAGCTA
2001 GCTGCTTACTCACTGCACGCATAGTTAAAAGATATACACATTTCTAATTTCAAAAATAGTTCTAGGAGCTACAGAGATGG
2081 CCGAGTGGTTATGTTTCTTGCTGAGGACCCAAGTTCAGTTCCCAGAACTCATGTAGAGTGTTTCACCAACTTCCTATAAC
2161 TTCAGCATTAGGGATTCTAATGCCTCTGGCTTCTCTGGGCATCTGCACACTGGCTTGTGTATGAACACACACACATATAC
2241 ACACACACATATATCTTAAAAATAAGTACATTTGCTAGGGGAGGTGGTGCAAGCCTTTAATCCCAGCACTTGGGAATCAG
2321 AGGCATGTGGATCTCTGAGTTTGAGGGCAGTCTGGACTACAGAACAAGTTCCAGGACAGCCAGGGCAACACAGAGAAAAG
2401 CCTGTCTTGAAAAACCAGATAAATAGATAAATAAAATTTAAAAACGTCCATGATTTGGGGTATACCTTAGTGGCACATCA
2481 CTGGCATGTATTGTGAAGCTCTTGGGTTGATCACCAGCAGCAGATGTGGGACAGAAAGATAAAGGGGAGACAACAAAAAT
2561 AACCCCAAAACTTCTAATACTAAAAGACAAGGAAACGTTTTTGTTTTTTGGGTTTTTTTGTTTTTTTTTTGTTTGGTTGG
2641 TTTTTTTTTTTTTTTTTTGGTTTTTCAAGACAGGGTTTCTCTGTATAGTCCTGGCTGTCCTGGAACTCACTTTGTAGACC
2721 AGGCTGGCCTCGAACTCAGAAATCCGCCTGTCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGCGCCACCACTGCCCGG
2801 CCGGAAAGTATTTTTTTAATTCATTGTTTTGCCTGCATGTGTGTCTTTATGAGGGTGTTGGATCCCCTGAAATTGGAGTT
2881 ACAGATAATTATGAGCTGCCATGTTGCTCCTGGGAATTGAATTCGGGTCGTCTTGAAGATCAGCCATCTTACCAGCTCCT
2961 GTTTTGTTTGTTTTTAAACCCGATCATGATGGCACATACATATAATCTTAGTAATTTGGAAGCATAAGAGTGCATAGTGG
3041 TTCAAGGCCAGCTTGGGCTACATATTGAGACCAAGTTTCAAAAAAATGTTTATGATCACAATTTCTCAAATATTAGGATT
3121 ATCATCTGTCTTCAGATGGTGGTTCACACTTTTAATCCCAGCACTTAGGAGGCAGAGGCAGGTGATTCTCTGTGAGTTTG
3201 AGGCTAGACTGGTCTACAAAGCCAAATCCAGGACCCCCAGGGCTCTGTTACACAGAAAAACCTTGTCTCAAGAAAAGTAA
3281 AAATGATGAGTCAGAGGAGATTAAAGAGAATTAAAGCTGTTCAAGGGATTCGGCCAAGTAAACTTTACTTTGTGCCTTAA
3361 AAACAGCACAAAACAAGTGGCTTTGTGATCCTGCTCTCAGATGATCACTTTGCTCAGTGATAATAACAGATGCTCAGCAC
3441 AGCCTCCTGTCACATCTGTCCAAGTGATGTCTTCTTTTTTTTTTTGTTGTTTTTTTTTGTTTTTTTTTTTTGTTTTTGGA
3521 GACAGGGTTTCTCTGTGTAGCCATGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCACC
3601 TGCCTCTGTCTCCCGAGTGCTAGGATTAAAGGCGTGCGCCACCACCGCCCAGCAAGTGATGTCTTCTTAACATTGGAAAG
3681 GGGTAAAGAAAGATGTTAGTACAGATGGGAAACAATGCCGGCTCCTCCTGAGATTGCATTTACCTATGTAACCCATAGTG
3761 TCCTTGAACTCTAGATTCTTCTAAGTCATCGTTCTCAGGACTGAGATTACAAGTACGTGTCACCACTTCTGACTCCTGCC
3841 TTTGAACATCAATCTTTTGTTTTTTCTTAACACGTAAATATTGATCTCCCTGTGAGGCGGCCTCTTCATCTCTTCATTCT
3921 CCCACCCTTCGTTTATTATGCTAGGCATAGTACTCAGGGCTTCAGGAATGCTAGGCTGCTATTCTTTCTCTGAGACATGG
4001 CCTCCAGCCTGTTTTTCTTAGTTTATCAATGCCTTTGCTCTCCCCATGAATTAGAACAGGACATGCTGATTGTGGACAAA
4081 TAGTATCCACCACAATTAGAGTGTAGTAGGTTTTAACTTCAGTGTCTCTGAAGTACGTTTTCCTGGGTACTCTGATCCTG
4161 ACTTTGCCAGCTGCTGGACCCTTCCTAATATGTCCAAGTTTAGTTTGAATTAAATCAAGTTGGCTAGTTGTGTGTTTGTG
4241 GGGTTTTTGTTTGTTTTTACTTTTCATTTCTGGGACTCAAGCTGCATACTAAATTCATTTGTAATGTCTGGACTTAATAA
4321 TAATGTAATTGTGAGTATGTTCGTTCAATGTTCGTTCAATGTTGGCACTTTGGAAAAGGCCACAGTTTAGGGTGGACAAT
4401 TGTCTGCATCAAAGCCAAGTCATATTTGCTTTATACCAAACAATACTAGAGAATTAAAACACATCATAAAATGTACACTG
4481 TTTTGTATTTCACCTCTTTCAGTATTTAAATAATTATATTAATGCCTCCTAGAAAAGAATTCTGTTAGATAATTCAGTGA
4561 TTCCTGAAATAAATTGGTATTGTGTAATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
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' ggUCG-AU-CGUUACGUGACGGa 5'
            :|| |: || |  ||||||| 
Target 5' aaGGCGTGCGCCA-CCACTGCCc 3'
 2777 - 2798 142.00 -14.90
2 
miRNA  3' ggUCGAUCG-----UUACGUGACGga 5'
            |||||||     | | ||||||  
Target 5' ccAGCTAGCTGCTTACT-CACTGCac 3'
 1994 - 2018 138.00 -21.70
3 
miRNA  3' ggUCGA-UCGUUACGU-GACGGa 5'
            | || || ||| || ||||| 
Target 5' cgAACTCAGAAATCCACCTGCCt 3'
 3583 - 3605 131.00 -12.40
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 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

Error report submission