miRTarBase - #MIRT596048


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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 Shisa7   
Synonyms ckamp59
Description shisa family member 7
Transcript NM_172737   
Expression
Putative miRNA Targets on Shisa7
3'UTR of Shisa7
(miRNA target sites are highlighted)		 
>Shisa7|NM_172737|3'UTR
   1 GGCCCGGTGGAGTGCTGGGGGCTGTGGCTTCCGAGGCCCCCTTCTCCCAGCCCAGATCTCCATTACAAGGCTTATCATAC
  81 ACACCAAGGCTCTGAGACCAGATGGGCCCTTGGACCGGAGACCACGCCTCCTTTTGGGATGTTACAGTAGATGAGATCTC
 161 TCCTTTTACTTTGTCACTGTTTGAACCAAGGCCTCCCTCCCATGATGTCATCCCAGAGGAAGGAGGCCTGTATATGAGGT
 241 CATTGCTAGCAAATATGTCTGTGTTTTATGATGTTGTTTGCAGGGACTAAACCTCCTTCCTATGAGGTCACCACAGAGGA
 321 AGAGCCCTGCCTGAGGTCATCACTAGAGGCTATGTCCATTTTGCATGACATCACCACAGAAACTCCTTTCCTGTGATGTC
 401 ACTACGACAATGCCTTGTCCCATCCCATCATCCCTACAAACAAAAATTTCTTCCTGCGTGTCACTACAGAGACAAGTCTC
 481 ACACTTCTTGACACTTGTTGACATCATCCTGACTGAGCACCAAGGCCTCTTGCAATTATCATCACAGGAAAAATGTTTCT
 561 CTGCCATGGAGAAGATAGCTCCATTCCATGATGCCACCACTACAGACAAAGCCATTTTCCTGGGACACATCGCAGTGGAC
 641 TACGCCCTGCCAGTTATGTCCTCACTAACAATTAGGCCTCCTTTCCACAATACTATCACAGGACTTTGCCTCCCTCCTGT
 721 GATGCCATCACCAGAATAGGTGCCTTGCCCAATGGCGCCATCACAGGGACTGTGCCTCTTCATGTGATGTCATTACCAGA
 801 AATGACCACCTGTTCTTGGGACTTCTCCAGAGTGAGGCCCTTCTGTGGTGTGACCACCAGTTACCACCCACTTGGAAATG
 881 ACACCAGGAGACACCTCTATCGCTGTGCCATGTCGTGAGAAAGTTGGGCATGTGTAGCCCAAGGCCACCTGGGAAGAGGC
 961 CAGAGAAAGTAACCTGTCCTGAGATGTCATGAGGGCGTCAGCACTAGGGATACTAGGGTCTTTCTATAGGATGCTGGGGG
1041 TGATGCCCTCTATTGCTTGGACATCATCATAGAGTGCTTCCTTCTCAGAGGTGTTCCCCACTCTAGATGACCAACAGTAG
1121 TGACTGCATAATGATTGTGTCATCAGAGTCCTTAAGTCCCTATAGCTGAGCTCTGTGCTTCTTTCTTTGCGTGACCCCAG
1201 GGGCATAGCCAACAGGATGTCTACTAGCCCCAGTAAAGGCAGACTGGGCCTGTGCAGTGAGCCCTGGGGATGCAGTGAGC
1281 CCTGGGGACGGCACCCATGGATGAGCTTCAGCTCCACAGCCGCTCTGATCCACAGGGCTGCTAAAGTCCTGGGACTCAAG
1361 GGTGAGCCAAAGGATGGCATCACTTCTTTCTGCCATATCTAAAGACATCAGCTCTCAACACAGTCCCCATCTCTATTGGA
1441 GGGGAAGGGTTAGGGTATATGTGCTGTTGACCTTGCCAATGACATCATCAATGCCACCCAGTGTCCTCCTTTCATGATGG
1521 CATAGCAGTTGGGGTCCAATGTTAACTGTGTCATTTCCCAGAATTCCATGACTCACCTCAATTACCATATCAACTTCCAG
1601 GCATTATCACCATTAATGGCATCATCATTGCCTCCCAAGATCCCTCCCAACCATGGTGTCATCATTTCCCAGGGTCCAAA
1681 CAACACATCATCATGATGTCCCAGGATCCACTATGTCCTCATTGCTTCCCAGAATCCTTCACAACATGCTCACCTCATCA
1761 CCTCCCAGCATCCATCACAGCCAGGGGGTCTTCATCTCCCAGCAATCACAACCATACAGTCCTCACCATCTCCCAGATGG
1841 TGAGATCCATCAGAACCACACTGTCCTCATCTCTCAGGACTTGTTAGGACTGATAGAGCCAGAGTCTCTCGTGACTCCAT
1921 ATAATTGCAGTGTCACCTCCCAGGACCCACTTTAGCCATGTCTTCATGTCTCAGTAGCCATCATAGCTATGATGTCACCA
2001 CTTCATAAAATCCACTCCAACTGTGGTGTCCCTGGATTCTTGTGACCATGTATCATCACATCCCAGTATCCATCTAATAG
2081 TGTCACAAGTATCATATACAATGAGCATCTATGAGGACCATCATTCTGTCACCTCCCTAGACACATCAGTCATGTCCTAT
2161 CACGACTCATCAGGATTTACTGTAACTGTGGTGCCATCACCTCCAAGCAGCCATAATAGCCAACAGTGTCTTCATTCTCC
2241 AGGACCTACTTCAACCCCAGTGTCTCCATGGCTTAGGGTCTACCATAATCACAGTTGTCATCACCTCCCTGGACCCATGG
2321 CAACAATAATGTTATCATTTCCAGAGTGTACTTCAGCGATGGTGCCATCATCCTCTCCCAGAATCCATGTAAAACCGTGT
2401 GTCCTCATCTTCTAGGACCCGTGGCAATTGTGTGCCATCTACCAGGACCCATCATCTTAGGGTCCAAATGTTGTGACAGG
2481 CTATATTTCAGTTGTCCTCTGGGGTCTCATGGCATTTACAGTTCCTCCCTTTAGGGGAACCAGCACAACAGGCCATTTCC
2561 CATTCCCTCCAATGGACTAGGGTGGAGCCAGCTGCCTCCTCTGATAATGTCACCCCACTCTGTCCCTTCTTAATGTGTCA
2641 CTGCCTCATTCCTGATCCGAATAGATACCTGGATCAGCTTCACCTACAGACTTGGCCTTGGCAAGCCTCCTTCCACTCAC
2721 TGGTGAGTGCATCTTAACTCTTCTTGGATTACCACTGTCCCTTGCCCAGCCATCTGATCGGTGACAGGGTCATCTTGGTG
2801 ACCTCTCCACAGCAGCAGCAGAGGGGGAGCTTCCCAGCCCTTAGATGGCATCACTGCCCTAACCCACTCCATTTCTGGTA
2881 CTTGGTCCCAACCAGGATCAGAACTTGCTGGCTTGGGCCATGCTCTGTCTAGAGAGGATGTAGGAGATGCCACAGCTGAT
2961 AAACCACCCGCTGGCCTATTCCTGGAGTATGTATATCTGAGAGCAATGGCCCCTGCTACCTTCACCTGAAAAGGCCAAGG
3041 GTGCTCCTTTGCCTCTTTCCCTAATATACCAGGGAGTGAGTACCCAGGGGCTTCAGGAAGTCCCTGACACCCAGTGCACA
3121 ATCTTTTCCTGCCACACCCAGTTCTCTGTACATATAGCCATGTTTCAGGGGGGCGGCCATTCCCCACTCTTAAAGGGCTA
3201 CATGCCCCCCTCCCAGCCCCTATGGCAAGGAGAGGGGCTCTTCTCCCTCCTCTGGGCCGCCCTCTCCCTCTTATGTCTCC
3281 CTCCCCCCACCAAATATTGGCCCCTGTGGCCATCCCTTCTTGCCCAGAGCCTGGATGGGATAGATGGTAACAGGCTCTCA
3361 CCATGCTGAGGAAAGTAGGGAGTTACCACCAATCTTCCTAAATGCCAGCACCAGGTTTTCGGCCTCCCAACTAATAGATG
3441 CTCCATGGGCTCCGCATCCATTCTAGGGCCTCCCTTCAAGTGTGCTTAACACTCCCATGGAACACACAGCTTTCTCCAAG
3521 CCCTGGAGAGGTTCAGGGGCTTTCAGCTTTTGTTTGCCCACTCTCTCTTTCCCTTCATCCCTCCCCAAACCTGAATTCCT
3601 TCCTTCCTGGGATCTGCCCTCACCCCAGCCTCCACCCTCCACCTGCCTGACCCTGAAGTCTTGACCTCTTATTTCAATAA
3681 AGCCATAGTGGGGAGAGGTCTTGAGGGTGGGCCAGCAGGCCCTGTTCTGCTCATCCCCCACCATCACCACGATGCTTCCA
3761 GAATTGGGACCTGGCCTTCTGAGTCTTCCCCTCCCCACCCCCACCCCTGCTCCCCAATAAACACAAATACACATAGGCAG
3841 GGTGTGCCCATGCAGGAAAGCTCCCTTCTGGCTGGGGGCTGCAGAGGGGGTGTCAGAGACAAGATCAAAGTGCCACACCA
3921 GAGGTTCCTCAGGCCTCTGAACCCCATTCTTACTCCCCTCCCCACACTTCCTTCCAGTGCTGGACTCACCTTCATCTTCC
4001 TGGTGAGGACAGCAAAAGGAGCAGGCACTTGGCTGGGGGTGGGGTGTTGGTTTTTGTTTTGGAATAAACAGCTGTTTTCC
4081 TGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
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' ttAGATGGC-AT-CACTGCCc 3'
 2841 - 2859 157.00 -17.20
2 
miRNA  3' ggucgaucGUUAC---GUGACGGa 5'
                  :||||   ||||||| 
Target 5' tcccttctTAATGTGTCACTGCCt 3'
 2623 - 2646 149.00 -16.90
3 
miRNA  3' ggucgAUCGU--UACGUGACGGa 5'
               |:|||  || ||:|||| 
Target 5' attaaTGGCATCAT-CATTGCCt 3'
 1612 - 1633 137.00 -14.50
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions CD4+ T cells (C57BL/6)
Disease MIMAT0003460
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 GSM1013581. RNA binding protein: AGO2. Condition:CD4+ T cells "HITS-CLIP data was present in GSM1013582. RNA binding protein: AGO2. Condition:CD4+ T cells ...

- Loeb GB; Khan AA; Canner D; Hiatt JB; et al., 2012, Molecular cell.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' ggucgaucGUUAC---GUGACgga 5'
                  :||||   |||||   
Target 5' ------cuUAAUGUGUCACUG--- 3'
 		1 - 15
Article - Loeb GB; Khan AA; Canner D; Hiatt JB; et al.
- Molecular cell, 2012
MicroRNAs (miRNAs) are essential components of gene regulation, but identification of miRNA targets remains a major challenge. Most target prediction and discovery relies on perfect complementarity of the miRNA seed to the 3' untranslated region (UTR). However, it is unclear to what extent miRNAs target sites without seed matches. Here, we performed a transcriptome-wide identification of the endogenous targets of a single miRNA-miR-155-in a genetically controlled manner. We found that approximately 40% of miR-155-dependent Argonaute binding occurs at sites without perfect seed matches. The majority of these noncanonical sites feature extensive complementarity to the miRNA seed with one mismatch. These noncanonical sites confer regulation of gene expression, albeit less potently than canonical sites. Thus, noncanonical miRNA binding sites are widespread, often contain seed-like motifs, and can regulate gene expression, generating a continuum of targeting and regulation.
LinkOut: [PMID: 23142080]
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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