pre-miRNA Information
pre-miRNA mmu-mir-3110   
Genomic Coordinates chrX: 38210441 - 38210520
Description Mus musculus miR-3110 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-3110-5p
Sequence 13| UUCUGCCUCCCCUGAAGGCUC |33
Evidence Experimental
Experiments Illumina
Putative Targets

Gene Information
Gene Symbol Mysm1   
Synonyms C130067A03Rik, C530050H10Rik
Description myb-like, SWIRM and MPN domains 1
Transcript NM_177239   
Expression
Putative miRNA Targets on Mysm1
3'UTR of Mysm1
(miRNA target sites are highlighted)
>Mysm1|NM_177239|3'UTR
   1 TTATTTTAAAGTAAGATGTTCTAATCTTGGCATGCTACTGTAAATAATTGAGATTTTAAAGCAATATAAATTATGTTTTT
  81 TTTTTAATCCATAAAACTCTAAACTTTCTCACATAGATAATGTGAGAAGGAAGAGAGAGCCCTTGTTCTCATAGTGGTAA
 161 TCAAGAGTGGTAGAGCCCTGCCTATGCTAAGCTGTGCAGTGGGCATGAAAGCTTGAGCTCTGCTCTGCCTCGTGGTGTGC
 241 GGCTTAATAACTAGGAGATGACCGAGCTCCGCTTTTTCTCAGAGGGACTGTTTCTCACTTTGCCATCTCATTACACACAC
 321 TTTCTTCCCATATGTTCTGGTGGTGAGATTGTGTGTGTGTGTGTGTGTGTTATTTGGATGTTGCAGCCTAGGTGTGGAAC
 401 ATTAATGGGGTTGAGAACTACTGACTAATAAATCTAACAGCATGCCAACACAGCAAAAGGGAGCATCCTTAGTAATGTTC
 481 AGACAGGAGTCCAAAGGGGAGAAGAACCAATTTTCAGTCTGCGGTGTGTGCTTCATCTTACTGTGTACACTATACCATAG
 561 GACAGTCAGCCTCCTCTGCGATTTAAATGTTTAAATGAATTTCACAAGGGAAATAATTAGCTCCAACTCTGTCCAATTGC
 641 AGTAGCATGTGACAAAATGTCATTGAACTAGACTTGGTAATGTAGCCCTCAACCTAGCTTTTTTCCCTACTGTCAGGAGA
 721 AAGAGAAAAATGAGTCACATATTACAATAGAAAAAAAAATGCCATCTGGTATTTTACATAGCTTAACCCAGTTTCATGCA
 801 CTTGCTGAATATTAAAAGTAAACTTTTTTCATGTTGTAAATTCAAATTGTTCATGTAAGTATTAGTGAATATTTCTGCTT
 881 GCTGGAGAACTGGTGTTTGACCCTGTCCAGGCCTTCTTATTGGCAACAGTTTTGTTATATTGAAACTGAATGTGAGTTTA
 961 GAGTTTTCTTTTTTCTTTTTTTTTTTTTTTTTTTTTGCTGTAGTTGTAGCCAAAGGGGGAGGCAGCACTGGATGGAGTGA
1041 CTGCAGTCATAGGTGACCTGAATCTGATTTGGGCACTGTGATTTAAAGAAAAGGCGTTTGCTTTCTCTAGGCCAAGTTTG
1121 TCTTATGTAGCTGAGGCTAATCCAGCCCTGAGTGTTGCTCCTACTCTGATTTATCTGCTGGCTTGTTAGGCTGCACTTTT
1201 GGAACTTTATAAGATCGTGTAATTGCAAAATTAATGTGTAGCTTTAAAAGAGAACTAGCAGTTTTTCCATTTCCCTCTGT
1281 ACATTTAATACGAACAATGAAACATACTTTGTAAAATCCTCTTGAAATCTGGAAGTGCAAGGACTCCAGAGCAAAAATCA
1361 GGAATCCTGAGCTCTCAACCTAATCTGCTTAAGCTTTGGTAAGGGGCCTCGCTCCACGCTCAGCTCTCTAAACTCATCAG
1441 TTGAGATTCAAAGAGCTGAATTCTATCACTTGTTGTCTCTTCAAGCACACAAGGCTACAAAAGTCAGTAGCAATTAATTC
1521 ATTCCTTTCTGTTTTCCTTCCTCTTCACCTGTCTCTTCATAGGCTGTTGGCACAGACCTGAAATGGATGATAATTTACTT
1601 TCTTGCAATTTTCCTAGAATGCTGTTGAATTTTAAAAAGTTCTTTCTCAAATCTGGACTTTACACATGCCAGTGGTTAAG
1681 AGTATTCACTACCCTGATCTATACATTGTAAGGACCCAACGGGTGCCAATAGTCAGAGTGTAGGGCCTTGAGAACAGAAG
1761 TTTTTAAGCAACTATTGAGAAAATACAACTATTTTCTGACTGTAGAATATATTTGTAATTTATCTTATGAAATATTTTTA
1841 AATACAGTGAAATATATACAAAGTGCAAGTATCTCAAACCTACTGTTGAGGAAATATTTTACATAGGAATCAGATTCTTA
1921 ACCAGTTTTTAACAGCATAAATTCAGGATATTCAGTTATTGTTTGTCTGCTTTTGTTTTCTGTCTGTTCTCTGTGCTGCC
2001 TTCTCTTCTCTTGTCCTAGTGTCTACTTGCTCTGGCAGCTGTAGGTGGCCAACCTAGGCCTCCTGAGACTGGTTAGAGCC
2081 AAGACCTTAAAGAAGCACAGATGAGTCTGGAACTTGAGGGGACATGTAACACAGAAGTTCATGGAGAGAGAGAGAGAGAG
2161 AGAGACAGAGACAGAGACAGAGAGAGACAGACAGAGACCGCCCTTCCCAACAGTGTTTGCAGAAGTGGAGGACCAGCAAT
2241 GCCTGAGTCTCTTTATCCTGGGTTCTATTTTTATTGGTGCATAAAAATAGAAATTGAGCTTAAATTTTGTCTCTTATTCT
2321 GACATGGTTAAGGACACTTAATAATAGTACTTCTCTTATATTAGACTTACTGTTCTTCAAAACTAATACTCAAGAAAGCA
2401 AAATCAGTGGAACAAGACCAGTAAGGTAAAACTCGCTGGCCATTGTTTAACCTTGGCCCTTCTTCTCCACTCCTTTTAAA
2481 TGGCTAGGAGCTCCCAGTCTTGGAGTTGGTATGGCCACCTGCTCAATGCTCATGAGGTTTTAGGCACCAAGCACTTTAGC
2561 TCACTTTGACCTCTTCCATATAGAATTTAAAATTACATTTTATAATTGTGTTTGTATAACATGACAGTATTCACATTTTG
2641 GATTAAAATATTCCTTTAATCTAAAACTTGGATTATTTTTCCTAATAAAATTAAGTAAAATGTTTGTTATACACCCTTCA
2721 AAATTCTGAGAATTTGAGACTGTACCTGATGAATGGTTTATGTTCTGAGAGGGTTGTTGGAAAAATGCAGACCGTGTTCT
2801 CCATCCCTTACCACCACTCAGGTGTTTGTTTCACTCCAGCCAGGAGCACTGCAGGTCCTCCTGTCACAAGCCTGGACATC
2881 TGAACTTCGTCCTTCCCATCCTAGCCAGAACTCAGTATGGCTTAGATCATCCATGGGAGGCGGAGGTGCAGTAGTTAGAA
2961 ATCAGTAGATAGGAATTTTATTTAGGTTCCTACTTTTACAGCTTGTGCGCCACCTCACAGGGTGAGGTGCCTTTTTTCCC
3041 TTTACTGTCAAACCCTCATATTCATCTATTCATCCATTCTCACAGCTCATAGGTACAAGAGCTTTATATCATTCATTGAA
3121 AGTAATTAAACAGACCCATTCAGAAAATGCCTGCAGTCATTTATTGTTTAGCATTGGTCCAGGCTTCTCCACAGAATGTT
3201 CCTCTCGGGCTAGGTGAGGTTGGTAGCATGCAGACTGGAAGCACCGTTAGCCTCTTCGTTTCTAAGGACAGAGAAAGTGG
3281 CAGCCCCGGCATTCCAGCCTAAGCTGTCCTACTGCTCTTTAGTTTACCTTTTCCCATGTACATTGCTGAGTCCTGACGGA
3361 AGGAAGGCGCTAGAGAAGCCAACAAAGCCTGTGCACGCCTCCACTCTGTCTCTGCTCTGTGCCAACTGAAGACACCCAAT
3441 TGGCCACCTGCTTGTGGACACACTTGAAGTTCACCGGCAGACATCCTATGTTGGTTTCTCAGCAGGAGAGGTGGCCACCC
3521 AAATTTCCCTTTTCTACTTACCAGCAAGGCACTTAATCTGGTGTCACGTGACACTCATAGAGAAAAGCACCTGCACAGAA
3601 GCACAAGAAGAGCACACACATTCTGTTGTGTTAGCATTAACAAACTTAACGAACAAACTTTATCTCTAGAGCTTCATCTC
3681 TAGTTTTGTATTTAGCTCTTAGAACAATATATCTTATAATGTATCCAGAAAAATCAGAATAATGTAATATCCTTCGATTA
3761 TTATTTCCTGACCTTTCTGAAAAAGTTTCATGCATGCTTTCATTTCCTGTAACTTTGTTTTCTGATATCTCTTCTACCTT
3841 ACTCCCTTATTGCCCCGACCAAATCAGGAGGAAATAAAAGCATCCAAGAGGAACTTAAAAGGTTCTAAATGAAACTAAAC
3921 TTTAAAGCCGAAATTAATTCGCAGCATCTGTGTAGCTTTTATTTTTGTCCTTTGCTGTTTCTGTCATATATTCATGTGAG
4001 TTCCAGGGAAAATAACCTGCTTTGTTGTGTCTGAGGGTTCCTAGTAGCTTATCAGGAATTCAATAAATTCATATTTCCGG
4081 TGTTATATGTTATCAAAAAATTGAGGCCTGTGTGGTGGTGCACACCTTTAATCCCAGAACTCAGAAGCAGAGTCAGGGAG
4161 CTCTCCAGTGCTCAAGGTTAGCCTGGAACAGGAGGACTACATAGTAAGACCCTGTCATTTAAAAATAAAACAAAACAAAC
4241 AAACAAACAAAAAAAACAAGACAAAACAAAGCTGGGCATGGTGGCGCACGCCTTTAATCCCAGCACTCGGGAGGCCGAGG
4321 CAGAGGCAGAGGCAGGCGAATTTCTGAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACATCCAGGGCTACAC
4401 AGAGAAACCCTGTCTTGAAAAGAAAAAAAAAAAAAAAAGATCATCTGCTTCAGCATATGAGTACTAAAGTTGTAATTAGA
4481 TTTTAGCATGATTTATGTAGAGGAGTCTTTTATAAACGCCTTTAAATGTGTAGATTGGAGTTGATTTATACAGTTGTGTT
4561 GTATATAAGATATTGCATGACAGTTTATGAACTTGTTGCTGTTTTCTCACAATATTAACAGTTTTGTAAATTTTTTCACT
4641 ATGCATTTACAGTGTTCTATAACAATATATGACTTAAAACTATTTTATACATTTAAATGTTATGTTGTATATATCTACAT
4721 TAAAGAATATTGTAAATATCAATGTTTGTAAAATTATAAGTTTTCCAAAAATATAAACTCATTTTTCCATATCTACTTGT
4801 GGCATATTAAAAATACCAGTTTTTAAGCTTTGACGTATTATCTTGTAGTGAAAGAGGAGGATCATGCTGTCAATTCAATG
4881 TAAGCAAATGTTAAAAATAAAACAGGTAGTTTTTGATGTCTTTG
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' cuCGGAAGUC--CC--CUCCGUCUu 5'
            ||  ||:|  ||  |||||||| 
Target 5' caGCACTCGGGAGGCCGAGGCAGAg 3'
4301 - 4325 155.00 -24.20
2
miRNA  3' cucGGAAGUCCCCUCCGUCUu 5'
             | | || |||||||:|| 
Target 5' gatCATCCATGGGAGGCGGAg 3'
2925 - 2945 150.00 -20.70
3
miRNA  3' cuCGGAAGUCCCCUCCGUCuu 5'
            |||   :||||||||||  
Target 5' taGCCAAAGGGGGAGGCAGca 3'
1007 - 1027 147.00 -27.70
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 ...

- 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' cucggaagucccCUCCGUCUu 5'
                      |||||||| 
Target 5' ------------GAGGCAGAg 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]
185 mmu-miR-3110-5p Target Genes:
Functional analysis: