miRTarBase - #MIRT604517


—
pre-miRNA Information
pre-miRNA mmu-mir-1948   
Genomic Coordinates chr18: 12714811 - 12714895
Synonyms mmu-mir-1948, Mir1948
Description Mus musculus miR-1948 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-1948-3p
Sequence 52| UUUAGGCAGAGCACUCGUACAG |73
Evidence Experimental
Experiments Illumina
Putative Targets

Gene Information
Gene Symbol 1700094D03Rik   
Synonyms -
Description RIKEN cDNA 1700094D03 gene
Transcript NM_028567   
Expression
Putative miRNA Targets on 1700094D03Rik
3'UTR of 1700094D03Rik
(miRNA target sites are highlighted)		 
>1700094D03Rik|NM_028567|3'UTR
   1 CAGCTGCCAAGACACTGTTCTTCCACCTCGTCACGCCTGCTAAGCAAGCCTTCATGCTTTACCCTGAGCTTCCCAAAACA
  81 CACCTGGACCTGGAACTTAAATCTTTTTCACTATTTTGTCAACCTAAATGTTGCCTCTGGACACAAGAGTGACACCTTGT
 161 GGTCAGTGTGGGATATGCACTGTGGCGGGAAGAGAGATTATGTACATTGTCTGGTTTTAAAAATCTGATTTGGTTTAACA
 241 AATAAAGCTAGCTCTTAAAGGTTCAGATTTGGGCTGGCAGGATGGCTCAGCAGGTAAGAGCACTGACTGCTTTTCCAAAG
 321 GTCCTGAGTTCAAATCCCAGCAACCACATGGTAGCTCACAACCACCCATAATGAAATCTGATGCCCTCTTCTAGTGTCTG
 401 AAGTCAGCTACAGTGTACTTACATATAATAATAAATAAATCTTTTTTTTAAAAAGTTCAGATTTAGGCCACAGGGCTTAT
 481 TCTCAGCCTTGAGTCTTGATTTGTTCTTGGCTGCCATAATTTTACTTCCTAGATTGTGGGCACTGCCTCAGACTTCAGTT
 561 TCACTGATCTTTCCTAAATTCGTGGACAAAAACCATGTTTAATGTCTATTAATCTGTAGGCACTGTGGTGCTTGAGTGTC
 641 AGGAGGCCCCAGTTGTATGTTTAGAAGTCACCTCATTGTGAAACCATGGATTAGCCTGAATTCCCACTCCTACTTTACAA
 721 AACTGAAGCCTCCAAACTCTAATCCCTCTAGGCATTTGGCTTGCAGTGGAGCAAGTGTCAAGTATCAAGCAGTAGGTTTG
 801 AGGAGCTGGAAAGATCATGTCTATTCTCAAGGTGTTTGACACTGAAAATCCTGGAAAGTATACACCTGTAGGTCACAAAG
 881 ATGCAAATGAGTAGCCTTGGCTGTCCTGAAACTCACTCTGTAGACCAGGCTGACCTCGAACTCAGAAATCTGCCTAACTC
 961 TGCCTCCCAAGTGCTGGGATTAAAGGCGTGCGCCACCACCCGGCAATGGCTAATATTTTAAATTTGGCTTCCATCGATAG
1041 TGCTGCTGTTCAGGCATGTGTGCCAAGGGATCTTTTCCTACCCTCAGTTTTGTGTGGCTGTCTCCACTGCAAAGTTCACA
1121 TTCTCGTCCTTTTTCCTTCCAGCCTGTCTCTAGCCTGCATCCCTTACTAAAGCCTGTAATTTTCATTAGCTGTCGGGAGC
1201 TACTACTTCTTGTCCCTCCATATCCCACCCATGGAAAGCACAAGCTTTAGGGTCAGGTATAAGTTCACAGTATCAGAACA
1281 TCGTTCCTCTTCTGGAAATGACAGACTCTCCTAGGATTTTCCTCGGGATTAAATAGGTAGAGAGCACAAGCCCAGTGATT
1361 GACCTAAAATACCCTCATTATATTTCTCTGTAACCCAGGGCCCTTTTCTGTGGTCCTGCAGTTAACGCACATCCAGTTAA
1441 ATGTCATCTTTCTTCTTTTGATCACATTCCTTCCTCTTTGCCTTCAATGCCACTGCTTCCTAATCCCTTGTCATTCGTAG
1521 CTGGTCATGGATACTTTCATTAAATGAGTTGGAGCTACAGGCTGGTGGGGAAAGCAGGCTTTGAACAGGAGTTACAAGTG
1601 TAGCATGTGTTTTGTAGATGAAGCCACAAAATGCCACCTGGATTTTGATTGACAAGACTGACTGAATCCTTCTGTCTGTC
1681 CCTGCCCTGTGTTAGTCTGGTCTGTACCCTCTTAGCCTCTTTAATCTTCCTTCTGTCTCCTGGACCACCTGCTGATTACC
1761 AGATAGTATGGCCTAGAGTTAATAGAATGGACAGATCTGGTTTTCAGGGTTGGCCTTTTCGCTTAGTTTGGTCTAGTCCA
1841 ATTTTTAATCTGAGAAGCGGGTAACTGGGGAAACGGCTCAGTGATTGGGAGCACTAGCTACTCTTGCAAAGAACCCAGAT
1921 TCAATTCCTAACATCTATATGGTTACTCAACAGTTCCAGAGTATCCCTTTCCCGGCCTTGGCAGGGACCAGGCAAACGCA
2001 TGGTACACAGACATGCAGATAAAACACCCATGCATATAAAACATTTTTAAATAATTTTAAGTCTGAGTTTTGGTTGCTAA
2081 TTTATGAAATGAAAACAATTCCAACCTTACTGGGTTACTGTGGGAATTAAATAAGACACCTAGAAGAAATCACACATAAT
2161 AAGTAATACAAACAGGAAGCCATAATGCTGTCTTCCTACTCCATGGTACTTTCTTCCCTAATTTCTACTCCCACTACACT
2241 TTATAACCAACCTCTTCAGTTCTCTCTTCCTTTGTTCATTTAGACTCACTGGATGCCCCATCCTGTCTGCCTGGATCTCT
2321 GACCTTGGCCTGTTGCCTCAGGGCTCATCAGTGCCAGGCCGACTCCTTTATTGGCAGGTTGGCTCACTACAGCGCTCATC
2401 TTCCCTGACCCTCCCTGCCAATACTGTGTGCACTCATCACATCGCTCAATTGTACCCCACCAGTCCATGCTGCTGCTGGA
2481 GCTGATGTCACACCCTGGCCTTGTGACTTGGGACTTAAACCTATTTGAAATAGCTGCCTAAAAACCACTGGCAGAGCTCT
2561 GTGAGATGGTGCAGTGGATAAAGACACTTCCTACTAGGCCCGATGACCTGAGTTAATCAACCCTCATAAAGGAGAGAACA
2641 GATTCCTGGAAATTGTCCTCTGACCTTCACATGGGCACCATGACACAACCACACAAAATATGAAAGTGTAATAAAAATAA
2721 AAGGAAAGATAAAGTA
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' gaCAUG-CUCACGAGACGGAUUu 5'
            | ||  ||   ||||||||| 
Target 5' tcGAACTCAGAAATCTGCCTAAc 3'
 936 - 958 152.00 -11.62
2 
miRNA  3' gacaugcucacgaGACGGAUUu 5'
                       |||||||| 
Target 5' ctatttgaaatagCTGCCTAAa 3'
 2521 - 2542 145.00 -12.70
3 
miRNA  3' gacauGCUCACGAGACGGAUUu 5'
               :| | || |||||| | 
Target 5' tagatTGTGGGCACTGCCTCAg 3'
 530 - 551 125.00 -12.30
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 ...

- 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' gacaugcucacGAGACGGAuuu 5'
                     ||||||||   
Target 5' ---------aaCUCUGCCUccc 3'
 		1 - 13
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]
9 mmu-miR-1948-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT580248 Trp63 transformation related protein 63 1 1
MIRT581816 Pkp1 plakophilin 1 1 3
MIRT593625 Tor1b torsin family 1, member B 1 1
MIRT593651 Stk3 serine/threonine kinase 3 1 1
MIRT594708 Irf2bpl interferon regulatory factor 2 binding protein-like 1 1
MIRT596077 Ttbk2 tau tubulin kinase 2 1 1
MIRT599656 B3galtl beta-3-glucosyltransferase 1 1
MIRT600593 Nfib nuclear factor I/B 1 1
MIRT604517 1700094D03Rik RIKEN cDNA 1700094D03 gene 1 1

Error report submission