miRTarBase - #MIRT605042


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pre-miRNA Information
pre-miRNA mmu-mir-876   
Genomic Coordinates chr4: 36645373 - 36645453
Synonyms Mirn876, mmu-mir-876, Mir876
Description Mus musculus miR-876 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-876-5p
Sequence 11| UGGAUUUCUCUGUGAAUCACUA |32
Evidence Experimental
Experiments Cloned
Putative Targets

Gene Information
Gene Symbol Efr3b   
Synonyms AI852640, C030014M07Rik, mKIAA0953
Description EFR3 homolog B
Transcript NM_001082483   
Expression
Putative miRNA Targets on Efr3b
3'UTR of Efr3b
(miRNA target sites are highlighted)		 
>Efr3b|NM_001082483|3'UTR
   1 ACTCCAGGAGACAGAGCTCCTTAGAGGACACAGTCTGCAAGAGGACCACCCCCCTGCTCACTCTCACCTTGGAAATCTAG
  81 CTGGGATGGCTAAGAACTTGTCACCTTGGACAGTGAGCAAAAGGTCCTCTCTGGTCCTCTGTGGTCCTCCTTCCTCCTTG
 161 TCGTCTTCCGTGAGAAGAGTCCAGCCACCTCTCCTCTGGGCTAATAAGCATCTGACCTGTCTTCTCTTGTATCAGCCAGG
 241 GACAGAGAATCACAAGGACATCTCCATTGAGAAGCAGAAGGGCCTGGGAAGCCTCCATTGGGGATGTGTCTATGAGGGAG
 321 TGTCAGCCACTCCCAAAGAAAGGAGCCTGATATCCACATGGTTGGTCAAAGGAGGGCAGAGGTGGCACCTGGGGAAATGA
 401 CCCTGTGAAAGCTCAGAAGTGATGTCTGCTCTCGCCTCTTAAGTCTTGGTTGTCTTACCCAGCATCCCGCCTACTCTCTA
 481 GTTGTCTGCATTTCTTTTTCTACTATTAATCAATGCTGAGGACTTACAGCCAGAGCTGGGGACAGACACTGGAGCCAGCA
 561 AGGCTAGCAGAAGAGCTGGGGATGGAGAGGGGCTGGGTCTCCCAGACTGGGTGGCAGCTTCAGCAAAGCACGAGTGTGGT
 641 GAGTCTGTGTCCTGGCTGCGTAGCATCTTCCCACATCTCTGTCCAGAGGAAGCTTGGGGTGGGTCTTCTCTGGTTCTCTC
 721 TCTTCTGGATGTTTCCTAGTTGTTAAGTTTGGTCCCTGATGTCTTTGTTTCCACAGCCTCTGGGATGAGAGAAAGCTGAG
 801 CAAGCTAGCTGGTTCTAGGTGGCTGGAGAGGGGGGGAGGAAGTGCCAGGGCCCTGAGGCCTGTCTGCATCACTTCCTCTG
 881 GAAGATGCTCCCAGCAGTAGTGAGGGCTTGAGAGAGAGGCAGGCAGTTGAGCAAGTGGCACTTTAGAATTTGGGGAAAGA
 961 AAGATTTAACAACTAGGATTGAAAAAATATTTTCCCTCTTTGGGCTAAGTCTGAGACACTGGGGATAATTGGCCTTGCTT
1041 GTAGCCTGGGTAGAGGTGTTAGGAATCACTTTGGCTTCCATTTTCCCTATGTGCTACCTCCCTGTCCCTATGTGACTTGG
1121 TGTGCTGGGAGCAGCTGACCCAGGACTGGGTGGGTGCAAACAAGGCCACTTGCAGTTATCTTGGTTTGGCCCTTTCCTGA
1201 TGTCCCTCGTGGTGTCTCCGTGCCTCTCAGAATGCCTAGCAGTGGGCATACTCCACGGTCCAAGATAGTCCATCTTTTCC
1281 CTTTCAAACTTCCCATACGTTTTCCAAGCTGTTTTTCTCTCAGGACCAACATTGCTCCAGAGATTTTTGGTTTGGTTTGG
1361 TTTGGTTTGGTTTTTTTCGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTTCGTAGACCAGGCTGGC
1441 CTTGAACTCAGAAATCCACCTGCCTCTGCCTCCCAAGTGCTAGGATTAAAGGCAGAGATTTTGCTTCTTGTAAAGGGGAA
1521 GTGGTTCTGTGGTCTGCAGGAATCATTTCTAAGGTATGGTTGTAGGCAGTGTGGCCTGGGGTCATAAAGGAGAAGTTGAG
1601 CTCCTCGGGACCCTGCATAGTGACAGCCTGCTCACTAGGACAGGTGGCAACATTTTCCAGAATTAGGAGAACTTGAGCAC
1681 ATGTACTTTTCGTTGCATATGTGATAAATATCACAGATGGGGCACTCCTGACCCTTTCCCCAGAGTTTCCCATTTGTAAT
1761 ACAACTCTTTCCCATGTTCTCTGCACTGAGCTACGGGCTCACGGCTCCAGCATGGCCTGCATGATCTCAGGTCCCTGAGG
1841 ACAACACCCCAACACCACTCACATGGCTTTGGAGCTGTGTGGCTACTGCTCAACCCAAGTTTATAAGCATGGCCTTGAAG
1921 GCAAGTTTAAGCATGAAGGCAAGTAACCTTTTAGAAACTAAGAAAATTTAAGCCTTGTGCTAAAAACTGTCTTTTTTCAC
2001 TTGCCGGCCACATCCTCTATCCTCTGCTTAGCTAGAGTAAGAGTCCATTAGTTTCTTTATTGTTCCCCACTGATGTCATT
2081 GTCCACCCCTGAGACACCTTAACCCTAGTTGTGGATTGGGAGAGACACTTCCTTGGAGTCTTTTGAGAGCCAGCATCAGA
2161 ACCAGATGCCTCCAGGCCCACACAGATATGTCTGTCTCTCACCTTGCCCTGGGAACAGAAGAAAGGCACAGCGTTCATGT
2241 CTGCAGAATCAATGGCTGCTCGGTCTAAGTATTTCTTTTTCTTCATGCCGTGGCTGTGTAGTAGGGACATGCTGCTTTTA
2321 GAGAACTGGTCACTTGTGTGCCCTCTTCTTGGTAGAATTGATTTAAATTTACATCCAGTAGGATACTGGGTTGCCTGTTG
2401 ACAGGAAATGGAATCTGATCGTGACCAAGTATGCCTCAGAGTCAGGAAGTCTAGATGGTGGGTGCAGGAGGATCTGTCCC
2481 TCCATCACAAGGCAGGGAAAAGAAGCACAGCGAGTGGAGGCCGGGGAGCAGCCCAGTGCCCATGCTTTTCTAGCCCCTGG
2561 TGTCTGATCGCACTGTCTCAAATTCTGTTCTCTTTCCCTATTGTAAACCAGAATCCAAAGGAGCCAACAAACCTATTAAG
2641 GCCAAGCAGTCCCTACCCCACCCCCATGATCAAAGCACCCAGGGCTCTGGCCTAGAGAGTGACATCCTACTGACAGAATG
2721 TAGCAGGTGGGAGTGTGTTTAGGGTTAGGAGTTAACGTGGTTGACCATAAAAGTGTAAACAGTAGATTAAGAGAAAATGC
2801 CTGATCCAGAAGCAGCTGCTGTTTTCCTATGCTGAGTCAGTTTCTTGTTTTCTCTTGACTAAAATAGATGGTTTCATGAC
2881 TCCTAAGTGGCCTCATCAGAAAACCTAGAAATGCCCCCTCTGGCTCCCACCTTCACGCAAAGCCGGAGAACGTAGGCTGG
2961 GACCAAGGACCCTGGTCAGAGCAGCCATATCCCATATGCTGCCTGTGCGTATGGGATATGTTACTGGTCTTGGTCCACAC
3041 GATGCAGTTCAGCTGAAGTAGGATTGGAAAAGCCTTAAGACTCTTGACTTCCTGAAAAGAAGCCCCAGACTTCTTGAGGG
3121 TCCCTGGGTCGTGGTGCCTTCCAGTTGTCCTTTTGGTGTCATAGACCTGCCAACCTGCTACAGAGAAAGCTGCTAAGCCC
3201 TGTGGCTTAGCTGTGTTTGGGGCCTGGGGGAAAGGCAAGGTCTAAGCTGTGGGTCTGAACTTTGTGTTTAAAAGTAGATT
3281 TGGAGGTCGGGAAGGGGTCTGCTTTTTTTGACCTTCTCCAGCAAGCAGATTGCACCAAAGCAAGAATTCTGTCCTCGGAA
3361 TCTGGGAATAAAATTTAGGGGAAACAGTCTGGTTTCTATGACCCTATAAAGCTGGGTCTTGTCTAAAGACTGCAGAGGGA
3441 AATCATGGGAGGCCCTGATCGTGATTCTGGGCACCAGCCTGGCTCCTCAGGGAGCACGGAGATCTTCTGAGCCCAGCACT
3521 TGCCCTTTCTGAACTCTTAATGACTGGAGTCTGGCACATGGAGTATAAAAGTGCACACCCATAGATGCTGCAGCCCATCA
3601 TCTCAGTGTGTCCGAGTTTTTGAGACCTTCATGCCTGGCTGAGTGTGTGTATGTGTCAATGTCCGTGCATGTGTGTGATG
3681 TAGTTTATAGTTGCCAACATTGTATATATAATAGCTGACATATTTATATGTGAGTACAGAATTGGCACCTGTGGCAGTCT
3761 TCTATGTTTTAAACTTGTTGAATCAACTTAGTTTTCCTTCCAGGGAAGGGGGTATTCTGAAGTCATTTTTTAGAACTATT
3841 AGCTGTGGTTGGTGCCCTTTTCAAATAAATGTTAATGTTGTCACCATA
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' aucACUAAGUGUCUCUUUAGGu 5'
             |||   ||  |||||||| 
Target 5' cctTGA---ACTCAGAAATCCa 3'
 1440 - 1458 152.00 -11.80
2 
miRNA  3' aucaCU-AAGUGUCUCUUUAGgu 5'
              || | || ||:||||||  
Target 5' taaaGACTGCAGAGGGAAATCat 3'
 3424 - 3446 142.00 -13.60
3 
miRNA  3' aucacuaAGU-GUCUCUUUAGGu 5'
                 ||| |  :||||||: 
Target 5' ctcactcTCACCTTGGAAATCTa 3'
 57 - 79 131.00 -9.80
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.

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]
CLIP-seq Support 1 for dataset GSM4751762
Method / RBP HITS-CLIP / AGO
Cell line / Condition adipose tissue / RNA sequencing of eWAT 3
Location of target site NM_001082483 | 3UTR | GCCCUGGCUGUCCUGGAACUCACUUCGUAGACCAGGCUGGCCUUGAACUCAGAAAUCCACCUGCCUCUGCCUCCCA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Accession Series GSE142677
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM622572
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / WT2
Location of target site NM_001082483 | 3UTR | CGUAGACCAGGCUGGCCUUGAACUCAGAAAUCCACCUGCCUCUGCCUCCCAAGUGCUAGGAUUAAAGGC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
120 mmu-miR-876-5p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT577002 Gpx5 glutathione peroxidase 5 2 2
MIRT577009 Zfhx3 zinc finger homeobox 3 2 2
MIRT577023 Fndc3b fibronectin type III domain containing 3B 2 4
MIRT577452 Tspan31 tetraspanin 31 2 4
MIRT578027 Pfas phosphoribosylformylglycinamidine synthase (FGAR amidotransferase) 2 2
MIRT578035 Pde4c phosphodiesterase 4C, cAMP specific 2 2
MIRT578432 Nmrk2 nicotinamide riboside kinase 2 1 1
MIRT579608 4930519G04Rik RIKEN cDNA 4930519G04 gene 2 4
MIRT579782 Zfp422 zinc finger protein 422 2 2
MIRT579948 Xpo7 exportin 7 2 4
MIRT581398 Rbms2 RNA binding motif, single stranded interacting protein 2 2 4
MIRT582830 Itih5 inter-alpha (globulin) inhibitor H5 2 4
MIRT584574 Bpnt1 bisphosphate 3'-nucleotidase 1 2 4
MIRT585235 Zfp459 zinc finger protein 459 2 4
MIRT585498 Ttc26 tetratricopeptide repeat domain 26 2 4
MIRT585512 Trub1 TruB pseudouridine (psi) synthase family member 1 2 4
MIRT585584 Tox4 TOX high mobility group box family member 4 2 2
MIRT585843 Slc3a2 solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2 2 2
MIRT585865 Slc23a1 solute carrier family 23 (nucleobase transporters), member 1 2 2
MIRT586042 Rps3 ribosomal protein S3 2 2
MIRT586299 Pnpla3 patatin-like phospholipase domain containing 3 2 4
MIRT586512 Neu3 neuraminidase 3 2 2
MIRT586788 Isg20l2 interferon stimulated exonuclease gene 20-like 2 2 4
MIRT586840 Il17rd interleukin 17 receptor D 2 6
MIRT586911 Helb helicase (DNA) B 2 4
MIRT586984 Gpr157 G protein-coupled receptor 157 2 4
MIRT587011 Gngt1 guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1 2 4
MIRT587338 Efcab4a calcium release activated channel regulator 2B 2 4
MIRT587594 Commd8 COMM domain containing 8 2 4
MIRT588116 Aco1 aconitase 1 2 4
MIRT589172 Rab11b RAB11B, member RAS oncogene family 2 2
MIRT589182 Ptprg protein tyrosine phosphatase, receptor type, G 2 2
MIRT589339 Ostf1 osteoclast stimulating factor 1 2 4
MIRT589353 Osbpl8 oxysterol binding protein-like 8 2 4
MIRT589489 Mzt1 mitotic spindle organizing protein 1 2 4
MIRT589817 Hnrnpab heterogeneous nuclear ribonucleoprotein A/B 2 4
MIRT590034 Fbxo43 F-box protein 43 2 2
MIRT590043 Fbxo30 F-box protein 30 2 2
MIRT590125 Ercc6 excision repair cross-complementing rodent repair deficiency, complementation group 6 2 4
MIRT590429 Cbfa2t2 core-binding factor, runt domain, alpha subunit 2, translocated to, 2 (human) 2 4
MIRT590994 Slc28a3 solute carrier family 28 (sodium-coupled nucleoside transporter), member 3 2 4
MIRT592907 Mmachc methylmalonic aciduria cblC type, with homocystinuria 2 4
MIRT593321 Slc25a51 solute carrier family 25, member 51 1 2
MIRT593776 Nfic nuclear factor I/C 2 2
MIRT594578 Znrf1 zinc and ring finger 1 2 2
MIRT594903 Homer1 homer scaffolding protein 1 2 2
MIRT594907 Hecw1 HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 2 2
MIRT595731 B2m beta-2 microglobulin 2 2
MIRT597330 Senp5 SUMO/sentrin specific peptidase 5 2 2
MIRT597339 Sema4b sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B 2 2
MIRT597499 Rbm34 RNA binding motif protein 34 2 2
MIRT597517 Rbak RB-associated KRAB zinc finger 2 2
MIRT597664 Prkcb protein kinase C, beta 2 2
MIRT597707 Ppih peptidyl prolyl isomerase H 2 2
MIRT597733 Polr3gl polymerase (RNA) III (DNA directed) polypeptide G like 2 2
MIRT597746 Polr1b polymerase (RNA) I polypeptide B 2 2
MIRT597780 Plin3 perilipin 3 2 2
MIRT597870 Pdxk pyridoxal (pyridoxine, vitamin B6) kinase 2 2
MIRT597901 Paxip1 PAX interacting (with transcription-activation domain) protein 1 2 2
MIRT598294 Mcm5 minichromosome maintenance complex component 5 2 2
MIRT598361 Man2a2 mannosidase 2, alpha 2 2 2
MIRT598747 Gpr68 G protein-coupled receptor 68 2 2
MIRT598915 Gje1 gap junction protein, epsilon 1 2 2
MIRT598934 Git2 G protein-coupled receptor kinase-interactor 2 2 2
MIRT598997 Fnip2 folliculin interacting protein 2 2 2
MIRT599120 Dynll1 dynein light chain LC8-type 1 2 2
MIRT599129 Dync1li1 dynein cytoplasmic 1 light intermediate chain 1 2 2
MIRT599209 Ddhd2 DDHD domain containing 2 2 2
MIRT599270 D14Abb1e family with sequence similarity 208, member A 2 2
MIRT599457 Cdnf cerebral dopamine neurotrophic factor 2 2
MIRT599491 Ccr9 chemokine (C-C motif) receptor 9 2 2
MIRT599545 Car5b carbonic anhydrase 5b, mitochondrial 2 2
MIRT599692 Aqp7 aquaporin 7 2 2
MIRT599818 Agl amylo-1,6-glucosidase, 4-alpha-glucanotransferase 2 2
MIRT599910 Abcc9 ATP-binding cassette, sub-family C (CFTR/MRP), member 9 2 2
MIRT599936 Rmi2 RecQ mediated genome instability 2 1 1
MIRT600061 Smco1 single-pass membrane protein with coiled-coil domains 1 1 1
MIRT600068 Knop1 lysine rich nucleolar protein 1 1 1
MIRT600089 2010315B03Rik RIKEN cDNA 2010315B03 gene 2 2
MIRT600338 Strbp spermatid perinuclear RNA binding protein 2 2
MIRT600469 Rbm4 RNA binding motif protein 4 2 2
MIRT600632 Mkl2 MKL/myocardin-like 2 2 2
MIRT600647 Med18 mediator complex subunit 18 2 2
MIRT600649 Mcc mutated in colorectal cancers 2 2
MIRT600717 Kif24 kinesin family member 24 2 2
MIRT600735 Ajuba ajuba LIM protein 1 1
MIRT600803 C5ar2 complement component 5a receptor 2 1 1
MIRT600924 Exoc8 exocyst complex component 8 2 2
MIRT601088 Cbln3 cerebellin 3 precursor protein 2 2
MIRT601272 Soga1 suppressor of glucose, autophagy associated 1 1 1
MIRT601425 Tubb5 tubulin, beta 5 class I 2 2
MIRT601557 Tapbp TAP binding protein 2 2
MIRT601630 Slc2a4 solute carrier family 2 (facilitated glucose transporter), member 4 2 2
MIRT601889 Pctp phosphatidylcholine transfer protein 2 2
MIRT601917 Ooep oocyte expressed protein 2 2
MIRT602062 Luc7l2 LUC7-like 2 (S. cerevisiae) 2 2
MIRT602149 Irgm2 immunity-related GTPase family M member 2 2 2
MIRT602256 Gnl3l guanine nucleotide binding protein-like 3 (nucleolar)-like 2 2
MIRT602278 Glt8d1 glycosyltransferase 8 domain containing 1 2 2
MIRT602285 Gls glutaminase 2 2
MIRT602324 Gal3st3 galactose-3-O-sulfotransferase 3 2 2
MIRT602385 Fam198b family with sequence similarity 198, member B 2 2
MIRT602406 Fadd Fas (TNFRSF6)-associated via death domain 2 2
MIRT602905 Fam219b family with sequence similarity 219, member B 1 1
MIRT602928 Zmat3 zinc finger matrin type 3 2 2
MIRT602977 Sgms2 sphingomyelin synthase 2 2 2
MIRT603139 Ufd1l ubiquitin recognition factor in ER-associated degradation 1 2 2
MIRT603235 Tle2 transducin-like enhancer of split 2 2 2
MIRT603269 Svopl SV2 related protein homolog (rat)-like 2 2
MIRT603292 Spib Spi-B transcription factor (Spi-1/PU.1 related) 2 2
MIRT604167 Cyb5d2 cytochrome b5 domain containing 2 2 2
MIRT604190 Cts8 cathepsin 8 2 2
MIRT604320 Car8 carbonic anhydrase 8 2 2
MIRT604483 2810006K23Rik RIKEN cDNA 2810006K23 gene 2 2
MIRT604612 Tbl1xr1 transducin (beta)-like 1X-linked receptor 1 2 2
MIRT604837 Mrpl35 mitochondrial ribosomal protein L35 2 2
MIRT605042 Efr3b EFR3 homolog B 2 2
MIRT605187 Bach2 BTB and CNC homology, basic leucine zipper transcription factor 2 2 2
MIRT605488 Slc35e2 solute carrier family 35, member E2 2 2
MIRT606171 Smtnl2 smoothelin-like 2 2 2

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