miRTarBase - #MIRT603304


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pre-miRNA Information
pre-miRNA mmu-mir-5114   
Genomic Coordinates chr19: 44303171 - 44303231
Description Mus musculus miR-5114 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA mmu-miR-5114
Sequence 1| ACUGGAGACGGAAGCUGCAAGA |22
Evidence Experimental
Experiments Illumina
Putative Targets

Gene Information
Gene Symbol Slc4a7   
Synonyms E430014N10Rik, NBC3, NBCn1, NBCn1-G
Description solute carrier family 4, sodium bicarbonate cotransporter, member 7
Transcript NM_001033270   
Expression
Putative miRNA Targets on Slc4a7
3'UTR of Slc4a7
(miRNA target sites are highlighted)		 
>Slc4a7|NM_001033270|3'UTR
   1 AGTCAAACCAAAAGGAATATATAGAGATATATGCCTATCTGTATATATACACATATATATGTATAAAAAGCACATGTGCC
  81 ATGCCATTATGTATAACAGTACTTTGGGGCTTTTTCAAGTAGCGTCAGATATTTGTTGTGGACACCATAGAGACTACATT
 161 AATTAAGTGCTCTCTTAGAAGCAAGGTTCATGAATTTTTACTCCAGATTTTTTTGGGGGGTGGGGTAAAGCCTTTCTGTT
 241 ATGCAATAGAAAGATGTGGAGCACTGCGTTCCATCTGCTTTTCTTTGATCTGTCAGTGGCAATCAATCATAACAATCTTA
 321 AGTCTACATACTTAAAATTCGACCTGAATTTCAAAAGATGTTTGTTTTCCCTTTTGGTAGTGTTTATAGGTAGAATAAGG
 401 AGTCTGCCCATGTGGTGGGAAAATGACATGTCCTGGCTTCTCTGTGGGCTTTCTTCATGTAACTGTCAATCATACTTCAC
 481 AGGATAGTGGAGATTTTCTAAGAAGGAACTTTATGTCTTAGGAGTTATTTTTAAATTTTAAAACTTTCTGAGTTTCCATT
 561 TTGATGGACAGGTTAAAAATTTTTATGTCACTTCTAATTTAACACCCACACAAGTCATAACGTTTTCAGTTTTAGAACCT
 641 ATGAAGTGCCCATTTACAGTAATTAACTATTGTTAGTTTTGTGGCAGGGCTTTGCCGGTACTCAGTACTTGCCTAGAAAC
 721 CAGAGTCCCACTCTTCTTTGTCTTTGTTTTTCTTTACTGAGGTGGTCTGGTGTGCCAGGCTCAGTTATCTTTCTGTTGTA
 801 AGTAGCAAAAAGAGTCAGCCCACTTTCAATAGGCTTGTGACCAGTGTGCCTGTAGAAGAATTACCTTTCATTTTCTGTGT
 881 GTATTCTTTCTATTTATATACAGTGTATTTAATTGGTTACCACCCATAATTTCCTTTTAAAATATTTTATTTATTATAGT
 961 TGATGTGATACTTCAATATATAAATATTTGAGACAGTAAAAATATAGAGTAAATTGTTCCTGTTGTAGATATTTGGTGCT
1041 TGTATTTCTTTTCACATCCTGAAAGCAGGTGACAAATTTTACATCTTTACTATAAAGCACTGCCATATTTATATTTTTAA
1121 AAGGAAGTTGGATATTTCCTGTACAGCTCAGATCAATGGCATTTTTTTCTGTTTTGTGATAGCATTGTGTTTCCAATATT
1201 TCTGAGCTGTTTCTTAAACATGTAGCAAATATTCATAGCTCCTCACAAAATAAGTAAAGGCTATTTTAGCCTTTGGGACA
1281 GAGAGTTTGGGGCTATGAAACTTGATTTGGCAAGAGGACAGATAATACATAGAAATGGTGAGCAACACTAGAGACACCGA
1361 AGGTGATGAAATGCGAAGGTTCAGGCAGATGTTTTAAGGAAATTCTAATGTTCTCTAGCCACTGCAAACTAACATTTAAA
1441 AGTATGAAGAAACTGATCTTTAAATCAAATTATTTTTAGCAAGTTTATTCTAAACTTTAGCAAATCATTTTCGTTTATTC
1521 TAAACAATGTACCAATTAATGTAATTCCCTCATCTGAGATCATGTAGTTGGATTCTTATTAGAATAGTAGCTGGCAGCAT
1601 TTGGTACTATCTGACGAGTTCTATTGGGCTTCTTAGCATGTGATAGGGAAGGTTGCCATGGTGCTTATGGTCACAGGTGA
1681 CCTCCATTGAAGTGGTTCCTTTGCACTCAGCAGCACATTCATTTCCAAAGTTCCCATTTGCTGCTAAATATAACCCTACC
1761 CCAACCCCTGAAGTACCCAAACAAGAGAATTTCCTCACACCATTTTCTTGTGTAAGGACATCAAAGGGTTAAATCTATTT
1841 TACAGGAAGTGATTTTAAAATTTAAACTGAAGACTACCTGTTATCATAATCTTCCTGTGATTTATTTAATTATATATGTT
1921 TTGTCCAGTGCCAGGGGCGGAAAAACCATGACTTACGGAATATTTTGTATCTAAGATGTTTCACTGTGGTTTTGGTTATT
2001 AATGGCTTCTGCTTTCTTTTGACTACTTGACTTACAAAGTGATCTAATAGGACTACTCCCCTGAAGAGCAGAGGTAATTT
2081 ACTGCTTCTTTCAGGTGGTTACATTTCTTGTGCTATTTTTGAAAATAACAATCATGAATAACATTCATTGCAAGACAGCA
2161 AGAGAGATAATTTTAAATATATATATACATATATATGTGTGTGTGTATATATATATATATTTTTAATGCTGCCTTAAATA
2241 GGTGTATATGAGCAGTAGTAATTGCTATGTACTGATTTACCTCAAGGTGCAAAATAATTAAATTTGTACATACCCATTTA
2321 CAGAATAAGTTCAGAGACACAGCCCTGCACTTTCTTAGATGCCTTGATTTTCAAACGGAGCTTAGTGCTACTGAACACCA
2401 CGGCCATGGGGCCACCTCAGGACGTTCTTCCCTCCACCATATTTTATTTATTTATAGATGTCCGTTTACAAAGACTATAA
2481 TGAAACCTGGTGTAAACTATCTGATACTTATTTCCTTTCTATTGCTATTTCAATCTAAAGTAGGAGCTTTTGAGAAAACA
2561 GTAAACTAGCTTCCCAATGCTAAAGGGTTGATTCTATATATATTTTTAATAATATTAGATATGCAAAAGTTAAAGTACAA
2641 GGTCTTTAAAATATTGTGTGAGTGTTTGTGTATGTGTATGAAATCACTCTTAACTCTCTTAACTTTTTTAAAACTCGTGG
2721 CATACCAATGTTCAGATTTGCCAAGCTTTCTCTAAGACATGTAGGATGAAATGTTTTTGTGTGTTAATGCATGTATTTAT
2801 AAAGATTTGTTTACTGCTGAGAATCACTAACTCTTGTTTTCATCCCCAAAGTGTTTGTTTCTTCCACATGCTGGAAGGCT
2881 TGGCTTGAGTATACGCTTTCTGGCTTTCCTTTCACAAAGGCACGTTCAAAATTGTTCAGAAAGAAGAATGGTCTCTGACA
2961 GTGAGGTGTGATGCCAGAGCTTTCTGAAGTTTGAGCAGTGTGTGCAGCTCTGCATGTGTGTCCTGACAGAGTCAGATATG
3041 TGAGCCATTAAAAGAACATTGTAATTCAGAGTGTTTATTTAAGTAACTTACATGTCTGAAATTTATTTATGTAGATTCCA
3121 TCATTGTTATCATTTGTAGTGCAAATACATGAACTGTCTTCATTTAGTCCCAACAATTATTTATTTTTAGAAAGTAAATT
3201 TAAAGCCAAGCTGCATTCAACTTTTAAAATAGTGTTCTAATCATAAGATGTGATCATTGTAAGGTCTCTTTTAACTTTCT
3281 GGAAAGTAAATGGTCAAAAGGAATCACATAAAGATTGTTTTACATTTTTAACCTGTATGTACTTAGAGGGTAAGCCCCAG
3361 TTCTCTGGTTTCTAATCATTTTTTGCACATTGATTGTTTCTGTTCTGTAGCTTTTCTTTTGCTCCTTTGGTTTTGGCTTT
3441 GTAGGGGTAAGGTGTCTTCCAATGTTTACTATGTTAGGCTTAAATTAAATTTTAAATTTATTGTCCATTTATATAATATT
3521 TGATACCTTGGTGTAACTTCTCAATACAATTACAATTTTTATGACATTTATAATTGCGATGGTATTTTCTTTTATAATAA
3601 AATCCAAAGTCAATTAAACAAATTGTAGACCTGATATTTTTCATCTATATGAAGTACAAGTCTCTACCTGAGTCTATAAT
3681 GTGAACCATCCTGCCTTTCACATTTGTTTCCTAATTGTTAGAGAAAACTATTTTCTGTAGATGTTATTGTAAGTTGAAAG
3761 AGCAATAAAAGTCTACATATCACGG
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' agAAC---GUCG-AAGGCAGAGGUca 5'
            |||   :||| || :||:||||  
Target 5' ttTTGTGATAGCATTGTGTTTCCAat 3'
 1172 - 1197 128.00 -14.60
2 
miRNA  3' agAACG--UCGAAGGCAGAGGUca 5'
            ||||  |||||   ||||:|  
Target 5' atTTGCCAAGCTT---TCTCTAag 3'
 2736 - 2756 127.00 -14.20
3 
miRNA  3' agaacgucGAAGGC-AGAGGUCa 5'
                  ||  :| ||||:|| 
Target 5' aggaaattCTAATGTTCTCTAGc 3'
 1397 - 1419 126.00 -10.00
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 GSM622572
Method / RBP HITS-CLIP / AGO2
Cell line / Condition mESCs / WT2
Location of target site NM_001033270 | 3UTR | CAGAUUUUUUUGGGGGGUGGGGUAAAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21258322 / GSE25310
CLIP-seq Viewer Link
39 mmu-miR-5114 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT577166 Madd MAP-kinase activating death domain 2 12
MIRT580377 Tmem206 transmembrane protein 206 2 4
MIRT580729 Srrm4 serine/arginine repetitive matrix 4 2 2
MIRT581165 Sec23ip Sec23 interacting protein 2 2
MIRT581310 Rnf150 ring finger protein 150 2 4
MIRT581568 Prtg protogenin 2 2
MIRT582280 Nav2 neuron navigator 2 2 2
MIRT582511 March5 membrane-associated ring finger (C3HC4) 5 2 4
MIRT584183 Cpeb3 cytoplasmic polyadenylation element binding protein 3 2 2
MIRT584252 Cmtm6 CKLF-like MARVEL transmembrane domain containing 6 2 2
MIRT584403 Cd63 CD63 antigen 2 2
MIRT586848 Ikbkg inhibitor of kappaB kinase gamma 2 4
MIRT586939 H2-T24 histocompatibility 2, T region locus 24 2 4
MIRT587266 Fam161b family with sequence similarity 161, member B 2 2
MIRT588386 Zfp113 zinc finger protein 113 2 2
MIRT590219 Dync1li2 dynein, cytoplasmic 1 light intermediate chain 2 2 4
MIRT592159 Paxip1 PAX interacting (with transcription-activation domain) protein 1 2 2
MIRT592188 Nanog Nanog homeobox 2 4
MIRT593309 Rmnd5a required for meiotic nuclear division 5 homolog A 2 2
MIRT594051 1200014J11Rik nuclear cap binding subunit 3 2 2
MIRT594495 Cspg4 chondroitin sulfate proteoglycan 4 2 2
MIRT595572 Mtf1 metal response element binding transcription factor 1 2 2
MIRT597122 Svopl SV2 related protein homolog (rat)-like 2 2
MIRT598947 Ggps1 geranylgeranyl diphosphate synthase 1 2 2
MIRT599498 Ccdc78 coiled-coil domain containing 78 2 2
MIRT601067 Cdc14b CDC14 cell division cycle 14B 2 2
MIRT601902 Padi2 peptidyl arginine deiminase, type II 2 2
MIRT602607 Chrna1 cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle) 2 2
MIRT602771 Armc2 armadillo repeat containing 2 2 2
MIRT602877 4931428F04Rik RIKEN cDNA 4931428F04 gene 2 2
MIRT602958 Xpo7 exportin 7 2 2
MIRT603304 Slc4a7 solute carrier family 4, sodium bicarbonate cotransporter, member 7 2 2
MIRT603315 Slc35d2 solute carrier family 35, member D2 2 2
MIRT603389 Sgol2 shugoshin 2A 2 2
MIRT605052 Efr3b EFR3 homolog B 2 2
MIRT605054 Arhgef39 Rho guanine nucleotide exchange factor (GEF) 39 1 1
MIRT605412 T2 brachyury 2 2 2
MIRT605550 Ppp1r16b protein phosphatase 1, regulatory (inhibitor) subunit 16B 2 2
MIRT606407 Glrx2 glutaredoxin 2 (thioltransferase) 2 2

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