pre-miRNA Information | |
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pre-miRNA | mmu-mir-669m-1 |
Genomic Coordinates | chr2: 10512790 - 10512887 |
Synonyms | mmu-mir-669m-1, Mir669m-1 |
Description | Mus musculus miR-669m-1 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
pre-miRNA | mmu-mir-669m-2 |
Genomic Coordinates | chr2: 10513434 - 10513531 |
Synonyms | mmu-mir-669m-2, Mir669m-2 |
Description | Mus musculus miR-669m-2 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |
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Mature miRNA | mmu-miR-669m-5p |
Sequence | 25| UGUGUGCAUGUGCAUGUGUGUAU |47 |
Evidence | Experimental |
Experiments | Illumina |
Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | Neurod2 | ||||||||||||||||||||
Synonyms | Ndrf, bHLHa1 | ||||||||||||||||||||
Description | neurogenic differentiation 2 | ||||||||||||||||||||
Transcript | NM_010895 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on Neurod2 | |||||||||||||||||||||
3'UTR of Neurod2 (miRNA target sites are highlighted) |
>Neurod2|NM_010895|3'UTR 1 GACCTCGCGCCGACCCCTTTCTTTTTCTTTGCCTTTGTCCGGCCCCTTAGCCCCAGCCCCACGAGCTCAGGGGCTCCCAC 81 CGACTCCAGAGCCGGGCGCTCGAGCGCGGGCCGCCGGTTCTGCAGCTCTCCAGAGCGGCGTGCTCTCTTACCTGTGGGTG 161 GCCCGTCCCAGGGGCCTCGCTTGCCTCTGGGGACTCGCCTTCTCTCTCTCCCCAGCGGGCTTCCTCCTCCCTTCTCTCGT 241 GGAGAGCATCTCTGGGGATCTCCCGCCAGGCCCTCCCAAGAGACTTCCTCCACATTCCCAAACTTGGGTTTTCTCTCCCC 321 ACCTCCCAACAGGCCAGAGGCAGTTGGTAAGGGGCTGCTGAGTCTCGGGATAGTGTCTCCCCCACTTATAGTTACTTTAA 401 AAAAACAAAAACAAAACAGACACAGAGCTTCCCAGGCCGAAAAGAGTTGGTATCTCTTCCTTCTCGAAGAGGCCACAGCC 481 AGGGAGCCCAAACGCCTTCACCCTAACACGAATCTCCGCGTTTTTTATTTTTTATTTTGGTGGGAGGGGATGTGGATTGA 561 GAGGAAAGAGAGAGGCCAAGCCAATTTGTAACTAGAACCATTTTTCCTTTTCCCTTTTTAAAGAAAACAAACAAACATAC 641 AAAAGGAAAAAAAAAAAAGAAAGAAAGAAAGAAAAAGGAAAAAATACTGAGAGGCAACGGAGGCCGAACTCAGAGTCCGG 721 ATCGGAGAGAAAACGCATTAAGAACTTTTAGAAGCAATAAAAGGCAAATAATAATAATAAAAAATACTACCAATAATAAT 801 TTTTAAAAAGACACAAATATCTATGCAAGGAGGTTCTGACTGAGCCTAGCAGCCTGACCTGGGTGCTCCTCGGGTCTGCT 881 GGCTGCCCCGCCCACGCGCGGATCTGTGCACTTTGGTGAAGTGGGGGCCCGCGCCGCCCCTCCCCCCCCCCAGTTTCTTA 961 CAATCAATGACTCGGAGATTTGGAACCCCAGTGCCACTGCCCTCCTCCCGCCCTGCCCCGTTGTGCGTCATACTGTTTTC 1041 TAAAAACCTGTTTCCAAATTTGTATGGAATGGCAAACTGTTAGGGGGGGTCGGTTTGGGGAGGGAGGGTTTGCATGAGAG 1121 ACACCACACACGCACACACACGCGCGCGCGCGAACACGCACACACACACACACACACACACACACACACACACACCACAC 1201 CGCACGCACACGCAGGCCCCGGGCGTCCGGGGACAGAAGGAGCTGTCTACTGGTACCTCCTCTCTATAGGCACTCTGGTC 1281 CGTCCCCTCTTGGGGTAAGGTGGAGGAGCCCAGACCTGGGAACAGCCTTACCCTTGTCCAGACTGTGCCTCCGTGGGCGC 1361 CAAGCTCCTGGTGATTTCTGGTGGCTAGAGAGGGTTGTTTTGGGTTTTTGTTTGTTTGTTTGTTGGGGGGGTTGTTGTTG 1441 CTTTTGTTTTTTGTTTTGTTTTGTGTTTCGGTTCTAGGCTCCTCCTGACTTTTGTCATCCAGTGAGCTGGGAGAACTGAG 1521 GGCTCCTCTGGAGGTTCCCCTCGCAAGAGGCAACAGGTGAAGCTCCCCCCCCACCGGAGGCAGGGAACCAGGCACCCAAA 1601 CACACGATGCAAAAAACGCAAACCCACAGGCGACACACCCCACACACGCAATTTTACCTTCCTCTTGTAGCGAAGATGAA 1681 ACTCCTGTCGGACACCCGAAGTGCATTGCGTGTTTCTGTTGAGTTTAATGACGATTAATAAATATTTATGTAAATGAGAT 1761 GCAAAGCA Target sites
Provided by authors
Predicted by miRanda
DRVs
SNPs
DRVs & SNPs
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miRNA-target interactions (Predicted by miRanda) |
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Experimental Support 1 for Functional miRNA-Target Interaction | |||||||
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miRNA:Target | ---- | ||||||
Validation Method |
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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. |
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miRNA-target interactions (Provided by authors) |
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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]
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Experimental Support 2 for Functional miRNA-Target Interaction | |||||||
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miRNA:Target | ---- | ||||||
Validation Method |
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Conditions | Liver | ||||||
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 ERR266286. RNA binding protein: AGO2. Condition:A_Liver partial hapatectomy 1h
... - Schug J; McKenna LB; Walton G; Hand N; et al., 2013, BMC genomics. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Schug J; McKenna LB; Walton G; Hand N; et al. - BMC genomics, 2013
BACKGROUND: Validation of physiologic miRNA targets has been met with significant challenges. We employed HITS-CLIP to identify which miRNAs participate in liver regeneration, and to identify their target mRNAs. RESULTS: miRNA recruitment to the RISC is highly dynamic, changing more than five-fold for several miRNAs. miRNA recruitment to the RISC did not correlate with changes in overall miRNA expression for these dynamically recruited miRNAs, emphasizing the necessity to determine miRNA recruitment to the RISC in order to fully assess the impact of miRNA regulation. We incorporated RNA-seq quantification of total mRNA to identify expression-weighted Ago footprints, and developed a microRNA regulatory element (MRE) prediction algorithm that represents a greater than 20-fold refinement over computational methods alone. These high confidence MREs were used to generate candidate 'competing endogenous RNA' (ceRNA) networks. CONCLUSION: HITS-CLIP analysis provide novel insights into global miRNA:mRNA relationships in the regenerating liver.
LinkOut: [PMID: 23597149]
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CLIP-seq Support 1 for dataset GSM622572 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | mESCs / WT2 |
Location of target site | NM_010895 | 3UTR | ACGCACACACACACACACACACACACACAC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 21258322 / GSE25310 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset ERR266286 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | Liver / A_Liver partial hapatectomy 1h |
Location of target site | NM_010895 | 3UTR | CACGCACACACACACACACACACACACACACACACA |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23597149 / E-MTAB-1612 |
CLIP-seq Viewer | Link |
87 mmu-miR-669m-5p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT577337 | Zfp157 | zinc finger protein 157 | ![]() |
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2 | 2 | ||||||
MIRT577486 | Tns4 | tensin 4 | ![]() |
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2 | 6 | ||||||
MIRT578069 | Oxsm | 3-oxoacyl-ACP synthase, mitochondrial | ![]() |
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2 | 2 | ||||||
MIRT578341 | Ltf | lactotransferrin | ![]() |
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2 | 2 | ||||||
MIRT578746 | Gm4841 | predicted gene 4841 | ![]() |
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2 | 4 | ||||||
MIRT578823 | Fermt1 | fermitin family member 1 | ![]() |
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2 | 2 | ||||||
MIRT579125 | Chrnd | cholinergic receptor, nicotinic, delta polypeptide | ![]() |
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2 | 2 | ||||||
MIRT579138 | Chrna1 | cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle) | ![]() |
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2 | 2 | ||||||
MIRT579308 | BC021785 | major facilitator superfamily domain containing 4B5 | ![]() |
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2 | 4 | ||||||
MIRT579418 | Agtrap | angiotensin II, type I receptor-associated protein | ![]() |
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2 | 2 | ||||||
MIRT579730 | Zfp92 | zinc finger protein 92 | ![]() |
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2 | 4 | ||||||
MIRT579980 | Wrn | Werner syndrome RecQ like helicase | ![]() |
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2 | 4 | ||||||
MIRT581036 | Sim1 | single-minded homolog 1 (Drosophila) | ![]() |
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2 | 4 | ||||||
MIRT581534 | Pten | phosphatase and tensin homolog | ![]() |
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2 | 2 | ||||||
MIRT582315 | Nab1 | Ngfi-A binding protein 1 | ![]() |
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2 | 4 | ||||||
MIRT582845 | Itga9 | integrin alpha 9 | ![]() |
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2 | 4 | ||||||
MIRT582975 | Igf2 | insulin-like growth factor 2 | ![]() |
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2 | 4 | ||||||
MIRT583471 | Foxk1 | forkhead box K1 | ![]() |
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2 | 4 | ||||||
MIRT584664 | B4galt6 | UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6 | ![]() |
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2 | 4 | ||||||
MIRT585223 | Zfp488 | zinc finger protein 488 | ![]() |
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2 | 4 | ||||||
MIRT585300 | Zfp26 | zinc finger protein 26 | ![]() |
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2 | 2 | ||||||
MIRT585313 | Zfp248 | zinc finger protein 248 | ![]() |
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2 | 4 | ||||||
MIRT585836 | Slc6a17 | solute carrier family 6 (neurotransmitter transporter), member 17 | ![]() |
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2 | 4 | ||||||
MIRT586076 | Rhobtb1 | Rho-related BTB domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT586328 | Pgm5 | phosphoglucomutase 5 | ![]() |
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2 | 4 | ||||||
MIRT587380 | Dzip3 | DAZ interacting protein 3, zinc finger | ![]() |
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2 | 2 | ||||||
MIRT587614 | Cml2 | N-acetyltransferase 8 (GCN5-related) family member 2 | ![]() |
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2 | 2 | ||||||
MIRT587630 | Clec7a | C-type lectin domain family 7, member a | ![]() |
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2 | 8 | ||||||
MIRT587724 | Cd28 | CD28 antigen | ![]() |
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2 | 2 | ||||||
MIRT587756 | Cd200r1 | CD200 receptor 1 | ![]() |
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2 | 2 | ||||||
MIRT588014 | Akap7 | A kinase (PRKA) anchor protein 7 | ![]() |
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2 | 2 | ||||||
MIRT588297 | 1700019G17Rik | N-acetyltransferase 8 (GCN5-related) family member 4 | ![]() |
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2 | 2 | ||||||
MIRT588558 | Uhrf1bp1l | UHRF1 (ICBP90) binding protein 1-like | ![]() |
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2 | 2 | ||||||
MIRT588688 | Tet2 | tet methylcytosine dioxygenase 2 | ![]() |
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2 | 2 | ||||||
MIRT588895 | Slc1a2 | solute carrier family 1 (glial high affinity glutamate transporter), member 2 | ![]() |
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2 | 4 | ||||||
MIRT589020 | Rnf11 | ring finger protein 11 | ![]() |
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2 | 2 | ||||||
MIRT589098 | Rasal2 | RAS protein activator like 2 | ![]() |
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2 | 4 | ||||||
MIRT590108 | Etv3 | ets variant 3 | ![]() |
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2 | 2 | ||||||
MIRT590173 | Elovl6 | ELOVL family member 6, elongation of long chain fatty acids (yeast) | ![]() |
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2 | 4 | ||||||
MIRT590925 | Tacr2 | tachykinin receptor 2 | ![]() |
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2 | 2 | ||||||
MIRT591064 | Ptpre | protein tyrosine phosphatase, receptor type, E | ![]() |
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2 | 4 | ||||||
MIRT591145 | Nsun3 | NOL1/NOP2/Sun domain family member 3 | ![]() |
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2 | 2 | ||||||
MIRT591206 | Mdm2 | transformed mouse 3T3 cell double minute 2 | ![]() |
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2 | 2 | ||||||
MIRT591428 | Car10 | carbonic anhydrase 10 | ![]() |
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2 | 4 | ||||||
MIRT591504 | Acot2 | acyl-CoA thioesterase 2 | ![]() |
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2 | 4 | ||||||
MIRT591558 | Zfp449 | zinc finger protein 449 | ![]() |
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2 | 2 | ||||||
MIRT591634 | Ubtf | upstream binding transcription factor, RNA polymerase I | ![]() |
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2 | 4 | ||||||
MIRT591949 | Ceacam1 | carcinoembryonic antigen-related cell adhesion molecule 1 | ![]() |
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2 | 2 | ||||||
MIRT591975 | Ap1ar | adaptor-related protein complex 1 associated regulatory protein | ![]() |
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2 | 2 | ||||||
MIRT592039 | Tnfrsf13c | tumor necrosis factor receptor superfamily, member 13c | ![]() |
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2 | 2 | ||||||
MIRT592090 | Smo | smoothened, frizzled class receptor | ![]() |
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2 | 2 | ||||||
MIRT592111 | Slc25a12 | solute carrier family 25 (mitochondrial carrier, Aralar), member 12 | ![]() |
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2 | 2 | ||||||
MIRT592172 | Oxtr | oxytocin receptor | ![]() |
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2 | 2 | ||||||
MIRT592215 | Map3k7 | mitogen-activated protein kinase kinase kinase 7 | ![]() |
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2 | 2 | ||||||
MIRT592225 | Magee2 | melanoma antigen, family E, 2 | ![]() |
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2 | 6 | ||||||
MIRT592248 | Lcp2 | lymphocyte cytosolic protein 2 | ![]() |
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2 | 4 | ||||||
MIRT592265 | Kcnj16 | potassium inwardly-rectifying channel, subfamily J, member 16 | ![]() |
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2 | 2 | ||||||
MIRT592389 | Trp53i11 | transformation related protein 53 inducible protein 11 | ![]() |
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2 | 6 | ||||||
MIRT592424 | Stxbp5l | syntaxin binding protein 5-like | ![]() |
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2 | 2 | ||||||
MIRT592444 | Snx12 | sorting nexin 12 | ![]() |
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2 | 2 | ||||||
MIRT592518 | Npr3 | natriuretic peptide receptor 3 | ![]() |
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2 | 2 | ||||||
MIRT592624 | Mbnl3 | muscleblind like splicing factor 3 | ![]() |
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2 | 4 | ||||||
MIRT592705 | Gfra2 | glial cell line derived neurotrophic factor family receptor alpha 2 | ![]() |
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2 | 2 | ||||||
MIRT592745 | Epas1 | endothelial PAS domain protein 1 | ![]() |
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2 | 2 | ||||||
MIRT592762 | Dmd | dystrophin, muscular dystrophy | ![]() |
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2 | 4 | ||||||
MIRT592846 | Akap2 | A kinase (PRKA) anchor protein 2 | ![]() |
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2 | 2 | ||||||
MIRT592988 | Cacna2d2 | calcium channel, voltage-dependent, alpha 2/delta subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT593001 | Bend4 | BEN domain containing 4 | ![]() |
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2 | 2 | ||||||
MIRT593230 | Fndc3a | fibronectin type III domain containing 3A | ![]() |
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2 | 2 | ||||||
MIRT593419 | Neurod2 | neurogenic differentiation 2 | ![]() |
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2 | 4 | ||||||
MIRT593451 | Rab11fip1 | RAB11 family interacting protein 1 (class I) | ![]() |
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2 | 2 | ||||||
MIRT593485 | Havcr2 | hepatitis A virus cellular receptor 2 | ![]() |
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2 | 2 | ||||||
MIRT593515 | Csf2ra | colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage) | ![]() |
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2 | 2 | ||||||
MIRT594036 | 2810006K23Rik | RIKEN cDNA 2810006K23 gene | ![]() |
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2 | 2 | ||||||
MIRT594128 | Fam104a | family with sequence similarity 104, member A | ![]() |
1 | 1 | |||||||
MIRT595669 | Rxrb | retinoid X receptor beta | ![]() |
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2 | 2 | ||||||
MIRT595702 | Fndc7 | fibronectin type III domain containing 7 | ![]() |
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2 | 2 | ||||||
MIRT596266 | Bnc2 | basonuclin 2 | ![]() |
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2 | 2 | ||||||
MIRT596280 | Slc6a8 | solute carrier family 6 (neurotransmitter transporter, creatine), member 8 | ![]() |
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2 | 2 | ||||||
MIRT598760 | Gpr68 | G protein-coupled receptor 68 | ![]() |
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2 | 2 | ||||||
MIRT601113 | Btrc | beta-transducin repeat containing protein | ![]() |
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2 | 2 | ||||||
MIRT601203 | Arhgef9 | CDC42 guanine nucleotide exchange factor (GEF) 9 | ![]() |
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2 | 2 | ||||||
MIRT603153 | Ubxn8 | UBX domain protein 8 | ![]() |
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2 | 2 | ||||||
MIRT603194 | Trim65 | tripartite motif-containing 65 | ![]() |
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2 | 2 | ||||||
MIRT604580 | Trim71 | tripartite motif-containing 71 | ![]() |
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2 | 2 | ||||||
MIRT605450 | St18 | suppression of tumorigenicity 18 | ![]() |
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2 | 2 | ||||||
MIRT605589 | Ncam1 | neural cell adhesion molecule 1 | ![]() |
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2 | 2 |