pre-miRNA Information | |
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pre-miRNA | hsa-mir-4260 |
Genomic Coordinates | chr1: 209623444 - 209623510 |
Description | Homo sapiens miR-4260 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||||||||
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Mature miRNA | hsa-miR-4260 | ||||||||||||
Sequence | 11| CUUGGGGCAUGGAGUCCCA |29 | ||||||||||||
Evidence | Experimental | ||||||||||||
Experiments | SOLiD | DRVs in miRNA |
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SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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Human miRNA Tissue Atlas | |
Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | POMGNT1 | ||||||||||||||||||||
Synonyms | GNTI.2, GnT I.2, LGMD2O, MEB, MGAT1.2, RP76, gnT-I.2 | ||||||||||||||||||||
Description | protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-) | ||||||||||||||||||||
Transcript | NM_017739 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on POMGNT1 | |||||||||||||||||||||
3'UTR of POMGNT1 (miRNA target sites are highlighted) |
>POMGNT1|NM_017739|3'UTR 1 GACCTCCTCCAGGACCCTGCGGGGCTGGGTACTGTGTACCCCCAGGCTGGCTAGCCCTTCCCTCCATCCTGTAGGATTTT 81 GTAGATGCTGGTAGGGGCTGGGGCTACCTTGTTTTTAACATGAGACTTAATTACTAACTCCAAGGGGAGGGTTCCCCTGC 161 TCCAACACCCCGTTCCTGAGTTAAAAGTCTATTTATTTACTTCCTTGTTGGAGAAGGGCAGGAGAGTACCTGGGAATCAT 241 TACGATCCCTAGCAGCTCATCCTGCCCTTTGAATACCCTCACTTTCCAGGCCTGGCTCAGAATCTAACCTATTTATTGAC 321 TGTCCTGAGGGCCTTGAAAACAGGCCGAACCTGGAGGGCCTGGATTTCTTTTTGGGCTGGAATGCTGCCCTGAGGGTGGG 401 GCTGGCTCTTACTCAGGAAACTGCTGTGCCCAACCCATGGACAGGCCCAGCTGGGGCCCACATGCTGACACAGACTCACT 481 CAGAGACCCTTAGACACTGGACCAGGCCTCCTCTCAGCCTTCTCTTTGTCCAGATTTCCAAAGCTGGATAAGTTGGTCAT 561 TGATTAAAAAAGGAGAAGCCCTCTGGGGAAAAAAAAAAAAAAAAAA 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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DRVs in gene 3'UTRs | |||||||||||||||||||||
SNPs in gene 3'UTRs |
Experimental Support 1 for Functional miRNA-Target Interaction | |||||||
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miRNA:Target | ---- | ||||||
Validation Method |
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Conditions | HEK293S | ||||||
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 GSM1084064. RNA binding protein: AGO2. Condition:CLIP_noemetine_AbnovaAb
HITS-CLIP data was present in GSM1084065. RNA binding protein: AGO2. Condition:CLIP_emetine_AbnovaAb
... - Karginov FV; Hannon GJ, 2013, Genes & development. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Karginov FV; Hannon GJ - Genes & development, 2013
When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Argonaute 2 (Ago2)/microRNA (miRNA) machinery has been shown to participate in stress-induced translational up-regulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (UTR) and coding sequence (CDS) sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2-binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA sequencing (RNA-seq). Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian miRNAs in mediating the translational component of the stress response.
LinkOut: [PMID: 23824327]
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CLIP-seq Support 1 for dataset GSM1084064 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_noemetine_AbnovaAb |
Location of target site | ENST00000396420.3 | 3UTR | caaaggaggagggagc |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM1084065 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293S / CLIP_emetine_AbnovaAb |
Location of target site | ENST00000396420.3 | 3UTR | caaaggaggagggagc |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23824327 / GSE44404 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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66 hsa-miR-4260 Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT074404 | TNRC6A | trinucleotide repeat containing 6A | ![]() |
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2 | 2 | ||||||
MIRT289774 | PER1 | period circadian clock 1 | ![]() |
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2 | 2 | ||||||
MIRT442576 | HOXD9 | homeobox D9 | ![]() |
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2 | 2 | ||||||
MIRT443878 | CNKSR3 | CNKSR family member 3 | ![]() |
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2 | 2 | ||||||
MIRT449080 | XPO6 | exportin 6 | ![]() |
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2 | 2 | ||||||
MIRT450294 | DRAXIN | dorsal inhibitory axon guidance protein | ![]() |
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2 | 2 | ||||||
MIRT461785 | FXR2 | FMR1 autosomal homolog 2 | ![]() |
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2 | 2 | ||||||
MIRT463931 | WNT10B | Wnt family member 10B | ![]() |
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2 | 2 | ||||||
MIRT464860 | UBB | ubiquitin B | ![]() |
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2 | 8 | ||||||
MIRT467619 | SLC7A5 | solute carrier family 7 member 5 | ![]() |
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2 | 2 | ||||||
MIRT469649 | RAC1 | Rac family small GTPase 1 | ![]() |
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2 | 2 | ||||||
MIRT473421 | MDM4 | MDM4, p53 regulator | ![]() |
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2 | 2 | ||||||
MIRT473646 | MARCKSL1 | MARCKS like 1 | ![]() |
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2 | 2 | ||||||
MIRT474213 | LCOR | ligand dependent nuclear receptor corepressor | ![]() |
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2 | 2 | ||||||
MIRT474335 | KMT2D | lysine methyltransferase 2D | ![]() |
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2 | 2 | ||||||
MIRT474871 | KDELR1 | KDEL endoplasmic reticulum protein retention receptor 1 | ![]() |
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2 | 2 | ||||||
MIRT477440 | ELOVL5 | ELOVL fatty acid elongase 5 | ![]() |
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2 | 2 | ||||||
MIRT478432 | DAZAP2 | DAZ associated protein 2 | ![]() |
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2 | 2 | ||||||
MIRT479851 | CCDC6 | coiled-coil domain containing 6 | ![]() |
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2 | 2 | ||||||
MIRT482507 | ACTB | actin beta | ![]() |
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2 | 2 | ||||||
MIRT485473 | IGF1R | insulin like growth factor 1 receptor | ![]() |
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2 | 8 | ||||||
MIRT485670 | CCDC64 | BICD family like cargo adaptor 1 | ![]() |
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2 | 4 | ||||||
MIRT485902 | PGPEP1 | pyroglutamyl-peptidase I | ![]() |
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2 | 4 | ||||||
MIRT488143 | PRRC2B | proline rich coiled-coil 2B | ![]() |
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2 | 4 | ||||||
MIRT489455 | MSC | musculin | ![]() |
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2 | 2 | ||||||
MIRT509568 | HIST2H2AB | histone cluster 2 H2A family member b | ![]() |
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2 | 4 | ||||||
MIRT513093 | DYNAP | dynactin associated protein | ![]() |
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2 | 2 | ||||||
MIRT513256 | CALM3 | calmodulin 3 | ![]() |
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2 | 2 | ||||||
MIRT514356 | UBBP4 | ubiquitin B pseudogene 4 | ![]() |
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2 | 6 | ||||||
MIRT522019 | PAQR3 | progestin and adipoQ receptor family member 3 | ![]() |
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2 | 4 | ||||||
MIRT523164 | HIST3H3 | histone cluster 3 H3 | ![]() |
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2 | 2 | ||||||
MIRT523297 | HIST1H1B | histone cluster 1 H1 family member b | ![]() |
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2 | 2 | ||||||
MIRT524782 | BAG5 | BCL2 associated athanogene 5 | ![]() |
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2 | 2 | ||||||
MIRT530921 | SCIN | scinderin | ![]() |
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2 | 2 | ||||||
MIRT533302 | USP44 | ubiquitin specific peptidase 44 | ![]() |
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2 | 2 | ||||||
MIRT552782 | YIPF4 | Yip1 domain family member 4 | ![]() |
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2 | 4 | ||||||
MIRT553981 | SRPR | SRP receptor alpha subunit | ![]() |
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2 | 2 | ||||||
MIRT563126 | ZNF215 | zinc finger protein 215 | ![]() |
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2 | 2 | ||||||
MIRT569025 | IL21R | interleukin 21 receptor | ![]() |
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2 | 2 | ||||||
MIRT573413 | RPL18A | ribosomal protein L18a | ![]() |
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2 | 2 | ||||||
MIRT574877 | Dnajc6 | DnaJ heat shock protein family (Hsp40) member C6 | ![]() |
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2 | 3 | ||||||
MIRT607538 | GLI2 | GLI family zinc finger 2 | ![]() |
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2 | 2 | ||||||
MIRT607682 | MAPK10 | mitogen-activated protein kinase 10 | ![]() |
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2 | 3 | ||||||
MIRT623791 | GK5 | glycerol kinase 5 (putative) | ![]() |
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2 | 2 | ||||||
MIRT628834 | FAM151B | family with sequence similarity 151 member B | ![]() |
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2 | 2 | ||||||
MIRT635547 | LEPREL1 | prolyl 3-hydroxylase 2 | ![]() |
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2 | 2 | ||||||
MIRT635698 | NMNAT2 | nicotinamide nucleotide adenylyltransferase 2 | ![]() |
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2 | 2 | ||||||
MIRT635906 | ARPC1B | actin related protein 2/3 complex subunit 1B | ![]() |
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2 | 2 | ||||||
MIRT649985 | MSI1 | musashi RNA binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT654900 | POMGNT1 | protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-) | ![]() |
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2 | 2 | ||||||
MIRT655116 | PHF7 | PHD finger protein 7 | ![]() |
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2 | 2 | ||||||
MIRT658958 | DNAJC6 | DnaJ heat shock protein family (Hsp40) member C6 | ![]() |
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2 | 3 | ||||||
MIRT659665 | CDC42EP4 | CDC42 effector protein 4 | ![]() |
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2 | 2 | ||||||
MIRT668946 | CNBP | CCHC-type zinc finger nucleic acid binding protein | ![]() |
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2 | 2 | ||||||
MIRT691164 | APOL6 | apolipoprotein L6 | ![]() |
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2 | 2 | ||||||
MIRT692696 | MEAF6 | MYST/Esa1 associated factor 6 | ![]() |
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2 | 2 | ||||||
MIRT693245 | HBS1L | HBS1 like translational GTPase | ![]() |
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2 | 2 | ||||||
MIRT695203 | SCAMP3 | secretory carrier membrane protein 3 | ![]() |
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2 | 2 | ||||||
MIRT701957 | MINK1 | misshapen like kinase 1 | ![]() |
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2 | 2 | ||||||
MIRT706802 | APOL4 | apolipoprotein L4 | ![]() |
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2 | 2 | ||||||
MIRT716899 | CACNB2 | calcium voltage-gated channel auxiliary subunit beta 2 | ![]() |
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2 | 2 | ||||||
MIRT717632 | HLX | H2.0 like homeobox | ![]() |
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2 | 2 | ||||||
MIRT719052 | ZNF281 | zinc finger protein 281 | ![]() |
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2 | 2 | ||||||
MIRT722973 | GDE1 | glycerophosphodiester phosphodiesterase 1 | ![]() |
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2 | 2 | ||||||
MIRT723643 | RPTN | repetin | ![]() |
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2 | 2 | ||||||
MIRT734708 | NR3C2 | nuclear receptor subfamily 3 group C member 2 | ![]() |
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4 | 0 |
miRNA-Drug Associations | ||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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