pre-miRNA Information | |
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pre-miRNA | hsa-mir-548al |
Genomic Coordinates | chr11: 74399237 - 74399333 |
Description | Homo sapiens miR-548al stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | ||||||||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-548al | |||||||||||||||||||||||||||||||||||
Sequence | 65| AACGGCAAUGACUUUUGUACCA |86 | |||||||||||||||||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||||||||||||||||
Experiments | Illumina | |||||||||||||||||||||||||||||||||||
Editing Events in miRNAs |
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SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | TRIM4 | ||||||||||||||||||||
Synonyms | RNF87 | ||||||||||||||||||||
Description | tripartite motif containing 4 | ||||||||||||||||||||
Transcript | NM_033017 | ||||||||||||||||||||
Other Transcripts | NM_033091 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on TRIM4 | |||||||||||||||||||||
3'UTR of TRIM4 (miRNA target sites are highlighted) |
>TRIM4|NM_033017|3'UTR 1 GGCTTTTCTTCCCCTGACCAAAACTCCTTCCCTGTAGTCCAGCTGAGGGACACACATCCCTGGGCCCTCTTCTGCCCTTC 81 ATGTCTCTATCCTGGATGGTCCATCTTCTGGGTCTCCCTAACGGTACCGTTTGGTATCTGCCCTTTGTGTGCTTCACAAG 161 AGGCAGTCCCATGGGAGGTGGGTCTGGCCAATGGAGATGGGACAGGAAATTTTCCAAGACGCTTTTGGGAAATCTTTTTG 241 TAGCTTTTAAAGAGATGTGCGGGGAAGACATATGGATGTTAGCAGCCATATTGGAACTGAGAACACAGGAATGGTGGAAA 321 GGTAGAAGAAACAGAGTTTTTGTTGCCGTTGTGAAATTGTTGAAATTTCCTTCATGCCAAGCTTCTTGTTATATGAGATA 401 ATTACGCCCTTATTGTATAAGACAATTTTAGTTGTATTTGGTTACTTGCAGCCTGAAGTACCGTAACTGCACTAAAGGGA 481 CGTAGTGTGAACATCCCGCAGTATAGGCTTAAGTCACTTTTGTGAAATTTGACAAAGGCATAGAATCTTTTTCTATCCAG 561 TCAGGCATTGCCTATTCTTTCCAGTAACTACTGATTCCCCCACTTTTCTGTCTTAGAAAATTGTGGGAATCCCCCCTCAC 641 TCTGCCTATGTTGCACTCTCTCTCTTCCCAACCATAACTCTGCCCTCAGCTATTAACTGTGCTGTGTATTTATCAAGTTG 721 GTATGTTGTATGTACAGTGTTATTCATGTCATCATGAGAATGTTGAACGCTTGTTAAATATCTTTTGCTAGCCTCTTCAT 801 ATGCTGTTGCATATGACTCTCATCACAACTCAGTGAGATGGAAAGTCAAATCCTATTTGTACAAATGAGAAAACTGAACT 881 CTTTAGAGTAACTAGCTCAGTATTGGCCAGCTGGTAAATGGCAGTGTTGGGATTAAAATCCAGTTCTTATCTACTCTCCC 961 TTTATTCAGAAGCATTTATTGGATGTTGATCTTTGTTTCAGGTTTTGATTTTGTTACTTTTTTATACTGTGTATATTTTC 1041 CTCAGTCTACCCTTCTGCTCTAGATTGTCTGGACTCAGGAGATTGTGGCAGTTACTGGATAGTTATTTTTAAGATAATGA 1121 TTGCTTTTCTCTGTTTATATAAGTCATGTGTACTTATTGTAGAAAGTTTGTAAGATGCAAAAAGTATAAAAATTAAAGTT 1201 ATGCACTACTAACATTTCAATATATTTTCTCCCAGATTTTCAGTAAAGACTTTCAGGCAGTGATTTAACGAGGATTTTAT 1281 TTTAACTTATATTTTAGTTTAAGGGGAACACGTGCAGGTTTGTTCTATAGATCAATTACATGTCACAGGGGTTTGGTGTA 1361 CATATTATTTCATTACCCAGGTAATAAGCATAGTACCCAATAGATACTTTTTTGATACCCCACCCTCCTCCACCCTCTAC 1441 CCTCAAGTAGTCCCTGGTGTCTGTTGTTCCCTTTTTTGTGTCCATGGGTACTCAATGTTTAGCTCTCCCTTATACGTGAG 1521 AACATGTGATGTTTGGTTTTCTGTTCATGTGTTGGTTTGCTTAGGGTAATGGCCTCCAGCTCCATCCATGTTGCTGCAAA 1601 GACATGATCTCATTCTTTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTACTATGTTTTCTTTATCCAGTCTACTG 1681 TTGATGGGCATTTAGGTTGATTCCATGTCTTTGCTATTGTGAATAGTGCTGCAATGAATATATACATGCATATGTC 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 | hESCs (WA-09) | ||||||
Disease | 89122.0 | ||||||
Location of target site | 3'UTR | ||||||
Tools used in this research | TargetScan , miRTarCLIP , Piranha | ||||||
Original Description (Extracted from the article) |
...
"PAR-CLIP data was present in SRR359787. RNA binding protein: AGO2. Condition:4-thiouridine
... - Lipchina I; Elkabetz Y; Hafner M; Sheridan et al., 2011, Genes & development. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Lipchina I; Elkabetz Y; Hafner M; Sheridan et al. - Genes & development, 2011
MicroRNAs are important regulators in many cellular processes, including stem cell self-renewal. Recent studies demonstrated their function as pluripotency factors with the capacity for somatic cell reprogramming. However, their role in human embryonic stem (ES) cells (hESCs) remains poorly understood, partially due to the lack of genome-wide strategies to identify their targets. Here, we performed comprehensive microRNA profiling in hESCs and in purified neural and mesenchymal derivatives. Using a combination of AGO cross-linking and microRNA perturbation experiments, together with computational prediction, we identified the targets of the miR-302/367 cluster, the most abundant microRNAs in hESCs. Functional studies identified novel roles of miR-302/367 in maintaining pluripotency and regulating hESC differentiation. We show that in addition to its role in TGF-beta signaling, miR-302/367 promotes bone morphogenetic protein (BMP) signaling by targeting BMP inhibitors TOB2, DAZAP2, and SLAIN1. This study broadens our understanding of microRNA function in hESCs and is a valuable resource for future studies in this area.
LinkOut: [PMID: 22012620]
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CLIP-seq Support 1 for dataset SRR359787 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | hESCs (WA-09) / 4-thiouridine, RNase T1 |
Location of target site | ENST00000355947.2 | 3UTR | UGCCGUUGUGAAAUUGUUGAAAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 22012620 / SRX103431 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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15 hsa-miR-548al Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT100248 | MRPS18B | mitochondrial ribosomal protein S18B | 2 | 2 | ||||||||
MIRT466864 | STX6 | syntaxin 6 | 2 | 2 | ||||||||
MIRT472971 | MSANTD3 | Myb/SANT DNA binding domain containing 3 | 2 | 2 | ||||||||
MIRT477531 | EIF4G2 | eukaryotic translation initiation factor 4 gamma 2 | 2 | 5 | ||||||||
MIRT483200 | PIP4K2A | phosphatidylinositol-5-phosphate 4-kinase type 2 alpha | 2 | 2 | ||||||||
MIRT496727 | NKD2 | naked cuticle homolog 2 | 2 | 2 | ||||||||
MIRT504947 | ZNRF2 | zinc and ring finger 2 | 2 | 6 | ||||||||
MIRT529248 | TRIM4 | tripartite motif containing 4 | 2 | 2 | ||||||||
MIRT529477 | THUMPD3 | THUMP domain containing 3 | 2 | 2 | ||||||||
MIRT576335 | Rapgefl1 | Rap guanine nucleotide exchange factor (GEF)-like 1 | 2 | 5 | ||||||||
MIRT607473 | RAPGEFL1 | Rap guanine nucleotide exchange factor like 1 | 2 | 7 | ||||||||
MIRT629228 | FAM186A | family with sequence similarity 186 member A | 2 | 2 | ||||||||
MIRT651501 | WT1 | Wilms tumor 1 | 2 | 2 | ||||||||
MIRT662296 | SLC29A4 | solute carrier family 29 member 4 | 2 | 2 | ||||||||
MIRT688897 | C1GALT1 | core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1 | 2 | 2 |
miRNA-Drug Associations | ||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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