pre-miRNA Information | |
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pre-miRNA | hsa-mir-28 |
Genomic Coordinates | chr3: 188688781 - 188688866 |
Synonyms | MIRN28, hsa-mir-28, miR-28, MIR28 |
Description | Homo sapiens miR-28 stem-loop |
Comment | None |
RNA Secondary Structure | |
Associated Diseases |
Mature miRNA Information | ||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-28-5p | |||||||||||||||||||||||||||
Sequence | 14| AAGGAGCUCACAGUCUAUUGAG |35 | |||||||||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||||||||
Experiments | Cloned | |||||||||||||||||||||||||||
Editing Events in miRNAs |
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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 | |
miRNAs in Extracellular Vesicles |
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Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | TUFM | ||||||||||||||||||||
Synonyms | COXPD4, EF-TuMT, EFTU, P43 | ||||||||||||||||||||
Description | Tu translation elongation factor, mitochondrial | ||||||||||||||||||||
Transcript | NM_003321 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on TUFM | |||||||||||||||||||||
3'UTR of TUFM (miRNA target sites are highlighted) |
>TUFM|NM_003321|3'UTR
1 GTGTGCAGATCTCTGCTCAGCTTCCCTTGCGTTTAAGGCCTGCCCTAGCCAGGGCTCCCTCCTGCTTCCAGTACCCTCTC
81 ATGGCATAGGCTGCAACCCAGCAGAGGGCAGCTAGATGGACATTTCCCCTGCTCGGAAGGGTTGGCCTGCCTGGCTGGGG
161 AGGTCAGTAAACTTTGAATAGTAAGCCAGCCTGTGTCCTGTGTCCTTTGTGCAAATTGGAGAGGATAGGGGAGGACAAAA
241 AGGGTGTTGAACCCCAGACAGATGGGGAGCTTGTGAGATCCCAGAGCAGTTTTAACGGATAAATCAAGTCCAGTGAGCTT
321 AGTGATTGCCTAGACACAGTAGGATGCCGTTATTCAGCCTCCTGGGAGATAGTGGGAAAGAATGTTCTATCGCTCTGGAG
401 CCAGCATGGCTTCAGCTCAGGTGCCAAACCCATCTTGTTTCCTCGGAATACTAAGTGAATGTCTAGCATCCATTCACATT
481 CTGTGGGAACAGGGACTGGACAGGCATACCTCAGATGCTGTAGGTTTGCTTCCAGACTACCACAATAAAGCAGGTCACAA
561 ATTTAAAAAAAAAAAAAAAAAA
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 | Flp-In T-REx 293-hAGO1 cells | ||||||
Location of target site | CDS | ||||||
Original Description (Extracted from the article) |
...
Validation of interactions identified by CLASH suppports their reliability.
... - Helwak A; Kudla G; Dudnakova T; Tollervey D, 2013, Cell. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Helwak A; Kudla G; Dudnakova T; Tollervey D - Cell, 2013
MicroRNAs (miRNAs) play key roles in gene regulation, but reliable bioinformatic or experimental identification of their targets remains difficult. To provide an unbiased view of human miRNA targets, we developed a technique for ligation and sequencing of miRNA-target RNA duplexes associated with human AGO1. Here, we report data sets of more than 18,000 high-confidence miRNA-mRNA interactions. The binding of most miRNAs includes the 5' seed region, but around 60% of seed interactions are noncanonical, containing bulged or mismatched nucleotides. Moreover, seed interactions are generally accompanied by specific, nonseed base pairing. 18% of miRNA-mRNA interactions involve the miRNA 3' end, with little evidence for 5' contacts, and some of these were functionally validated. Analyses of miRNA:mRNA base pairing showed that miRNA species systematically differ in their target RNA interactions, and strongly overrepresented motifs were found in the interaction sites of several miRNAs. We speculate that these affect the response of RISC to miRNA-target binding.
LinkOut: [PMID: 23622248]
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MiRNA-Target Expression Profile | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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MiRNA-Target Expression Profile (TCGA) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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82 hsa-miR-28-5p Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT000595 | CDKN1A | cyclin dependent kinase inhibitor 1A | 4 | 1 | ||||||||
MIRT006402 | MPL | MPL proto-oncogene, thrombopoietin receptor | 3 | 1 | ||||||||
MIRT006411 | N4BP1 | NEDD4 binding protein 1 | 1 | 1 | ||||||||
MIRT006414 | OTUB1 | OTU deubiquitinase, ubiquitin aldehyde binding 1 | 1 | 1 | ||||||||
MIRT006416 | TEX261 | testis expressed 261 | 1 | 1 | ||||||||
MIRT006418 | MAPK1 | mitogen-activated protein kinase 1 | 1 | 1 | ||||||||
MIRT006419 | E2F6 | E2F transcription factor 6 | 1 | 1 | ||||||||
MIRT049989 | ZCCHC3 | zinc finger CCHC-type containing 3 | 1 | 1 | ||||||||
MIRT049990 | TPM4 | tropomyosin 4 | 1 | 1 | ||||||||
MIRT049991 | TULP4 | tubby like protein 4 | 1 | 1 | ||||||||
MIRT049992 | SNX1 | sorting nexin 1 | 1 | 1 | ||||||||
MIRT049993 | IMPDH1 | inosine monophosphate dehydrogenase 1 | 1 | 1 | ||||||||
MIRT049994 | AAAS | aladin WD repeat nucleoporin | 1 | 1 | ||||||||
MIRT049995 | CENPV | centromere protein V | 1 | 1 | ||||||||
MIRT049996 | NRN1 | neuritin 1 | 1 | 1 | ||||||||
MIRT049997 | GEMIN4 | gem nuclear organelle associated protein 4 | 1 | 1 | ||||||||
MIRT049998 | ZBTB47 | zinc finger and BTB domain containing 47 | 1 | 1 | ||||||||
MIRT049999 | UNG | uracil DNA glycosylase | 1 | 1 | ||||||||
MIRT050000 | CNN3 | calponin 3 | 1 | 1 | ||||||||
MIRT050001 | KLHL12 | kelch like family member 12 | 1 | 1 | ||||||||
MIRT050002 | TLK1 | tousled like kinase 1 | 1 | 1 | ||||||||
MIRT050003 | SREBF2 | sterol regulatory element binding transcription factor 2 | 4 | 1 | ||||||||
MIRT050004 | RAB36 | RAB36, member RAS oncogene family | 1 | 1 | ||||||||
MIRT050005 | ZNF106 | zinc finger protein 106 | 1 | 1 | ||||||||
MIRT050006 | SETD7 | SET domain containing lysine methyltransferase 7 | 1 | 1 | ||||||||
MIRT050007 | DENND4B | DENN domain containing 4B | 1 | 1 | ||||||||
MIRT050008 | CS | citrate synthase | 1 | 1 | ||||||||
MIRT050009 | CD276 | CD276 molecule | 1 | 1 | ||||||||
MIRT050010 | TUFM | Tu translation elongation factor, mitochondrial | 1 | 1 | ||||||||
MIRT050011 | SMYD1 | SET and MYND domain containing 1 | 2 | 5 | ||||||||
MIRT050012 | SIK1 | salt inducible kinase 1 | 1 | 1 | ||||||||
MIRT054748 | MAD2L1 | mitotic arrest deficient 2 like 1 | 3 | 1 | ||||||||
MIRT054749 | BAG1 | BCL2 associated athanogene 1 | 3 | 1 | ||||||||
MIRT054750 | RAP1B | RAP1B, member of RAS oncogene family | 3 | 1 | ||||||||
MIRT317835 | CCND3 | cyclin D3 | 2 | 2 | ||||||||
MIRT367642 | ARHGAP42 | Rho GTPase activating protein 42 | 2 | 4 | ||||||||
MIRT443876 | DDTL | D-dopachrome tautomerase like | 2 | 2 | ||||||||
MIRT447544 | RNF165 | ring finger protein 165 | 2 | 2 | ||||||||
MIRT447611 | PCYOX1 | prenylcysteine oxidase 1 | 2 | 2 | ||||||||
MIRT447838 | CTIF | cap binding complex dependent translation initiation factor | 2 | 2 | ||||||||
MIRT448193 | FAM168A | family with sequence similarity 168 member A | 2 | 2 | ||||||||
MIRT448713 | KLHL11 | kelch like family member 11 | 2 | 2 | ||||||||
MIRT450179 | KLF7 | Kruppel like factor 7 | 2 | 2 | ||||||||
MIRT450312 | DRAXIN | dorsal inhibitory axon guidance protein | 2 | 2 | ||||||||
MIRT460792 | VPS37B | VPS37B, ESCRT-I subunit | 2 | 2 | ||||||||
MIRT466332 | THRA | thyroid hormone receptor, alpha | 2 | 2 | ||||||||
MIRT467610 | SLC7A5 | solute carrier family 7 member 5 | 2 | 2 | ||||||||
MIRT471609 | PAQR5 | progestin and adipoQ receptor family member 5 | 2 | 2 | ||||||||
MIRT472144 | NKIRAS2 | NFKB inhibitor interacting Ras like 2 | 2 | 4 | ||||||||
MIRT476588 | G3BP1 | G3BP stress granule assembly factor 1 | 2 | 4 | ||||||||
MIRT486265 | LINC00346 | long intergenic non-protein coding RNA 346 | 2 | 4 | ||||||||
MIRT486480 | TSC22D1 | TSC22 domain family member 1 | 2 | 2 | ||||||||
MIRT487978 | IQSEC2 | IQ motif and Sec7 domain 2 | 2 | 2 | ||||||||
MIRT489428 | TUBB2A | tubulin beta 2A class IIa | 2 | 2 | ||||||||
MIRT500781 | TMED4 | transmembrane p24 trafficking protein 4 | 2 | 6 | ||||||||
MIRT501235 | SEMA4C | semaphorin 4C | 2 | 6 | ||||||||
MIRT511045 | NRF1 | nuclear respiratory factor 1 | 2 | 2 | ||||||||
MIRT512837 | IER3 | immediate early response 3 | 2 | 2 | ||||||||
MIRT513091 | USP9X | ubiquitin specific peptidase 9, X-linked | 2 | 2 | ||||||||
MIRT513543 | PRDM2 | PR/SET domain 2 | 2 | 4 | ||||||||
MIRT532391 | UMPS | uridine monophosphate synthetase | 2 | 2 | ||||||||
MIRT535846 | MSI2 | musashi RNA binding protein 2 | 2 | 2 | ||||||||
MIRT537892 | EDA2R | ectodysplasin A2 receptor | 2 | 2 | ||||||||
MIRT552769 | YIPF6 | Yip1 domain family member 6 | 2 | 2 | ||||||||
MIRT553549 | TMEM167A | transmembrane protein 167A | 2 | 4 | ||||||||
MIRT557228 | HNRNPC | heterogeneous nuclear ribonucleoprotein C (C1/C2) | 2 | 2 | ||||||||
MIRT566756 | MORF4L1 | mortality factor 4 like 1 | 2 | 2 | ||||||||
MIRT567505 | FOXJ3 | forkhead box J3 | 2 | 2 | ||||||||
MIRT568165 | CCDC6 | coiled-coil domain containing 6 | 2 | 2 | ||||||||
MIRT570263 | PRSS16 | protease, serine 16 | 2 | 2 | ||||||||
MIRT614727 | TEAD3 | TEA domain transcription factor 3 | 2 | 2 | ||||||||
MIRT668894 | CRISPLD2 | cysteine rich secretory protein LCCL domain containing 2 | 2 | 2 | ||||||||
MIRT691021 | CRTC3 | CREB regulated transcription coactivator 3 | 2 | 2 | ||||||||
MIRT697421 | ZFP91 | ZFP91 zinc finger protein | 2 | 2 | ||||||||
MIRT711474 | SRD5A1 | steroid 5 alpha-reductase 1 | 2 | 2 | ||||||||
MIRT720189 | CMC4 | C-X9-C motif containing 4 | 2 | 2 | ||||||||
MIRT720622 | PIANP | PILR alpha associated neural protein | 2 | 2 | ||||||||
MIRT731420 | IGF1 | insulin like growth factor 1 | 3 | 1 | ||||||||
MIRT732850 | LINC00265 | long intergenic non-protein coding RNA 265 | 3 | 0 | ||||||||
MIRT732851 | PCNA | proliferating cell nuclear antigen | 3 | 0 | ||||||||
MIRT736342 | FOXO1 | forkhead box O1 | 3 | 0 | ||||||||
MIRT755341 | YWHAZ | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta | 3 | 1 |
miRNA-Drug Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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