pre-miRNA Information | |
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pre-miRNA | hsa-mir-4749 |
Genomic Coordinates | chr19: 49854591 - 49854651 |
Description | Homo sapiens miR-4749 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-4749-3p | ||||||||||||||||||||||||||||||
Sequence | 42| CGCCCCUCCUGCCCCCACAG |61 | ||||||||||||||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||||||||||||||
Experiments | Illumina | 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 | ATF5 | ||||||||||||||||||||
Synonyms | ATFX, HMFN0395 | ||||||||||||||||||||
Description | activating transcription factor 5 | ||||||||||||||||||||
Transcript | NM_012068 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on ATF5 | |||||||||||||||||||||
3'UTR of ATF5 (miRNA target sites are highlighted) |
>ATF5|NM_012068|3'UTR 1 AAGGGCAGGGGTGTGGCTTCTGGGGGCTGGTCTTCAGCTCTGGCGCCTTCATCCCCCTGCCTCTACCTTCATTCCAAACC 81 CCTCTCGGCCGGGTGCAGTGGCTTATGCTTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGAGGATCGTTTGAGGCCAG 161 GAGGTCAATACCAGCCTGGGCAACATAGTAAGACCCTGTCTCTATTAAAAAAAAAAAATCAACCCTTCTTCCCCACCAAA 241 CCACCCAACTCCTCTCTACTCTTATCCTTTTATCCTCTGTCTCTGCTTATCACCTCTCTTGCGTATTTCTGGATCTCCTT 321 CCCTCCTTTCTCGTCCAAATCATGAAATGTTTGGCCTTAGTCAATGTCTATGCCCGTCACATAACAGCCGAGGCACCGAG 401 GCCCACAGGGAAGCAGCTGGGAGCTTGGAAACCTGGTCTCTTGAATTTCAAACCTGGTTTCTTACAGGTGGTTGTCTGGG 481 GTGGGTGGAGTGGCGACAGGATAGAGCTGAAGGACTATGCAAATGAGGAAGTAAGTCAGGGCGGGCTTTGAGAAGGGGAC 561 CCATATCCTACAGGCAAAAAGCAGGCTAGGTGACCTTGGGACACTACGCTAAGGGAGGGAGGCTAAAGGCGGCCAGGTTT 641 GCAGTGCGGGAAGATGAGCAGGCCAGTGGGAGGAGGGGCAGGGCAGGGCTGTAGTTGGTGACTGGGTGTTCATTTTAGCT 721 CTAAGAAAAAAAATCAGTGTTTCGTGAAGGTGTTGGAGAGGGGCTGTGTCTGGGTGAGGGATGGCGGGGTACTGATTTTT 801 TTGGGAGGTTATGAGCAAAAATAAAACGAAACATTTCCTCTGGCAAAAAAAAAAAAAAAAAA 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 | HeLa | ||||||
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 Chi_124B_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell miR-124 + B
... - Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Chi SW; Zang JB; Mele A; Darnell RB - Nature, 2009
MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
LinkOut: [PMID: 19536157]
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CLIP-seq Support 1 for dataset Chi_124B_2A8_130_50 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | HeLa / HeLa cell miR-124 + B |
Location of target site | ENST00000423777.2 | 3UTR | AGGUGUUGGAGAGGGGCUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 19536157 / Chi_HITSCLIP |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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63 hsa-miR-4749-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT082256 | MED29 | mediator complex subunit 29 | ![]() |
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2 | 4 | ||||||
MIRT112161 | OTUD3 | OTU deubiquitinase 3 | ![]() |
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2 | 2 | ||||||
MIRT150036 | MIDN | midnolin | ![]() |
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2 | 2 | ||||||
MIRT246308 | HIST2H2AA3 | histone cluster 2 H2A family member a3 | ![]() |
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2 | 4 | ||||||
MIRT246320 | HIST2H2AA4 | histone cluster 2 H2A family member a4 | ![]() |
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2 | 4 | ||||||
MIRT248254 | SP1 | Sp1 transcription factor | ![]() |
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2 | 2 | ||||||
MIRT257944 | GIGYF1 | GRB10 interacting GYF protein 1 | ![]() |
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2 | 2 | ||||||
MIRT466973 | STARD7 | StAR related lipid transfer domain containing 7 | ![]() |
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2 | 4 | ||||||
MIRT492322 | SETD1B | SET domain containing 1B | ![]() |
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2 | 2 | ||||||
MIRT496204 | EFCAB1 | EF-hand calcium binding domain 1 | ![]() |
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2 | 2 | ||||||
MIRT497568 | CCR6 | C-C motif chemokine receptor 6 | ![]() |
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2 | 2 | ||||||
MIRT502990 | CCDC71L | coiled-coil domain containing 71 like | ![]() |
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2 | 8 | ||||||
MIRT508300 | SIX5 | SIX homeobox 5 | ![]() |
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2 | 4 | ||||||
MIRT522472 | ZAK | mitogen-activated protein kinase kinase kinase 20 | ![]() |
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2 | 2 | ||||||
MIRT525825 | VIMP | selenoprotein S | ![]() |
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2 | 4 | ||||||
MIRT528154 | BCL2L1 | BCL2 like 1 | ![]() |
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2 | 2 | ||||||
MIRT532606 | SPTLC2 | serine palmitoyltransferase long chain base subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT551302 | RPRM | reprimo, TP53 dependent G2 arrest mediator homolog | ![]() |
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2 | 2 | ||||||
MIRT568777 | FAM53C | family with sequence similarity 53 member C | ![]() |
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2 | 6 | ||||||
MIRT570896 | METTL21A | methyltransferase like 21A | ![]() |
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2 | 2 | ||||||
MIRT570963 | TMBIM4 | transmembrane BAX inhibitor motif containing 4 | ![]() |
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2 | 2 | ||||||
MIRT571167 | ZNF85 | zinc finger protein 85 | ![]() |
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2 | 2 | ||||||
MIRT576751 | Tmem127 | transmembrane protein 127 | ![]() |
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2 | 2 | ||||||
MIRT609854 | DAZAP2 | DAZ associated protein 2 | ![]() |
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2 | 2 | ||||||
MIRT627101 | PDRG1 | p53 and DNA damage regulated 1 | ![]() |
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2 | 2 | ||||||
MIRT637060 | PRKAG1 | protein kinase AMP-activated non-catalytic subunit gamma 1 | ![]() |
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2 | 2 | ||||||
MIRT639423 | PKP1 | plakophilin 1 | ![]() |
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2 | 2 | ||||||
MIRT643208 | TYW3 | tRNA-yW synthesizing protein 3 homolog | ![]() |
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2 | 4 | ||||||
MIRT646251 | PRSS38 | protease, serine 38 | ![]() |
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2 | 2 | ||||||
MIRT647145 | CYP27C1 | cytochrome P450 family 27 subfamily C member 1 | ![]() |
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2 | 2 | ||||||
MIRT647429 | ZKSCAN2 | zinc finger with KRAB and SCAN domains 2 | ![]() |
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2 | 2 | ||||||
MIRT650666 | GAPDHP44 | glyceraldehyde 3 phosphate dehydrogenase pseudogene 44 | ![]() |
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2 | 2 | ||||||
MIRT651816 | USP49 | ubiquitin specific peptidase 49 | ![]() |
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2 | 2 | ||||||
MIRT657376 | HMGA1 | high mobility group AT-hook 1 | ![]() |
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2 | 2 | ||||||
MIRT658105 | FOXK1 | forkhead box K1 | ![]() |
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2 | 2 | ||||||
MIRT658161 | FCHSD1 | FCH and double SH3 domains 1 | ![]() |
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2 | 2 | ||||||
MIRT662754 | LRRC3C | leucine rich repeat containing 3C | ![]() |
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2 | 2 | ||||||
MIRT667209 | NIPAL1 | NIPA like domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT687003 | RPL35 | ribosomal protein L35 | ![]() |
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2 | 2 | ||||||
MIRT707057 | NACC2 | NACC family member 2 | ![]() |
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2 | 2 | ||||||
MIRT709048 | MRO | maestro | ![]() |
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2 | 2 | ||||||
MIRT709054 | MGAT5B | mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B | ![]() |
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2 | 2 | ||||||
MIRT709446 | VWA2 | von Willebrand factor A domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT709847 | SNX12 | sorting nexin 12 | ![]() |
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2 | 2 | ||||||
MIRT710790 | IFNLR1 | interferon lambda receptor 1 | ![]() |
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2 | 2 | ||||||
MIRT711696 | GMPR | guanosine monophosphate reductase | ![]() |
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2 | 2 | ||||||
MIRT712462 | KCNC3 | potassium voltage-gated channel subfamily C member 3 | ![]() |
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2 | 2 | ||||||
MIRT713884 | MOB3A | MOB kinase activator 3A | ![]() |
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2 | 2 | ||||||
MIRT715329 | NTN1 | netrin 1 | ![]() |
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2 | 2 | ||||||
MIRT715927 | CHD4 | chromodomain helicase DNA binding protein 4 | ![]() |
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2 | 2 | ||||||
MIRT716533 | ATF5 | activating transcription factor 5 | ![]() |
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2 | 2 | ||||||
MIRT716937 | CACNB1 | calcium voltage-gated channel auxiliary subunit beta 1 | ![]() |
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2 | 2 | ||||||
MIRT717007 | MFSD6 | major facilitator superfamily domain containing 6 | ![]() |
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2 | 2 | ||||||
MIRT719139 | DPYSL5 | dihydropyrimidinase like 5 | ![]() |
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2 | 2 | ||||||
MIRT720853 | MEF2D | myocyte enhancer factor 2D | ![]() |
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2 | 2 | ||||||
MIRT721484 | LTB4R2 | leukotriene B4 receptor 2 | ![]() |
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2 | 2 | ||||||
MIRT721517 | DKK3 | dickkopf WNT signaling pathway inhibitor 3 | ![]() |
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2 | 2 | ||||||
MIRT722895 | LRRC20 | leucine rich repeat containing 20 | ![]() |
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2 | 2 | ||||||
MIRT723066 | GGA1 | golgi associated, gamma adaptin ear containing, ARF binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT723086 | INSIG1 | insulin induced gene 1 | ![]() |
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2 | 2 | ||||||
MIRT723353 | ASCL2 | achaete-scute family bHLH transcription factor 2 | ![]() |
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2 | 2 | ||||||
MIRT723483 | MINOS1 | mitochondrial inner membrane organizing system 1 | ![]() |
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2 | 2 | ||||||
MIRT724576 | NOTCH2 | notch 2 | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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