pre-miRNA Information | |
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pre-miRNA | hsa-mir-3678 |
Genomic Coordinates | chr17: 75406069 - 75406162 |
Description | Homo sapiens miR-3678 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-3678-3p | ||||||||||||||||||||||||||||||
Sequence | 69| CUGCAGAGUUUGUACGGACCGG |90 | ||||||||||||||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||||||||||||||
Experiments | Illumina | ||||||||||||||||||||||||||||||
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 | GPX8 | ||||||||||||||||||||
Synonyms | EPLA847, GPx-8, GSHPx-8, UNQ847 | ||||||||||||||||||||
Description | glutathione peroxidase 8 (putative) | ||||||||||||||||||||
Transcript | NM_001008397 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on GPX8 | |||||||||||||||||||||
3'UTR of GPX8 (miRNA target sites are highlighted) |
>GPX8|NM_001008397|3'UTR 1 GAATGCCATTGCGTTTCTAATAGAACAGAGAAATGTCTCCATGAGGGTTTGGTCTCATTTTAAACATTTTTTTTTTGGAG 81 ACAGTGTCTCACTCTGTCACCCAGGCTGGAGTGCAGTAGTGCGTTCTCAGCTCATTGCAACCTCTGCCTTTTTAAACATG 161 CTATTAAATGTGGCAATGAAGGATTTTTTTTTAATGTTATCTTGCTATTAAGTGGTAATGAATGTTCCCAGGATGAGGAT 241 GTTACCCAAAGCAAAAATCAAGAGTAGCCAAAGAATCAACATGAAATATATTAACTACTTCCTCTGACCATACTAAAGAA 321 TTCAGAATACACAGTGACCAATGTGCCTCAATATCTTATTGTTCAACTTGACATTTTCTAGGACTGTACTTGATGAAAAT 401 GCCAACACACTAGACCACTCTTTGGATTCAAGAGCACTGTGTATGACTGAAATTTCTGGAATAACTGTAAATGGTTATGT 481 TAATGGAATAAAACACAAATGTTGAAAAATGTAAAATATATATACATAGATTCAAATCCTTATATATGTATGCTTGTTTT 561 GTGTACAGGATTTTGTTTTTTCTTTTTAAGTACAGGTTCCTAGTGTTTTACTATAACTGTCACTATGTATGTAACTGACA 641 TATATAAATAGTCATTTATAAATGACCGTATTATAACATTTGAAAAAGTCTTCATCATTTTCAGTATTTCTCTCTGCATT 721 ATTTTTTAGAAGCAACTCAAATTCTGTAATCATAATATTACCAAGTAAGTCAGTCTTTATTTTTGCGTGAAAATCCCAAG 801 TGTAGAAAAAAGGACATGAGTATAAGATCATTTAACTTGATTCCTTATAGGCTGATTTGGGTTGCTAATGTATTCGTACT 881 AGATTAGCCACTTGGGAGGAATTCAATGCTGCATCATTCTGATAGCTGAAATAGTAAAAGTCAACTCCAAACAGCCTAAA 961 TTCTAGTATAAAAAGGGGGTGATCATACAAGTCCTAAAGTGTAGATCAGCAGTCACTGAACCTCTTAGAGTCACAAGGCA 1041 TTTCTTCTCCCAAAGTCATGACCTTTATATTTTGTTAGCCTTATAATTGACTAACAAAGCAACCTGCCAAGTTGGTGAAG 1121 GTTAATTATTGCCTCATGAAATATACATTCATCGCATAAAAGAATTAAATAGGAAGATGGCCAAAAATGTAAAAAAGTCG 1201 TATAAATTTGTCTAAGAAGAAAAAGACCCAATTTAAGTAGTCTGTGACTTGACTCCCAAATTCTGACCTGATGGATGAAA 1281 GTGAAGATGTTTCGTATGGCAAATTCAGTAATGCTACCTCAGTATATAGTTCTGTATACGTATTTGGACCAAAGTTATTA 1361 GATAAACCAAAAATATTTCATGAAGCATCTTCTGCTTCAGAGTCCATATCCAGCCACCCAGCTATGAATGTATTTAGAAA 1441 GATATTTGGTGGAGGTGGAATTTCTACCAGAGGTCAAGAGGATTTGTAGGGATAGCCTCAAGAATGCCAGATGAGTGTGT 1521 CAGAAAGCCTGCTCCTACCTCTCGCCAGCTGCGTGACTTTAGGCAAGTCACTTAAGTACCTTATTTCAGTTTCCTCACCT 1601 GTAAATTGAACAGGGGTTGAATGGAATAAAAAGCCCTTTGCAACTCTAAAAGTCAATTAACACACTTACTAAGGTGTTTT 1681 AAGTGACCAGGAAGGAAATCAGAACTAACCTGGATTGTTAGCGAAGAAAACAGAAGCCACCAACAAGCCTATCTGTCCTT 1761 TGCAATTTTGCTCCAAGAGCCTATTAGCAATTTGAATTCTGAGCCTCTAAGAAAACTTATGCTCAGGTGGCCCCTCCAAG 1841 TGTTGGTGCCAGAGCACTCTTGCCTTGTATCCTCACCTACGCCTTCCATGAACTCATAGCAGTGCTGTGGCACTGCAGGG 1921 GTGTTTTATGCATTCACGTTAGGAGCATGAGCAGAACTGCATATGCCAGCACCACATGGGCAGCAGAGACTCCCCACTGC 2001 CAGATGGATGATAATGGAGCTGCACTGGGAACAACCAGGACTGTCCCAGTCAACATGATACAGATGAACATCCTGCCTTA 2081 AGTCACTAGCTCTCTCCAAAGCCAGATAAAGTGGGTTTCTTCACTTACATCTCTCTAATCTTGGCTGCCTTATTCAACCT 2161 ACAGACTCTATGTCAGTGCTGGATTTTCTCCCCTTGCCCTTTAGGTAAGCAGAGTAGGCAGGAGGAGATTTGAAAGCGTG 2241 TCATACATATTGCCTTGAAAGAAAGGACATTCAGGTGTCCCTTCGGGGTTCTGTAACAATTAGGCTATGTGTGCTGAGAG 2321 AGGGAGCGGAGTCATTTGCTGATGTGCTGCTACCTGTAACTCAAATGCCTCATAGGAATACCAGCGGACAAACACATAGA 2401 GGAAAAGTTGAATCTTTCCTATATTGGACAATCTTCCTTCAGTCTTGTTTCTGCATCAAAAAGTCTGGGACACAGAGTGC 2481 TACAGGATGCCTGGGCTAAGGACTGTAACAGAAAAATATCAACATCAGAGCCTGGCACAGTGGCTCACACCGGTAATCCC 2561 AGCACTTTGGGAGGCCGAGGCGGGTGGATCACTTCAGGTCAGGAGTTCGAGACCATCCTGGCCAACATGGTGAAACCCCC 2641 ATCTCTACTAAAAATACAAAAATTAGCCGGGCACGGTGGCACATGCCTGTAATCCCAGCTACCTGGGAGGCTGAGTCAGA 2721 AGAATCACTTGAAAACAGGAGGCTGAGGTTGCAATGAGCCAAGATTGCACCACTGCACTCCAACCTGGGCAACAGAGCGA 2801 GACCCCATCTTAAAGACCCTGTCTCAAAAAAGAGAGAAAAAGAAAAAGAAAAATATCAGGCATCACATGAAAGAGTATTC 2881 AGCTGTCGTTCTTGTGAAAAAGGAAAAGGACAAAATCAAATGCATTTTAACTGTGGTAACTAATTCACTGACTTGAAGTT 2961 TGCTTTGTTTGTTTTCTTTGGTGCGTAGAGAAGAATACTTCATACTAACTCCTGATCATCTTACAGCAGACATAACAACA 3041 GAGTGTTAGAGACTGGAATAAATATGAATTTGGCTGAAATGTGAAAAAAAAAAAAAAAAAA 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 | MCF7 | ||||||
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 SRR1045082. RNA binding protein: AGO2. Condition:Untreated
... - Farazi TA; Ten Hoeve JJ; Brown M; et al., 2014, Genome biology. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Farazi TA; Ten Hoeve JJ; Brown M; et al. - Genome biology, 2014
BACKGROUND: Various microRNAs (miRNAs) are up- or downregulated in tumors. However, the repression of cognate miRNA targets responsible for the phenotypic effects of this dysregulation in patients remains largely unexplored. To define miRNA targets and associated pathways, together with their relationship to outcome in breast cancer, we integrated patient-paired miRNA-mRNA expression data with a set of validated miRNA targets and pathway inference. RESULTS: To generate a biochemically-validated set of miRNA-binding sites, we performed argonaute-2 photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (AGO2-PAR-CLIP) in MCF7 cells. We then defined putative miRNA-target interactions using a computational model, which ranked and selected additional TargetScan-predicted interactions based on features of our AGO2-PAR-CLIP binding-site data. We subselected modeled interactions according to the abundance of their constituent miRNA and mRNA transcripts in tumors, and we took advantage of the variability of miRNA expression within molecular subtypes to detect miRNA repression. Interestingly, our data suggest that miRNA families control subtype-specific pathways; for example, miR-17, miR-19a, miR-25, and miR-200b show high miRNA regulatory activity in the triple-negative, basal-like subtype, whereas miR-22 and miR-24 do so in the HER2 subtype. An independent dataset validated our findings for miR-17 and miR-25, and showed a correlation between the expression levels of miR-182 targets and overall patient survival. Pathway analysis associated miR-17, miR-19a, and miR-200b with leukocyte transendothelial migration. CONCLUSIONS: We combined PAR-CLIP data with patient expression data to predict regulatory miRNAs, revealing potential therapeutic targets and prognostic markers in breast cancer.
LinkOut: [PMID: 24398324]
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CLIP-seq Support 1 for dataset SRR1045082 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | MCF7 / Untreated |
Location of target site | ENST00000296734.6 | 3UTR | UCUUCAUCAUUUUCAGUAUUUCUCUCUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 24398324 / SRX388831 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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86 hsa-miR-3678-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT074327 | TNRC6A | trinucleotide repeat containing 6A | ![]() |
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2 | 10 | ||||||
MIRT107705 | CLTA | clathrin light chain A | ![]() |
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2 | 2 | ||||||
MIRT114113 | AGO1 | argonaute 1, RISC catalytic component | ![]() |
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2 | 2 | ||||||
MIRT155293 | IFNAR2 | interferon alpha and beta receptor subunit 2 | ![]() |
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2 | 4 | ||||||
MIRT159171 | NRBP1 | nuclear receptor binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT185795 | ZNF678 | zinc finger protein 678 | ![]() |
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2 | 2 | ||||||
MIRT282672 | SYNM | synemin | ![]() |
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2 | 2 | ||||||
MIRT294386 | ZNF264 | zinc finger protein 264 | ![]() |
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2 | 2 | ||||||
MIRT295818 | CHMP4B | charged multivesicular body protein 4B | ![]() |
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2 | 2 | ||||||
MIRT332777 | CAPRIN1 | cell cycle associated protein 1 | ![]() |
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2 | 4 | ||||||
MIRT334112 | PPP6R3 | protein phosphatase 6 regulatory subunit 3 | ![]() |
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2 | 2 | ||||||
MIRT340971 | IPO5 | importin 5 | ![]() |
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2 | 2 | ||||||
MIRT354679 | CDV3 | CDV3 homolog | ![]() |
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2 | 2 | ||||||
MIRT366662 | PLP2 | proteolipid protein 2 | ![]() |
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2 | 2 | ||||||
MIRT404272 | PLEKHA8 | pleckstrin homology domain containing A8 | ![]() |
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2 | 2 | ||||||
MIRT447536 | RNF165 | ring finger protein 165 | ![]() |
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2 | 2 | ||||||
MIRT449139 | UQCRB | ubiquinol-cytochrome c reductase binding protein | ![]() |
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2 | 2 | ||||||
MIRT451301 | LGALS3BP | galectin 3 binding protein | ![]() |
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2 | 2 | ||||||
MIRT451488 | FOPNL | FGFR1OP N-terminal like | ![]() |
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2 | 2 | ||||||
MIRT455198 | GNL1 | G protein nucleolar 1 (putative) | ![]() |
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2 | 2 | ||||||
MIRT459215 | MRPS21 | mitochondrial ribosomal protein S21 | ![]() |
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2 | 2 | ||||||
MIRT461764 | MPDU1 | mannose-P-dolichol utilization defect 1 | ![]() |
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2 | 2 | ||||||
MIRT463273 | ZFX | zinc finger protein, X-linked | ![]() |
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2 | 2 | ||||||
MIRT464862 | UBB | ubiquitin B | ![]() |
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2 | 8 | ||||||
MIRT464950 | TWIST1 | twist family bHLH transcription factor 1 | ![]() |
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2 | 2 | ||||||
MIRT467378 | SON | SON DNA binding protein | ![]() |
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2 | 4 | ||||||
MIRT469282 | RHOA | ras homolog family member A | ![]() |
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2 | 2 | ||||||
MIRT470293 | PPTC7 | PTC7 protein phosphatase homolog | ![]() |
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2 | 2 | ||||||
MIRT470639 | POM121C | POM121 transmembrane nucleoporin C | ![]() |
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2 | 2 | ||||||
MIRT477163 | FABP3 | fatty acid binding protein 3 | ![]() |
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2 | 2 | ||||||
MIRT477686 | EFHD2 | EF-hand domain family member D2 | ![]() |
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2 | 2 | ||||||
MIRT479725 | CCNF | cyclin F | ![]() |
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2 | 2 | ||||||
MIRT481726 | APH1A | aph-1 homolog A, gamma-secretase subunit | ![]() |
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2 | 2 | ||||||
MIRT485673 | CCDC64 | BICD family like cargo adaptor 1 | ![]() |
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2 | 2 | ||||||
MIRT498280 | PADI2 | peptidyl arginine deiminase 2 | ![]() |
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2 | 2 | ||||||
MIRT499921 | GPX8 | glutathione peroxidase 8 (putative) | ![]() |
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2 | 2 | ||||||
MIRT503616 | SLC25A36 | solute carrier family 25 member 36 | ![]() |
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2 | 4 | ||||||
MIRT506927 | IGDCC4 | immunoglobulin superfamily DCC subclass member 4 | ![]() |
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2 | 6 | ||||||
MIRT507348 | FAM129A | family with sequence similarity 129 member A | ![]() |
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2 | 6 | ||||||
MIRT508265 | DYNLL2 | dynein light chain LC8-type 2 | ![]() |
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2 | 4 | ||||||
MIRT508284 | YES1 | YES proto-oncogene 1, Src family tyrosine kinase | ![]() |
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2 | 4 | ||||||
MIRT509353 | COPS8 | COP9 signalosome subunit 8 | ![]() |
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2 | 2 | ||||||
MIRT510892 | RAB1A | RAB1A, member RAS oncogene family | ![]() |
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2 | 4 | ||||||
MIRT511882 | GAS1 | growth arrest specific 1 | ![]() |
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2 | 6 | ||||||
MIRT511990 | E2F1 | E2F transcription factor 1 | ![]() |
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2 | 4 | ||||||
MIRT512239 | ARPP19 | cAMP regulated phosphoprotein 19 | ![]() |
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2 | 4 | ||||||
MIRT512392 | BUB1 | BUB1 mitotic checkpoint serine/threonine kinase | ![]() |
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2 | 4 | ||||||
MIRT514086 | EPS15L1 | epidermal growth factor receptor pathway substrate 15 like 1 | ![]() |
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2 | 6 | ||||||
MIRT514358 | UBBP4 | ubiquitin B pseudogene 4 | ![]() |
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2 | 6 | ||||||
MIRT523149 | HNRNPU | heterogeneous nuclear ribonucleoprotein U | ![]() |
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2 | 2 | ||||||
MIRT525511 | FSIP2 | fibrous sheath interacting protein 2 | ![]() |
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2 | 2 | ||||||
MIRT526333 | SH3TC2 | SH3 domain and tetratricopeptide repeats 2 | ![]() |
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2 | 2 | ||||||
MIRT529962 | ZNF71 | zinc finger protein 71 | ![]() |
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2 | 2 | ||||||
MIRT530337 | GABRB3 | gamma-aminobutyric acid type A receptor beta3 subunit | ![]() |
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2 | 2 | ||||||
MIRT530884 | PHOX2A | paired like homeobox 2a | ![]() |
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2 | 2 | ||||||
MIRT533097 | YOD1 | YOD1 deubiquitinase | ![]() |
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2 | 2 | ||||||
MIRT533250 | VCAM1 | vascular cell adhesion molecule 1 | ![]() |
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2 | 2 | ||||||
MIRT534786 | RAB8B | RAB8B, member RAS oncogene family | ![]() |
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2 | 2 | ||||||
MIRT537917 | DSTYK | dual serine/threonine and tyrosine protein kinase | ![]() |
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2 | 2 | ||||||
MIRT547799 | JARID2 | jumonji and AT-rich interaction domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT548714 | CRK | CRK proto-oncogene, adaptor protein | ![]() |
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2 | 2 | ||||||
MIRT555509 | PMEPA1 | prostate transmembrane protein, androgen induced 1 | ![]() |
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2 | 2 | ||||||
MIRT555984 | NFYB | nuclear transcription factor Y subunit beta | ![]() |
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2 | 2 | ||||||
MIRT557942 | FAM222B | family with sequence similarity 222 member B | ![]() |
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2 | 2 | ||||||
MIRT560830 | ZNF786 | zinc finger protein 786 | ![]() |
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2 | 2 | ||||||
MIRT562720 | ZNF714 | zinc finger protein 714 | ![]() |
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2 | 2 | ||||||
MIRT565337 | TMEM104 | transmembrane protein 104 | ![]() |
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2 | 2 | ||||||
MIRT614453 | REL | REL proto-oncogene, NF-kB subunit | ![]() |
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2 | 2 | ||||||
MIRT639474 | SLC6A4 | solute carrier family 6 member 4 | ![]() |
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2 | 2 | ||||||
MIRT644056 | IQCE | IQ motif containing E | ![]() |
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2 | 2 | ||||||
MIRT651652 | VWA1 | von Willebrand factor A domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT651866 | UNC119B | unc-119 lipid binding chaperone B | ![]() |
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2 | 2 | ||||||
MIRT653490 | SLC43A2 | solute carrier family 43 member 2 | ![]() |
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2 | 2 | ||||||
MIRT657039 | KCNJ6 | potassium voltage-gated channel subfamily J member 6 | ![]() |
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2 | 2 | ||||||
MIRT657985 | GAN | gigaxonin | ![]() |
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2 | 2 | ||||||
MIRT672117 | ATP6V0A2 | ATPase H+ transporting V0 subunit a2 | ![]() |
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2 | 2 | ||||||
MIRT683583 | GSTCD | glutathione S-transferase C-terminal domain containing | ![]() |
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2 | 2 | ||||||
MIRT688689 | CPS1 | carbamoyl-phosphate synthase 1 | ![]() |
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2 | 2 | ||||||
MIRT695375 | NSA2 | NSA2, ribosome biogenesis homolog | ![]() |
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2 | 2 | ||||||
MIRT696351 | EIF2S3 | eukaryotic translation initiation factor 2 subunit gamma | ![]() |
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2 | 2 | ||||||
MIRT700614 | PRKAA2 | protein kinase AMP-activated catalytic subunit alpha 2 | ![]() |
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2 | 2 | ||||||
MIRT703512 | FKBP15 | FK506 binding protein 15 | ![]() |
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2 | 2 | ||||||
MIRT705051 | C5orf15 | chromosome 5 open reading frame 15 | ![]() |
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2 | 2 | ||||||
MIRT705180 | BTG1 | BTG anti-proliferation factor 1 | ![]() |
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2 | 2 | ||||||
MIRT709409 | FBXL20 | F-box and leucine rich repeat protein 20 | ![]() |
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2 | 2 | ||||||
MIRT721053 | DCC | DCC netrin 1 receptor | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||
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