pre-miRNA Information | |
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pre-miRNA | hsa-mir-3180-1 |
Genomic Coordinates | chr16: 14911220 - 14911313 |
Description | Homo sapiens miR-3180-1 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
pre-miRNA | hsa-mir-3180-2 |
Genomic Coordinates | chr16: 16309879 - 16309966 |
Description | Homo sapiens miR-3180-2 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
pre-miRNA | hsa-mir-3180-3 |
Genomic Coordinates | chr16: 18402178 - 18402271 |
Description | Homo sapiens miR-3180-3 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |
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Mature miRNA | hsa-miR-3180-3p |
Sequence | 62| UGGGGCGGAGCUUCCGGAGGCC |83 |
Evidence | Experimental |
Experiments | Illumina |
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 | SLC10A7 | ||||||||||||||||||||
Synonyms | C4orf13, P7 | ||||||||||||||||||||
Description | solute carrier family 10 member 7 | ||||||||||||||||||||
Transcript | NM_001029998 | ||||||||||||||||||||
Other Transcripts | NM_032128 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on SLC10A7 | |||||||||||||||||||||
3'UTR of SLC10A7 (miRNA target sites are highlighted) |
>SLC10A7|NM_001029998|3'UTR 1 CAAAGGAGGTGGACTTTCTGTAGCAATGTATATATGTACAGGATTGTACATACTAGCAATTCTGAAGACTTGTACTTGTG 81 AATGTTGCCTCAATGCATATTTTATTTTTTTACACAAAAATATGAGATCCTGTTTAAGTGCCTTAAAATGTATTTGACAA 161 GAGCGTTATTTCCAAAATATGCTTTGTTGATTACTGCCAGGGGTGGTACAATATTTGGGGGTTAATTTTGCTTTCCTAAT 241 GCAGGAATCAGTCATGGTAAGTGACAAAAAGCAAACATGCTTTCCCTGCAGCACCTTTGTGCAATACAACCCTATAGTAG 321 TTACTGTAATGTTTGAAATGAGGTCACACCATCAGGAAAATGCCCTTCTGATGACAGTGAAAATTTCCAAAGTCTTATTC 401 ATGCATACTTTGATTTACTGTGTGATTCTTTTTTTCTACGACTGTGACATGCCTCTTCCTTATCAACTCAGCAGGGGTCA 481 TAGATCGAATAGATGCTGAAAAGCGTAAGATATATGCATTCCTTGACATCATTTTTAAAGACATTCCTTCAAATAGTTTC 561 CACACAGAAATTCCTCACTCCCATTATGAGAGATTGTGGTTATATGTCTTAAATTTATTATAAGCTGCTTCAAAGAAAGG 641 GTCTGAATGTTTGAATTATGAGTGAAATCATGTGAAATTTTGAGTTAAACTCTGTGATTTGATTTTCAGGGTCTTTAAAA 721 TATATCTTAATATCTTCTTCCTCTTTATTCAATAATTTCTGTCTTGCACTTACACACTCATAACAGCCAAATATGAGGCA 801 CAAAAATGTTACAATCAGTTTGAAAGCAGCATCAATTAATGGTAGATTCTATTCACATTCCACAACCCAGACCAAATTTT 881 TTTCCTATTACGCAGATGTGCTGAGCACTTTCCAGATTGCCCCTGTTGGCCAAAAGCAGCCTGTTACATCCTGGAATTAA 961 GCACACTTAAGGTATTTGAGACAATTTATTAATGAAAATTTCCTTGGCAGATTTGACAAATGTTGGCAATATTTTTTTAG 1041 AAGTTAAATCATATTGCTTTCATGAATAAATGAAAATATAAAGGTCATGGATGCAAACAAATGTTACATATACACATTCT 1121 GTCTCTCCAGATGAAAAGAACATGCAAAACCATTTAATAACCAAAATATCAAGTAAAATTAGTTCCCAACGGGGCAGCAG 1201 CTTTCAAATGAGTGTCCAATATTTGCTTCTGCTATAGCTGCAAGAACTGTAACTGGACCCAAGTAGAGAATGAAGCCACG 1281 TATAGAACTACGAGAACACTTTTCTGTGTTTCCCCCATGCCGTCCTGTCACATCCTCTTACACGTCCTCTCTTGATTTGA 1361 TAGACAATATTGGCATCCTGGGTCTCACTGAGGCCGTGCTATGTCCTCAGCAGCTGTTTTTGTTGTTTCGTTATTATGCC 1441 CACAACAAAAAATCATTCCTTAGAAACTCACCAAGTTTATCTACTGTGTAAATTTATATTATTGTTACTACCAGGTCTCA 1521 TCTTTTGTCAATGTCATTGAATAAATTTCATAAGAGTTATTCTCAGTGTGAATTTTAAGGCTAATGCCAGATCCTGCAAA 1601 AATCTATGCTAACCAGGCTGTAGTACACACTGTTATAAAGAATTTTACTTGTGTCTAAAACTACAGTAATTTTGCTTAGG 1681 TAATTGTGCTTACCTATGGAGCACAGGAAGGCTCTTAGGTTTTGTTCCTACAAGTTTCTTTGAATTTTGGAGTAAATGGA 1761 AGTGTCTGTCTGTCTGTCATCTATCTGCCCTATCATAAAAATCTTTCTCCCTAACATTAAAATACTGATCCCCGCCCCCA 1841 ACTTATCTACCTCTATTGTCTAACACCTATAGTAGGTGTGATCATGGGATAAAATTCAACTGAAAATGCTATGATAACAT 1921 TTTATCGTTTGCTTTAAAAATGTGCTTTGTTTTCAAATAATCTTTACATAGTGAACTTTGGTGGCGTTAGTGATATGTTT 2001 ATGCCTATTTCTTTTTTTTACACAAATTCCTTGGCATATTTTTTCATAAAGAACAAAAAATAAAATCAAAATTTATTTTT 2081 AATTCATGCTTATTGGGATTTAATTATTCAGAGCTTAAAATATTTTGTTATGTTTATACACTGTAAAGCTATCTGTTTTA 2161 TGCATTTGTTTTGTCTAAATGTATTTATGAAAGAAATACATTAGATTATATTTATGTTTACTCATTTTTCCACCTGGATT 2241 TTTTTTAATGGTTGTTACAAAATTAGATTTTTTAATGGGTAATAATGTTGGTATTTTCATGTTTTTTCTTAGTATTAAAA 2321 TTTTTGTGGGTTTTTTAAAATTTTTCCCTATTCTGTTAAAAATTAACACACCTCTAGCTAATGTTCAGTGTTTGTGCTAA 2401 ATACCAAATTTTTTCAAAAGGATTGGTTAAGTCATAAAGTGGATTATTTATGATGACTGGAAGATGAAAATAATTATATG 2481 ATTAAACAAAGAATGTTTCAGAAAAAAAAAAAAAAAA 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 | HEK293 | ||||||
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 GSM545217. RNA binding protein: AGO2. Condition:miR-7 transfection
... - Hafner M; Landthaler M; Burger L; Khorshid et al., 2010, Cell. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Hafner M; Landthaler M; Burger L; Khorshid et al. - Cell, 2010
RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.
LinkOut: [PMID: 20371350]
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Experimental Support 2 for Functional miRNA-Target Interaction | |||||||
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miRNA:Target | ---- | ||||||
Validation Method |
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Conditions | HEK293 | ||||||
Disease | 84068.0 | ||||||
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 GSM714644. RNA binding protein: AGO2. Condition:completeT1
... - Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Kishore S; Jaskiewicz L; Burger L; Hausser et al. - Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
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Experimental Support 3 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. |
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 GSM545217 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / miR-7 transfection |
Location of target site | ENST00000264986.3 | 3UTR | CCCCCAACUUAUCUACCUCUAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 20371350 / GSE21578 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM714644 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / completeT1, repA |
Location of target site | ENST00000264986.3 | 3UTR | CCCCCAACUUAUCUACCUCUAUUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 21572407 / GSE28865 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 for dataset SRR1045082 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | MCF7 / Untreated |
Location of target site | ENST00000264986.3 | 3UTR | CCCCCAACUUAUCUACCUCUAUUG |
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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66 hsa-miR-3180-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT133792 | SKI | SKI proto-oncogene | ![]() |
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2 | 2 | ||||||
MIRT146658 | MINK1 | misshapen like kinase 1 | ![]() |
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2 | 4 | ||||||
MIRT441337 | C19orf26 | CACN beta subunit associated regulatory protein | ![]() |
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2 | 4 | ||||||
MIRT449088 | XPO6 | exportin 6 | ![]() |
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2 | 2 | ||||||
MIRT464967 | TULP1 | tubby like protein 1 | ![]() |
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2 | 6 | ||||||
MIRT471706 | OTUB1 | OTU deubiquitinase, ubiquitin aldehyde binding 1 | ![]() |
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2 | 2 | ||||||
MIRT473252 | MIDN | midnolin | ![]() |
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2 | 2 | ||||||
MIRT483494 | STMN3 | stathmin 3 | ![]() |
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2 | 4 | ||||||
MIRT483726 | THSD4 | thrombospondin type 1 domain containing 4 | ![]() |
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2 | 2 | ||||||
MIRT485684 | CCDC64 | BICD family like cargo adaptor 1 | ![]() |
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2 | 4 | ||||||
MIRT486046 | WSCD1 | WSC domain containing 1 | ![]() |
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2 | 4 | ||||||
MIRT486522 | CLCN7 | chloride voltage-gated channel 7 | ![]() |
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2 | 2 | ||||||
MIRT486779 | SESTD1 | SEC14 and spectrin domain containing 1 | ![]() |
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2 | 4 | ||||||
MIRT486852 | DPF1 | double PHD fingers 1 | ![]() |
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2 | 2 | ||||||
MIRT487035 | C10orf55 | chromosome 10 open reading frame 55 | ![]() |
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2 | 2 | ||||||
MIRT487082 | C3orf36 | chromosome 3 open reading frame 36 | ![]() |
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2 | 2 | ||||||
MIRT487284 | AGPAT6 | glycerol-3-phosphate acyltransferase 4 | ![]() |
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2 | 4 | ||||||
MIRT487992 | RXRB | retinoid X receptor beta | ![]() |
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2 | 2 | ||||||
MIRT488101 | POU3F1 | POU class 3 homeobox 1 | ![]() |
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2 | 2 | ||||||
MIRT488547 | POU3F3 | POU class 3 homeobox 3 | ![]() |
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2 | 8 | ||||||
MIRT488582 | ST7L | suppression of tumorigenicity 7 like | ![]() |
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2 | 2 | ||||||
MIRT488757 | FXYD1 | FXYD domain containing ion transport regulator 1 | ![]() |
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2 | 2 | ||||||
MIRT489217 | ASCL2 | achaete-scute family bHLH transcription factor 2 | ![]() |
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2 | 4 | ||||||
MIRT489350 | SYNGR1 | synaptogyrin 1 | ![]() |
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2 | 4 | ||||||
MIRT489385 | RAB11B | RAB11B, member RAS oncogene family | ![]() |
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2 | 2 | ||||||
MIRT489459 | MSC | musculin | ![]() |
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2 | 2 | ||||||
MIRT489469 | SLITRK5 | SLIT and NTRK like family member 5 | ![]() |
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2 | 2 | ||||||
MIRT489749 | TACC3 | transforming acidic coiled-coil containing protein 3 | ![]() |
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2 | 2 | ||||||
MIRT490244 | MFI2 | melanotransferrin | ![]() |
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2 | 2 | ||||||
MIRT490423 | VPS51 | VPS51, GARP complex subunit | ![]() |
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2 | 4 | ||||||
MIRT490644 | FEM1A | fem-1 homolog A | ![]() |
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2 | 2 | ||||||
MIRT491977 | UNK | unkempt family zinc finger | ![]() |
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2 | 2 | ||||||
MIRT492469 | RASD1 | ras related dexamethasone induced 1 | ![]() |
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2 | 4 | ||||||
MIRT492837 | NRGN | neurogranin | ![]() |
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2 | 2 | ||||||
MIRT492956 | NEUROD2 | neuronal differentiation 2 | ![]() |
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2 | 2 | ||||||
MIRT493002 | NANOS1 | nanos C2HC-type zinc finger 1 | ![]() |
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2 | 2 | ||||||
MIRT493430 | KCNK3 | potassium two pore domain channel subfamily K member 3 | ![]() |
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2 | 2 | ||||||
MIRT493709 | H2AFX | H2A histone family member X | ![]() |
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2 | 6 | ||||||
MIRT493886 | FAM43A | family with sequence similarity 43 member A | ![]() |
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2 | 4 | ||||||
MIRT493955 | ENG | endoglin | ![]() |
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2 | 2 | ||||||
MIRT500168 | MSI1 | musashi RNA binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT500196 | MAPK8IP3 | mitogen-activated protein kinase 8 interacting protein 3 | ![]() |
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2 | 4 | ||||||
MIRT500366 | ZNF385A | zinc finger protein 385A | ![]() |
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2 | 2 | ||||||
MIRT501159 | SLC10A7 | solute carrier family 10 member 7 | ![]() |
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2 | 6 | ||||||
MIRT501698 | PCGF3 | polycomb group ring finger 3 | ![]() |
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2 | 6 | ||||||
MIRT512173 | CASP16 | caspase 16, pseudogene | ![]() |
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2 | 6 | ||||||
MIRT512237 | ATG2A | autophagy related 2A | ![]() |
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2 | 6 | ||||||
MIRT512879 | PITX3 | paired like homeodomain 3 | ![]() |
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2 | 2 | ||||||
MIRT531184 | SIGLEC12 | sialic acid binding Ig like lectin 12 (gene/pseudogene) | ![]() |
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2 | 2 | ||||||
MIRT548362 | ENTPD5 | ectonucleoside triphosphate diphosphohydrolase 5 | ![]() |
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2 | 4 | ||||||
MIRT569093 | FSCN1 | fascin actin-bundling protein 1 | ![]() |
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2 | 2 | ||||||
MIRT574133 | MARVELD1 | MARVEL domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT635542 | LEPROTL1 | leptin receptor overlapping transcript like 1 | ![]() |
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2 | 2 | ||||||
MIRT654098 | RSBN1L | round spermatid basic protein 1 like | ![]() |
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2 | 2 | ||||||
MIRT664919 | BHMT2 | betaine--homocysteine S-methyltransferase 2 | ![]() |
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2 | 2 | ||||||
MIRT669843 | OLR1 | oxidized low density lipoprotein receptor 1 | ![]() |
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2 | 2 | ||||||
MIRT670502 | LYRM4 | LYR motif containing 4 | ![]() |
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2 | 2 | ||||||
MIRT670526 | SLC9A7 | solute carrier family 9 member A7 | ![]() |
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2 | 2 | ||||||
MIRT670550 | SHISA2 | shisa family member 2 | ![]() |
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2 | 2 | ||||||
MIRT671031 | PCDHB2 | protocadherin beta 2 | ![]() |
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2 | 2 | ||||||
MIRT695219 | SCAMP3 | secretory carrier membrane protein 3 | ![]() |
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2 | 2 | ||||||
MIRT700129 | RNF144B | ring finger protein 144B | ![]() |
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2 | 2 | ||||||
MIRT709280 | MAPK8IP2 | mitogen-activated protein kinase 8 interacting protein 2 | ![]() |
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2 | 2 | ||||||
MIRT712750 | GMDS | GDP-mannose 4,6-dehydratase | ![]() |
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2 | 2 | ||||||
MIRT720753 | FAM193A | family with sequence similarity 193 member A | ![]() |
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2 | 2 | ||||||
MIRT724920 | VPS18 | VPS18, CORVET/HOPS core subunit | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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