pre-miRNA Information | |
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pre-miRNA | hsa-mir-6830 |
Genomic Coordinates | chr5: 132217849 - 132217918 |
Description | Homo sapiens miR-6830 stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | |||||||||||||||||||||||||
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Mature miRNA | hsa-miR-6830-3p | ||||||||||||||||||||||||
Sequence | 48| UGUCUUUCUUCUCUCCCUUGCAG |70 | ||||||||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||||||||
Experiments | Meta-analysis | ||||||||||||||||||||||||
SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | DCK | ||||||||||||||||||||
Synonyms | - | ||||||||||||||||||||
Description | deoxycytidine kinase | ||||||||||||||||||||
Transcript | NM_000788 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on DCK | |||||||||||||||||||||
3'UTR of DCK (miRNA target sites are highlighted) |
>DCK|NM_000788|3'UTR 1 TCTTGCTGAAGACTACAGGCAGCCAAATGGTTCCAGATACTTCAGCTTTGTGTATCTTCGTAACTTCATATTAATATAAG 81 TTTCTTTAGAAAACCCAAGTTTTTAATCGTTTTTGTTTTAAGGAAAAAAGATTTTTAAAATGAATCTTATGCAAAACTTT 161 TTGACCAGTTTCTTTTCTTTTGTTTTTTTTTTAAAAAAGACATTTAAAGACAAAGACATTATTTCTCATAGCAGGAAATG 241 TAGAGGTAGATGGTTCCAGTATCAGCATAGTGACTAAACTACATTATAAAAGATCCAGCTTCCTTCTGTCATTCCCCTCT 321 TTTGTCTTCCTCAGCAGGTTGGCTTTTTTCCCTGGTGCCTCTCACTTCGTTGGTGACCAGTTTCTTAAACTGAAAGCTTT 401 AATGTTACATAGTAAATGGTAGTGTGTCCTGTGTAAATTAGTGTACCTATTAAAAGTTGCAAAGTGGAATTAAAGGAATC 481 CCTAGAATAAGGATTCTGAAGTTTTATTTTAAATTATTATCTTCTTAACAGTTTAGTCCCACCTCTTACTTCCTGCCTCA 561 GTCTGCTTTCTCTACTGTCTGGATTAATTAGGCAGCCTGCTATAAAGTTAAAGTCACACATTTCTATTTTGCAAACACTG 641 TGATTACTCTTTGCTTTGTAGTTTGCTTTGCTTTGTAGGGTTCTGCTTTTAAGTTTTTCTCTTTTTCAGACAAATTACTG 721 ATAAAAATGATATTGCTCTATATGTAATATATCCTGAAAGCATTATTTTTTGTTGAATAGGAAATAAAATTAATGAAGAC 801 AGAGGCTAGAAAGCATCCATTAATTAATGAGACACACTTAACTACTTATCTCTAAACCATCTATGTGAATATTTGTAAAA 881 ATAATGAATGGACTCATCTTAGTTCTGTATATAAATATATTTTCTTTCTAGTTTGTTTAGTTAAGGTGTGCAGTGTTTTT 961 CCTGTGTATTAAACCTTTCCATTTTACGTTTTAGAAAATTTTATGTATTTTAAAATAAGGGGAAGAGTCATTTTCACTTT 1041 TAAACTACTATTTTTCTTTCCAAGTCATTTTTGTTTTTGGTTTCTTATTCAAAGATGATAATTTAGTGGATTAACCAGTC 1121 CAGACGCACTGATCTTTGCAAAGGAGACTTAATTTCAAATCTGTAATTACCATACATAAACTGTCTCATTATACGTATGC 1201 ATTTTTTTAGTTTGTTTTTGTTTGGTATAAATTAATTTGTTAATTAAATATTTCTTAAGTATAAACCTTATGAACTACAG 1281 TGGAGCTACACTCATTGAAATGTAATTTCAGTTCTAAAAAGATGTAATAATCATTTTAGAATTAAAATTTATTCTACTTT 1361 TAAATAAATTATGAATATTAAAGGTGAAAATTGTATAAATTACTTTGATTCCATTTTAAGTGGAGACATATTTCAGTGAT 1441 TTTTAGTAACCTTTAAAAATGTATAATGACTTTTAAAATTTGTAGAATTGAAAAGACGCTAATAAAAATTTATTATTTAT 1521 TTGTCATGACTCAAAAAAAAAAAAAAA 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 GSM545212. RNA binding protein: AGO1. Condition:Control
PAR-CLIP data was present in GSM545214. RNA binding protein: AGO3. Condition:Control
PAR-CLIP data was present in GSM545216. RNA binding protein: AGO2. Condition:miR-124 transfection
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. |
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 | 1633.0 |
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 GSM1065667. RNA binding protein: AGO1. Condition:4-thiouridine
"PAR-CLIP data was present in GSM1065669. RNA binding protein: AGO1. Condition:4-thiouridine
... - Memczak S; Jens M; Elefsinioti A; Torti F; et al., 2013, Nature. |
Article |
- Memczak S; Jens M; Elefsinioti A; Torti F; et al. - Nature, 2013
Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.
LinkOut: [PMID: 23446348]
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CLIP-seq Support 1 for dataset GSM545212 | |
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Method / RBP | PAR-CLIP / AGO1 |
Cell line / Condition | HEK293 / Control |
Location of target site | ENST00000504730.1 | 3UTR | ACAUUAUUUCUCAUAGCAGGAAAUG |
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 GSM545214 | |
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Method / RBP | PAR-CLIP / AGO3 |
Cell line / Condition | HEK293 / Control |
Location of target site | ENST00000504730.1 | 3UTR | ACAUUAUUUCUCAUAGCAGGAAAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 20371350 / GSE21578 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 for dataset GSM545216 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / miR-124 transfection |
Location of target site | ENST00000504730.1 | 3UTR | ACAUUAUUUCUCAUAGCAGGAAAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 20371350 / GSE21578 |
CLIP-seq Viewer | Link |
CLIP-seq Support 4 for dataset GSM545217 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / miR-7 transfection |
Location of target site | ENST00000504730.1 | 3UTR | ACAUUAUUUCUCAUAGCAGGAAAU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 20371350 / GSE21578 |
CLIP-seq Viewer | Link |
CLIP-seq Support 5 for dataset GSM1065667 | |
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Method / RBP | PAR-CLIP / AGO1 |
Cell line / Condition | HEK293 / 4-thiouridine, ML_MM_6 |
Location of target site | ENST00000504730.1 | 3UTR | ACAUUAUUUCUCAUAGCAGGAAAUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23446348 / GSE43573 |
CLIP-seq Viewer | Link |
CLIP-seq Support 6 for dataset GSM1065669 | |
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Method / RBP | PAR-CLIP / AGO1 |
Cell line / Condition | HEK293 / 4-thiouridine, ML_MM_8 |
Location of target site | ENST00000504730.1 | 3UTR | ACAUUAUUUCUCAUAGCAGGAAAUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23446348 / GSE43573 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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82 hsa-miR-6830-3p Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT081461 | SSBP4 | single stranded DNA binding protein 4 | 2 | 2 | ||||||||
MIRT132029 | IER5 | immediate early response 5 | 2 | 2 | ||||||||
MIRT187279 | DAZAP2 | DAZ associated protein 2 | 2 | 6 | ||||||||
MIRT350303 | TMEM189-UBE2V1 | TMEM189-UBE2V1 readthrough | 2 | 8 | ||||||||
MIRT350307 | UBE2V1 | ubiquitin conjugating enzyme E2 V1 | 2 | 8 | ||||||||
MIRT372105 | EIF3H | eukaryotic translation initiation factor 3 subunit H | 2 | 2 | ||||||||
MIRT408159 | DCK | deoxycytidine kinase | 2 | 4 | ||||||||
MIRT442623 | LOX | lysyl oxidase | 2 | 2 | ||||||||
MIRT442952 | ASXL2 | additional sex combs like 2, transcriptional regulator | 2 | 2 | ||||||||
MIRT469401 | REL | REL proto-oncogene, NF-kB subunit | 2 | 6 | ||||||||
MIRT476631 | G2E3 | G2/M-phase specific E3 ubiquitin protein ligase | 2 | 2 | ||||||||
MIRT485039 | TMEM189 | transmembrane protein 189 | 2 | 8 | ||||||||
MIRT485133 | RASSF8 | Ras association domain family member 8 | 2 | 6 | ||||||||
MIRT498963 | ORC4 | origin recognition complex subunit 4 | 2 | 8 | ||||||||
MIRT500082 | L2HGDH | L-2-hydroxyglutarate dehydrogenase | 2 | 8 | ||||||||
MIRT503018 | CAND1 | cullin associated and neddylation dissociated 1 | 2 | 2 | ||||||||
MIRT503374 | SCAMP1 | secretory carrier membrane protein 1 | 2 | 2 | ||||||||
MIRT504975 | ZNF711 | zinc finger protein 711 | 2 | 2 | ||||||||
MIRT518984 | NNT | nicotinamide nucleotide transhydrogenase | 2 | 4 | ||||||||
MIRT520754 | TFDP1 | transcription factor Dp-1 | 2 | 6 | ||||||||
MIRT526785 | SGCD | sarcoglycan delta | 2 | 2 | ||||||||
MIRT533868 | TBL1XR1 | transducin beta like 1 X-linked receptor 1 | 2 | 2 | ||||||||
MIRT535107 | PMEPA1 | prostate transmembrane protein, androgen induced 1 | 2 | 2 | ||||||||
MIRT538991 | BAG4 | BCL2 associated athanogene 4 | 2 | 2 | ||||||||
MIRT543518 | PRSS21 | protease, serine 21 | 2 | 2 | ||||||||
MIRT543813 | SNX10 | sorting nexin 10 | 2 | 2 | ||||||||
MIRT543825 | GSG1 | germ cell associated 1 | 2 | 2 | ||||||||
MIRT545334 | CCDC83 | coiled-coil domain containing 83 | 2 | 2 | ||||||||
MIRT545669 | DECR1 | 2,4-dienoyl-CoA reductase 1 | 2 | 2 | ||||||||
MIRT547798 | KAT7 | lysine acetyltransferase 7 | 2 | 2 | ||||||||
MIRT548068 | GIGYF1 | GRB10 interacting GYF protein 1 | 2 | 2 | ||||||||
MIRT549577 | ZNF850 | zinc finger protein 850 | 2 | 2 | ||||||||
MIRT550753 | ENTPD1 | ectonucleoside triphosphate diphosphohydrolase 1 | 2 | 2 | ||||||||
MIRT550808 | FAM229B | family with sequence similarity 229 member B | 2 | 2 | ||||||||
MIRT551457 | CARKD | NAD(P)HX dehydratase | 2 | 2 | ||||||||
MIRT551852 | RPS3 | ribosomal protein S3 | 2 | 2 | ||||||||
MIRT554218 | SLC30A1 | solute carrier family 30 member 1 | 2 | 2 | ||||||||
MIRT556588 | LEPROT | leptin receptor overlapping transcript | 2 | 2 | ||||||||
MIRT557344 | HDGF | heparin binding growth factor | 2 | 4 | ||||||||
MIRT571945 | LARP1 | La ribonucleoprotein domain family member 1 | 2 | 2 | ||||||||
MIRT574374 | YY1 | YY1 transcription factor | 2 | 2 | ||||||||
MIRT611142 | CRISP1 | cysteine rich secretory protein 1 | 2 | 4 | ||||||||
MIRT611799 | FCRL4 | Fc receptor like 4 | 2 | 2 | ||||||||
MIRT612834 | KCNN3 | potassium calcium-activated channel subfamily N member 3 | 2 | 2 | ||||||||
MIRT617257 | GLIPR1L2 | GLI pathogenesis related 1 like 2 | 2 | 2 | ||||||||
MIRT619781 | NRIP2 | nuclear receptor interacting protein 2 | 2 | 2 | ||||||||
MIRT620440 | SEMA3E | semaphorin 3E | 2 | 2 | ||||||||
MIRT621725 | TNR | tenascin R | 2 | 2 | ||||||||
MIRT622905 | PCDH17 | protocadherin 17 | 2 | 2 | ||||||||
MIRT623428 | KLF6 | Kruppel like factor 6 | 2 | 2 | ||||||||
MIRT627856 | PITPNM3 | PITPNM family member 3 | 2 | 2 | ||||||||
MIRT633894 | FGF10 | fibroblast growth factor 10 | 2 | 2 | ||||||||
MIRT636257 | SEC24D | SEC24 homolog D, COPII coat complex component | 2 | 2 | ||||||||
MIRT640654 | FRY | FRY microtubule binding protein | 2 | 2 | ||||||||
MIRT640857 | TSHZ2 | teashirt zinc finger homeobox 2 | 2 | 4 | ||||||||
MIRT641220 | LRCH1 | leucine rich repeats and calponin homology domain containing 1 | 2 | 2 | ||||||||
MIRT642526 | ANKRD9 | ankyrin repeat domain 9 | 2 | 2 | ||||||||
MIRT646011 | TNFAIP8L2 | TNF alpha induced protein 8 like 2 | 2 | 2 | ||||||||
MIRT653317 | SMOC1 | SPARC related modular calcium binding 1 | 2 | 2 | ||||||||
MIRT657940 | GATM | glycine amidinotransferase | 2 | 2 | ||||||||
MIRT658291 | FAM83F | family with sequence similarity 83 member F | 2 | 2 | ||||||||
MIRT660607 | ANTXR2 | anthrax toxin receptor 2 | 2 | 2 | ||||||||
MIRT664675 | LMBR1L | limb development membrane protein 1 like | 2 | 2 | ||||||||
MIRT664889 | PRRG4 | proline rich and Gla domain 4 | 2 | 2 | ||||||||
MIRT666972 | PHF20L1 | PHD finger protein 20 like 1 | 2 | 2 | ||||||||
MIRT669128 | CD200 | CD200 molecule | 2 | 2 | ||||||||
MIRT673267 | RUNDC1 | RUN domain containing 1 | 2 | 2 | ||||||||
MIRT704609 | CLN8 | CLN8, transmembrane ER and ERGIC protein | 2 | 2 | ||||||||
MIRT709404 | TADA2A | transcriptional adaptor 2A | 2 | 2 | ||||||||
MIRT710963 | CMKLR1 | chemerin chemokine-like receptor 1 | 2 | 2 | ||||||||
MIRT711745 | DTX1 | deltex E3 ubiquitin ligase 1 | 2 | 2 | ||||||||
MIRT715009 | CYP1B1 | cytochrome P450 family 1 subfamily B member 1 | 2 | 2 | ||||||||
MIRT715467 | NEGR1 | neuronal growth regulator 1 | 2 | 2 | ||||||||
MIRT715737 | CD226 | CD226 molecule | 2 | 2 | ||||||||
MIRT716526 | KSR2 | kinase suppressor of ras 2 | 2 | 2 | ||||||||
MIRT718311 | TMPRSS11B | transmembrane protease, serine 11B | 2 | 2 | ||||||||
MIRT719006 | TMEM184C | transmembrane protein 184C | 2 | 2 | ||||||||
MIRT719319 | STAC | SH3 and cysteine rich domain | 2 | 2 | ||||||||
MIRT722092 | SUSD1 | sushi domain containing 1 | 2 | 2 | ||||||||
MIRT723198 | TNRC6C | trinucleotide repeat containing 6C | 2 | 2 | ||||||||
MIRT723239 | BTLA | B and T lymphocyte associated | 2 | 2 | ||||||||
MIRT724850 | IGFBP5 | insulin like growth factor binding protein 5 | 2 | 2 |