pre-miRNA Information | |
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pre-miRNA | hsa-mir-2116 |
Genomic Coordinates | chr15: 59171183 - 59171262 |
Description | Homo sapiens miR-2116 stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | ||||||||||||||||||||||
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Mature miRNA | hsa-miR-2116-5p | |||||||||||||||||||||
Sequence | 14| GGUUCUUAGCAUAGGAGGUCU |34 | |||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||
Experiments | 454 | |||||||||||||||||||||
Editing Events in miRNAs |
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SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | ADSS | ||||||||||||||||||||
Synonyms | ADEH, ADSS 2 | ||||||||||||||||||||
Description | adenylosuccinate synthase | ||||||||||||||||||||
Transcript | NM_001126 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on ADSS | |||||||||||||||||||||
3'UTR of ADSS (miRNA target sites are highlighted) |
>ADSS|NM_001126|3'UTR 1 TGATTGCCAGTAATGCAAGAAACACTCCTTGAGAGGGAGGGGAAAAGACTTTCTTAAATATTTCATTTATGACCTGCAAA 81 TTCAAGAATAAAGACACTGAAGTAAGTTTGAAGCCCTACAGTTGTTTCCAGTCTTTTCAGATGGATGCCTACTGTGGAGA 161 TTAACTTTGGCATATTCCAGTGTCAGCTTTCTTTAGCTGGAATTGCCAAATCATTTGTTGCTCCTGCTGCTCTCATGGTG 241 CCACGTTTTTTTTTTCAATGTTTAGTAATAGTATAATCCATGTTGTTTGATATCAAAAGTAGAATTACTTTTAATGTAGT 321 TTTTCTTCATTATTGTCATTGCGTGTTCTTAAGTTTTACCCCTATTAGATGGTAAGAACAATTAATGCAGTTTTGCACAA 401 ATATTTTTACATTCTGATCATTCAGTTCTGTCATTGTAATCTTTGTTGTTAGAAACAAATGATGAAAACATAGGGGTTCT 481 GTAAACTTTTGTAATGCTATGAATTCTGTTTAAATTTTGGGCTGTCTATTTTCTGCTGAAACCATGCAAAATTGAGCTTT 561 GGTGGGGCTGGGAGGGGGTTATGTATTCATGGGACCTTTAATTTGTACAGAACACAGAACTTATTTCTGTCAGTTATTTA 641 ATACATTGAAAATTTAGTGAAATGTTCAAAGAGAATAGATGTTTCCCAAAACAACAATCTTTATGTTAAAAATAGTCATT 721 AAAAGATCTGTTGTAATATATGGTGGATATTTTTCTTTAATTTCAAACATTACCTCTGAAATGTGTATCTTTTCTTTTTT 801 ATCTTACCATTAATTTTAAATCTAGTGGATTGGTTTTCAACATCGTGCCTGCCGATATGCCTACAGAATCATCTGTAAGT 881 GTCAAAATGAACCCACGTTGTTAGCCATAATTTTGATTATGCCTTTATTTCTCCTTTCTTGAAAAAAAAAAGGTGTTATT 961 TTGACAATTAGGCATAACATTGTTTTGTAGATTATCTTTTAATGAACTATTTTAAATGTTAAATTAGGTGCCACTTAAAT 1041 TTATTTTATTACACCATGAATAGCTGATTAAAAGAACCAAATATTTCTAGTATGAAAAAAAAA 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 GSM545214. RNA binding protein: AGO3. Condition:Control
... - 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 | 159.0 |
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. |
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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CLIP-seq Support 1 for dataset GSM545214 | |
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Method / RBP | PAR-CLIP / AGO3 |
Cell line / Condition | HEK293 / Control |
Location of target site | ENST00000366535.3 | 3UTR | AACAAUUAAUGCAGUUUUGCACAAAUAUUUUUACAUU |
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 | ENST00000366535.3 | 3UTR | UUUUACCCCUAUUAGAUGGUAAGAACAAUUAAUGCAGUUUUGCACAAAUAUUUUUACAUUCUGAUCAUUCA |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 21572407 / GSE28865 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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62 hsa-miR-2116-5p Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT080547 | PMAIP1 | phorbol-12-myristate-13-acetate-induced protein 1 | 2 | 2 | ||||||||
MIRT135054 | ADSS | adenylosuccinate synthase | 2 | 4 | ||||||||
MIRT147317 | KPNA2 | karyopherin subunit alpha 2 | 2 | 4 | ||||||||
MIRT154323 | CEBPB | CCAAT/enhancer binding protein beta | 2 | 2 | ||||||||
MIRT326799 | SYAP1 | synapse associated protein 1 | 2 | 2 | ||||||||
MIRT357963 | GRPEL2 | GrpE like 2, mitochondrial | 2 | 2 | ||||||||
MIRT384296 | GOLT1B | golgi transport 1B | 2 | 2 | ||||||||
MIRT442316 | UBE2Q1 | ubiquitin conjugating enzyme E2 Q1 | 2 | 2 | ||||||||
MIRT443785 | ST13 | ST13, Hsp70 interacting protein | 2 | 2 | ||||||||
MIRT446868 | NBPF3 | NBPF member 3 | 2 | 2 | ||||||||
MIRT447647 | RAB3GAP1 | RAB3 GTPase activating protein catalytic subunit 1 | 2 | 2 | ||||||||
MIRT448470 | SLC45A4 | solute carrier family 45 member 4 | 2 | 2 | ||||||||
MIRT449121 | XRRA1 | X-ray radiation resistance associated 1 | 2 | 2 | ||||||||
MIRT450245 | TRIM66 | tripartite motif containing 66 | 2 | 2 | ||||||||
MIRT450270 | F2RL2 | coagulation factor II thrombin receptor like 2 | 2 | 2 | ||||||||
MIRT450688 | RPN2 | ribophorin II | 2 | 2 | ||||||||
MIRT481123 | AZIN1 | antizyme inhibitor 1 | 2 | 4 | ||||||||
MIRT497207 | CDH7 | cadherin 7 | 2 | 4 | ||||||||
MIRT502956 | CCNT2 | cyclin T2 | 2 | 2 | ||||||||
MIRT509226 | KIF14 | kinesin family member 14 | 2 | 6 | ||||||||
MIRT515395 | ARHGAP21 | Rho GTPase activating protein 21 | 2 | 4 | ||||||||
MIRT525559 | MTRNR2L7 | MT-RNR2-like 7 | 2 | 6 | ||||||||
MIRT525608 | MTRNR2L3 | MT-RNR2-like 3 | 2 | 4 | ||||||||
MIRT533254 | VCAM1 | vascular cell adhesion molecule 1 | 2 | 2 | ||||||||
MIRT535782 | MTRNR2L11 | MT-RNR2-like 11 | 2 | 6 | ||||||||
MIRT535803 | MTRNR2L10 | MT-RNR2-like 10 | 2 | 4 | ||||||||
MIRT543211 | TMEM117 | transmembrane protein 117 | 2 | 2 | ||||||||
MIRT552792 | YAF2 | YY1 associated factor 2 | 2 | 2 | ||||||||
MIRT553947 | STAMBP | STAM binding protein | 2 | 2 | ||||||||
MIRT556217 | MB21D2 | Mab-21 domain containing 2 | 2 | 2 | ||||||||
MIRT566351 | POLDIP2 | DNA polymerase delta interacting protein 2 | 2 | 2 | ||||||||
MIRT568429 | GDNF | glial cell derived neurotrophic factor | 2 | 2 | ||||||||
MIRT568521 | ANP32E | acidic nuclear phosphoprotein 32 family member E | 2 | 2 | ||||||||
MIRT573359 | PDE3A | phosphodiesterase 3A | 2 | 2 | ||||||||
MIRT574653 | LMAN2 | lectin, mannose binding 2 | 2 | 2 | ||||||||
MIRT608172 | ERBB2 | erb-b2 receptor tyrosine kinase 2 | 2 | 2 | ||||||||
MIRT610692 | FAM89A | family with sequence similarity 89 member A | 2 | 2 | ||||||||
MIRT618459 | TMCO1 | transmembrane and coiled-coil domains 1 | 2 | 2 | ||||||||
MIRT622281 | SH3TC2 | SH3 domain and tetratricopeptide repeats 2 | 2 | 2 | ||||||||
MIRT624615 | B3GALT5 | beta-1,3-galactosyltransferase 5 | 2 | 2 | ||||||||
MIRT631041 | TAS2R30 | taste 2 receptor member 30 | 2 | 2 | ||||||||
MIRT638335 | RCAN1 | regulator of calcineurin 1 | 2 | 2 | ||||||||
MIRT641630 | KIAA1244 | ARFGEF family member 3 | 1 | 1 | ||||||||
MIRT649117 | SRD5A1 | steroid 5 alpha-reductase 1 | 2 | 2 | ||||||||
MIRT652246 | TPI1 | triosephosphate isomerase 1 | 2 | 2 | ||||||||
MIRT659865 | CAPRIN1 | cell cycle associated protein 1 | 2 | 4 | ||||||||
MIRT669219 | CAND1 | cullin associated and neddylation dissociated 1 | 2 | 2 | ||||||||
MIRT682585 | CPA4 | carboxypeptidase A4 | 2 | 2 | ||||||||
MIRT690129 | EPHX2 | epoxide hydrolase 2 | 2 | 2 | ||||||||
MIRT699793 | SEC24A | SEC24 homolog A, COPII coat complex component | 2 | 2 | ||||||||
MIRT699991 | RPS24 | ribosomal protein S24 | 2 | 2 | ||||||||
MIRT710376 | LMBR1 | limb development membrane protein 1 | 2 | 2 | ||||||||
MIRT710412 | YTHDC1 | YTH domain containing 1 | 2 | 2 | ||||||||
MIRT710574 | TNPO1 | transportin 1 | 2 | 2 | ||||||||
MIRT712045 | STYK1 | serine/threonine/tyrosine kinase 1 | 2 | 2 | ||||||||
MIRT713292 | ADAMTS20 | ADAM metallopeptidase with thrombospondin type 1 motif 20 | 2 | 2 | ||||||||
MIRT718211 | TNRC6C | trinucleotide repeat containing 6C | 2 | 2 | ||||||||
MIRT718809 | SLC25A33 | solute carrier family 25 member 33 | 2 | 2 | ||||||||
MIRT719341 | VGLL4 | vestigial like family member 4 | 2 | 2 | ||||||||
MIRT720841 | C1orf52 | chromosome 1 open reading frame 52 | 2 | 2 | ||||||||
MIRT724076 | NCKAP1L | NCK associated protein 1 like | 2 | 2 | ||||||||
MIRT724602 | AP3B1 | adaptor related protein complex 3 beta 1 subunit | 2 | 2 |
miRNA-Drug Associations | ||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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