pre-miRNA Information | |
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pre-miRNA | hsa-mir-1284 |
Genomic Coordinates | chr3: 71541970 - 71542089 |
Synonyms | MIRN1284, hsa-mir-1284, MIR1284 |
Description | Homo sapiens miR-1284 stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | |||||||||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-1284 | ||||||||||||||||||||||||||||||||||||
Sequence | 30| UCUAUACAGACCCUGGCUUUUC |51 | ||||||||||||||||||||||||||||||||||||
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 | |
miRNAs in Extracellular Vesicles |
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Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | ADCYAP1 | ||||||||||||||||||||
Synonyms | PACAP | ||||||||||||||||||||
Description | adenylate cyclase activating polypeptide 1 | ||||||||||||||||||||
Transcript | NM_001099733 | ||||||||||||||||||||
Other Transcripts | NM_001117 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on ADCYAP1 | |||||||||||||||||||||
3'UTR of ADCYAP1 (miRNA target sites are highlighted) |
>ADCYAP1|NM_001099733|3'UTR 1 CGATGGGTTACCAGCTACCCTGTGTATACAGCCCTGACGCAATGAAAAGTCGTTTTCCAAACTGACTCAACAGTCATCGC 81 TCGTGTGTTCTATCCAAACATGTATTTATGTAATGAAGTAAAGCCATTAAATGAATATTTTGATAATAATATTGTTTTTC 161 TTTCTACAAAGCACTAGAGAATGCACAGATATACTTTGTGGACCAATTATTGATATATATTATAAATATATATAAAGAAT 241 ATATATATATATATATATATATATATATATAAAGTATAGAGAGAAGTTCATACAAAGCGTGCACAAGGATTGAAAATTCG 321 CCCGAGCTGTTTATGTTTTTATAAAAATAAATAGAAAAGTAGACAATCATTGTTTTGAATATTACTCCTATTTTTGTAAA 401 CTGGAATTAAAAGGATAGTATTTTTATCCATGACAGGCCTGAAGATATTACTACTTACCATTTGCTACTGTACATAAACA 481 ATGATGCCCTGCTCCAGGGAGATTTTGAGGTAAAGATATGGAGAATTGCTGAAGGGCATTCTTTCCCAGTGAGTCTCTGG 561 GGCAGGCTGCTTCAATCCCAGCCTAACTCAACTGGGCTCTGTCCCCCTGGTTGGGTGGCAATTCCAATATTTCTGCTTTC 641 TTTGATTCTCCTTTTATGTGTAGTTGTCTCTCTTCAGACTCTCAGCCCAGAAGAAAATTCTCCTGATAAAACAACAGCTC 721 GATCCAAATTGTGCTTCTCCCCAGAATTCACGCCTCTCCCTAGGAGAAGAGTTGAGGAACTGTACAGAAAAGGGCGGCTT 801 CGTTAGACCGCTCTCTTTTCTGTACTTCCTGAGTGGCCAGGGAATCTAATATCCCCAAATTAGGGCAATTGGAACAAAGT 881 GAAGGACATAGAGGTATATTGGAAGAGGCAGAGCCTGAGGTGGTAGGAGGAGGACCCTGGAAATGGACTGGTTTGAGATT 961 GCCCCAGGTCTGGGAAGCTGAGGGCAAATCCAGTCCCAATGGTCCTGACTTTGGGCGCTGGGTATTGGAAATGGATGCAA 1041 AGTACAATGTGTTTTTCTCCAGTGCTGTCCATGCTTCTCATCTTGTGAAATGGCCAGGATCCTCTCCTTTGAAACCTGCT 1121 CTGTAGGAGCTACCCTTTTCCTTTGTGGTTTTATGGAGACCTCTCCTTCCTACCCTCCTGCACTGTTTAAGTACTGTTTA 1201 CCATTTTTCATTCACTTCTCTTAAACTTGTGAATGCTTCTCACTTTTTTTTTTTGTTTGATGCAGGCACTTATTGTAAAT 1281 TTTAGAAACCCCTCTGTAGCCACTAGTAAGTAATTATGCACTAAATATGAACCCTTTGTTTCTTGTTTATTGAGTTTGTA 1361 GGTAAAATGTATTTTTCTACATTATTGCTTATTGCTTAGTAAAATTTATTTCATAAAACCAACCTTTGTCATATTAGAAT 1441 GTGTAGTGTTCACATGTTGCTCAGTTTTGCTAACTGATAAATCATTTAATCCTCTTCTTCATATGTATGAGTACTATCTT 1521 ATATCTGTGGTCAAGAGTGAGGTAAGCAAGCTCCAACAGACCCTGAGAACCTACGCTTGTATCCTTTCTTTGGCTAAAGA 1601 AAGCATGTCTGTTTCCTGTCAATTCTTTGAACATACAGAGTAATCTTTATAAACAAAAGAACCTTCACCCAGCAATCAGA 1681 TCGAGCAGCAACAGACAAACCAGCCAGCCAATCTCCCAAATTTCAGGCACAAGTTTATTTATTTATTTTTTTATGTTTTG 1761 AAAAAAGAAGATGAAGAAGAAGAAAAAAAAAAGAACAAGGAAAGATTAAACGTTAGCTTGTAAAGTTTAAAGGACCTTTC 1841 CTTTTCCTTTACGGATTTGATCAGTATGAAGTCATAAATCAAAGAAAACAGAATTGGATTTGCATTCCCAGGCGGGATGG 1921 ATGCTGCCAGGAGATCACATTGCAAATAGTGAAAACAGAGGCATTCGGTCTATGCCTGAGTCCTGTGTATAGGATCAATC 2001 TTCCTTTAATTCCGCAGTCTCCTCAGGCAATGTGACACGGGATGCAGTTTGCAGCTTTAGTGCCTTTCTTCGCCTTTTAA 2081 ATTGCCACGAATCACAGATGGCTATTTAGTGGCCCTACAATGCTGCAACACATCAGCTTGCATTTTAGTCTTAATTATTT 2161 GTTTCTTGGATAATGGGCAGAGTTTTCTGTATTTGTATCAGCTGTTAGTGGTGAAATAGGGCTCTAGTTAACCTTTTATT 2241 TATGAAGTCTAATTTAGTGTTCCCGTGGCTAGTTGCAAGCATTTTACAGTGATCACCCAGTTTAATCTTTTGTATACTTT 2321 TTAGAAATGCCAAGAGCCTTACTAAACTGAAGCAGATTTATGATATAGTGATAATTTAGGTAGATGTTAGTCTTGAAGCT 2401 CTTATTTTGTGTGCAACTGATTATAAAAACACCTTAACCAAGTATTATTACACACATGATATCTATAACTAGGACTTTGA 2481 TAACTGTTATATAAAGTGTGTAAAATTTGTATGAATAAATTTTTGTAAACAATGCAA 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 GSM545216. RNA binding protein: AGO2. Condition:miR-124 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 | 116.0 |
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 GSM545216 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / miR-124 transfection |
Location of target site | ENST00000579794.1 | 3UTR | AUAUAUAUAUAUAUAUAUAUAUAUAUAAAGU |
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 | ENST00000579794.1 | 3UTR | AGAAUAUAUAUAUAUAUAUAUAUAUAUAUAUAUAUAAAG |
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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46 hsa-miR-1284 Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT035831 | PRRC2B | proline rich coiled-coil 2B | 1 | 1 | ||||||||
MIRT079621 | DNAJB4 | DnaJ heat shock protein family (Hsp40) member B4 | 2 | 2 | ||||||||
MIRT149901 | LDLR | low density lipoprotein receptor | 2 | 2 | ||||||||
MIRT182786 | TOR1AIP2 | torsin 1A interacting protein 2 | 2 | 2 | ||||||||
MIRT188827 | TMTC3 | transmembrane and tetratricopeptide repeat containing 3 | 2 | 2 | ||||||||
MIRT198187 | EIF4A1 | eukaryotic translation initiation factor 4A1 | 3 | 1 | ||||||||
MIRT245472 | ARID5B | AT-rich interaction domain 5B | 2 | 2 | ||||||||
MIRT252245 | PMAIP1 | phorbol-12-myristate-13-acetate-induced protein 1 | 2 | 6 | ||||||||
MIRT269363 | WEE1 | WEE1 G2 checkpoint kinase | 2 | 2 | ||||||||
MIRT320406 | HOXA9 | homeobox A9 | 2 | 4 | ||||||||
MIRT474722 | KIF13A | kinesin family member 13A | 2 | 6 | ||||||||
MIRT497926 | BTG1 | BTG anti-proliferation factor 1 | 2 | 2 | ||||||||
MIRT504264 | C1orf147 | chromosome 1 open reading frame 147 | 2 | 4 | ||||||||
MIRT520449 | TSPAN2 | tetraspanin 2 | 2 | 4 | ||||||||
MIRT524092 | DNAJB14 | DnaJ heat shock protein family (Hsp40) member B14 | 2 | 4 | ||||||||
MIRT528639 | SENP6 | SUMO1/sentrin specific peptidase 6 | 2 | 2 | ||||||||
MIRT537385 | FGF2 | fibroblast growth factor 2 | 2 | 2 | ||||||||
MIRT538902 | BRI3BP | BRI3 binding protein | 2 | 2 | ||||||||
MIRT542095 | KCNK10 | potassium two pore domain channel subfamily K member 10 | 2 | 6 | ||||||||
MIRT543976 | PRR23A | proline rich 23A | 2 | 2 | ||||||||
MIRT549625 | ADCYAP1 | adenylate cyclase activating polypeptide 1 | 2 | 4 | ||||||||
MIRT554298 | SIPA1L2 | signal induced proliferation associated 1 like 2 | 2 | 2 | ||||||||
MIRT554872 | RCAN2 | regulator of calcineurin 2 | 2 | 2 | ||||||||
MIRT567623 | FAM210A | family with sequence similarity 210 member A | 2 | 2 | ||||||||
MIRT571137 | TTC33 | tetratricopeptide repeat domain 33 | 2 | 2 | ||||||||
MIRT576361 | Pxdn | peroxidasin | 2 | 2 | ||||||||
MIRT611088 | PHF8 | PHD finger protein 8 | 2 | 2 | ||||||||
MIRT612380 | TCTE1 | t-complex-associated-testis-expressed 1 | 2 | 4 | ||||||||
MIRT613725 | MTPN | myotrophin | 2 | 2 | ||||||||
MIRT614627 | YAE1D1 | Yae1 domain containing 1 | 2 | 2 | ||||||||
MIRT615818 | KIAA1549L | KIAA1549 like | 2 | 2 | ||||||||
MIRT620949 | TBCK | TBC1 domain containing kinase | 2 | 2 | ||||||||
MIRT622339 | SCN4A | sodium voltage-gated channel alpha subunit 4 | 2 | 2 | ||||||||
MIRT623219 | MTA3 | metastasis associated 1 family member 3 | 2 | 4 | ||||||||
MIRT628932 | SLC1A4 | solute carrier family 1 member 4 | 2 | 2 | ||||||||
MIRT632121 | FKBP9 | FK506 binding protein 9 | 2 | 2 | ||||||||
MIRT635877 | COX17 | COX17, cytochrome c oxidase copper chaperone | 2 | 2 | ||||||||
MIRT636485 | IKBKG | inhibitor of nuclear factor kappa B kinase subunit gamma | 2 | 2 | ||||||||
MIRT653097 | SRSF7 | serine and arginine rich splicing factor 7 | 2 | 2 | ||||||||
MIRT655048 | PKN2 | protein kinase N2 | 2 | 2 | ||||||||
MIRT686946 | SFT2D3 | SFT2 domain containing 3 | 2 | 2 | ||||||||
MIRT692724 | INPP5B | inositol polyphosphate-5-phosphatase B | 2 | 2 | ||||||||
MIRT697282 | ZNF800 | zinc finger protein 800 | 2 | 2 | ||||||||
MIRT698995 | SPAG9 | sperm associated antigen 9 | 2 | 2 | ||||||||
MIRT704462 | CRNKL1 | crooked neck pre-mRNA splicing factor 1 | 2 | 2 | ||||||||
MIRT715163 | FIG4 | FIG4 phosphoinositide 5-phosphatase | 2 | 2 |
miRNA-Drug Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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