pre-miRNA Information | |
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pre-miRNA | hsa-mir-1268a |
Genomic Coordinates | chr15: 22225278 - 22225329 |
Description | Homo sapiens miR-1268a stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | |||||||||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-1268a | ||||||||||||||||||||||||||||||||||||
Sequence | 5| CGGGCGUGGUGGUGGGGG |22 | ||||||||||||||||||||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||||||||||||||||||||
Experiments | Illumina | ||||||||||||||||||||||||||||||||||||
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 | DHCR7 | ||||||||||||||||||||
Synonyms | SLOS | ||||||||||||||||||||
Description | 7-dehydrocholesterol reductase | ||||||||||||||||||||
Transcript | NM_001163817 | ||||||||||||||||||||
Other Transcripts | NM_001360 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on DHCR7 | |||||||||||||||||||||
3'UTR of DHCR7 (miRNA target sites are highlighted) |
>DHCR7|NM_001163817|3'UTR
1 GGGCACGCCCTAGGGAGAAGCCCTGTGGGGCTGTCAAGAGCGTGTTCTGCCAGGTCCATGGGGGCTGGCATCCCAGCTCC
81 AACTCGAGGAGCCTCAGTTTCCTCATCTGTAAACTGGAGAGAGCCCAGCACTTGGCAGGTGTCCAGTACCTAATCACGCT
161 CTGTTCCTTGCTTTTGCCTTCAAGGGAATTCCGAGTGTCCAGCACTGCCGTATTGCCAGCACAGACGGATTTTCTCTAAT
241 CAGTGTCCCTGGGGCAGGAGGATGACCCAGTCACCTTTACTAGTCCTTTGGAGACAATTTACCTGTATTAGGAGCCCAGG
321 CCACGCTACACTCTGCCCACACTGGTGAGCAGGAGGTCTTCCCACGCCCTGTCATTAGGCTGCATTTACTCTTGCTAAAT
401 AAAAGTGGGAGTGGGGCGTGCGCGTTATCCATGTATTGCCTTTCAGCTCTAGATCCCCCTCCCCTGCCTGCTCTGCAGTC
481 GTGGGTGGGGCCCGTGCGCCGTTTCTCCTTGGTAGCGTGCACGGTGTTGAACTGGGACACTGGGGAGAAAGGGGCTTTCA
561 TGTCGTTTCCTTCCTGCTCCTGCTGCACAGCTGCCAGGAGTGCTCTGCCTGGAGTCTGCAGACCTCAGAGAGGTCCCAGC
641 ACCGGCTGTGGCCTTTCAGGTGTAGGCAGGTGGGCTCTGCTTCCCGATTCCCTGTGAGCGCCCACCCTCTCGAAAGAATT
721 TTCTGCTTGCCCTATGACTGTGCAGACTCTGGCTCGAGCAACCCGGGGAACTTCACCCTCAGGGGCCTCCCACACCTTCT
801 CCAGCGAGGAGGTCTCAGTCCCAGCCTCGGGAGGGCACCTCCTTTTCTGTGCTTTCTTCCCTGAGGCATTCTTCCTCATC
881 CCTAGGGTGTTGTGTAGAACTCTTTTTAAACTCTATGCTCCGAGTAGAGTTCATCTTTATATTAAACTTCCCCTGTTCAA
961 ATAA
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 | ||||||
Disease | 1717.0 | ||||||
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 GSM714645. 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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CLIP-seq Support 1 for dataset GSM714645 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / completeT1, repB |
Location of target site | ENST00000407721.2 | 3UTR | UCUUCCCACGCCCUGUCAUUAGGCUGCAUUUACUCUUG |
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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44 hsa-miR-1268a Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT035845 | POLR2I | RNA polymerase II subunit I | 1 | 1 | ||||||||
MIRT035847 | FASN | fatty acid synthase | 1 | 1 | ||||||||
MIRT053736 | SOX12 | SRY-box 12 | 1 | 1 | ||||||||
MIRT053737 | CAMK2G | calcium/calmodulin dependent protein kinase II gamma | 1 | 1 | ||||||||
MIRT473717 | MAPK1 | mitogen-activated protein kinase 1 | 2 | 2 | ||||||||
MIRT483654 | QSOX2 | quiescin sulfhydryl oxidase 2 | 2 | 4 | ||||||||
MIRT484277 | AIP | aryl hydrocarbon receptor interacting protein | 2 | 4 | ||||||||
MIRT486674 | WDR81 | WD repeat domain 81 | 2 | 2 | ||||||||
MIRT488672 | WWP2 | WW domain containing E3 ubiquitin protein ligase 2 | 2 | 4 | ||||||||
MIRT493453 | ITFG3 | family with sequence similarity 234 member A | 2 | 2 | ||||||||
MIRT495902 | ZNF641 | zinc finger protein 641 | 2 | 2 | ||||||||
MIRT500188 | BARX1 | BARX homeobox 1 | 2 | 4 | ||||||||
MIRT512015 | DNAJC10 | DnaJ heat shock protein family (Hsp40) member C10 | 2 | 2 | ||||||||
MIRT521134 | SGPL1 | sphingosine-1-phosphate lyase 1 | 2 | 4 | ||||||||
MIRT530047 | TRIM72 | tripartite motif containing 72 | 2 | 2 | ||||||||
MIRT531519 | NOM1 | nucleolar protein with MIF4G domain 1 | 2 | 2 | ||||||||
MIRT543736 | DHCR7 | 7-dehydrocholesterol reductase | 2 | 2 | ||||||||
MIRT558054 | EVI5L | ecotropic viral integration site 5 like | 2 | 2 | ||||||||
MIRT569603 | TRIM29 | tripartite motif containing 29 | 2 | 2 | ||||||||
MIRT570027 | FAM228A | family with sequence similarity 228 member A | 2 | 2 | ||||||||
MIRT573595 | CERS1 | ceramide synthase 1 | 2 | 2 | ||||||||
MIRT623884 | FRMPD4 | FERM and PDZ domain containing 4 | 2 | 2 | ||||||||
MIRT630000 | PDE6B | phosphodiesterase 6B | 2 | 2 | ||||||||
MIRT632716 | MSANTD4 | Myb/SANT DNA binding domain containing 4 with coiled-coils | 2 | 2 | ||||||||
MIRT633497 | ERO1L | endoplasmic reticulum oxidoreductase 1 alpha | 1 | 1 | ||||||||
MIRT637076 | SELPLG | selectin P ligand | 2 | 2 | ||||||||
MIRT638183 | TLN1 | talin 1 | 2 | 2 | ||||||||
MIRT638767 | EPB41 | erythrocyte membrane protein band 4.1 | 2 | 2 | ||||||||
MIRT668073 | GMPS | guanine monophosphate synthase | 2 | 2 | ||||||||
MIRT669874 | RAET1E | retinoic acid early transcript 1E | 2 | 2 | ||||||||
MIRT670664 | KIAA1551 | KIAA1551 | 2 | 2 | ||||||||
MIRT671283 | RPL37A | ribosomal protein L37a | 2 | 2 | ||||||||
MIRT675055 | OR7D2 | olfactory receptor family 7 subfamily D member 2 | 2 | 2 | ||||||||
MIRT682784 | BLOC1S3 | biogenesis of lysosomal organelles complex 1 subunit 3 | 2 | 2 | ||||||||
MIRT683344 | SCARF1 | scavenger receptor class F member 1 | 2 | 2 | ||||||||
MIRT690283 | ZNF154 | zinc finger protein 154 | 2 | 2 | ||||||||
MIRT695172 | SLC25A33 | solute carrier family 25 member 33 | 2 | 2 | ||||||||
MIRT695222 | SCAMP3 | secretory carrier membrane protein 3 | 2 | 2 | ||||||||
MIRT700485 | PTPRF | protein tyrosine phosphatase, receptor type F | 2 | 2 | ||||||||
MIRT700601 | PRKCA | protein kinase C alpha | 2 | 2 | ||||||||
MIRT701410 | NKRF | NFKB repressing factor | 2 | 2 | ||||||||
MIRT703995 | EIF5A2 | eukaryotic translation initiation factor 5A2 | 2 | 2 | ||||||||
MIRT711232 | RETSAT | retinol saturase | 2 | 2 | ||||||||
MIRT719510 | TMEM175 | transmembrane protein 175 | 2 | 2 |
miRNA-Drug Associations | ||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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