pre-miRNA Information | |
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pre-miRNA | hsa-mir-4656 |
Genomic Coordinates | chr7: 4788565 - 4788639 |
Description | Homo sapiens miR-4656 stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | |||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-4656 | ||||||||||||||||||||||||||||||
Sequence | 10| UGGGCUGAGGGCAGGAGGCCUGU |32 | ||||||||||||||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||||||||||||||
Experiments | Illumina | ||||||||||||||||||||||||||||||
SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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Human miRNA Tissue Atlas | |
Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | LAPTM5 | ||||||||||||||||||||
Synonyms | CLAST6 | ||||||||||||||||||||
Description | lysosomal protein transmembrane 5 | ||||||||||||||||||||
Transcript | NM_006762 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on LAPTM5 | |||||||||||||||||||||
3'UTR of LAPTM5 (miRNA target sites are highlighted) |
>LAPTM5|NM_006762|3'UTR 1 CCCTCGCCAGGCCCCAGCCCCAGTGCTGGGAGGGGTGGAGCTGCCTCATAATCTGCTTTTTTGCTTTGGTGGCCCCTGTG 81 GCCTGGGTGGGCCCTCCCGCCCCTCCCTGGCAGGACAATCTGCTTGTGTCTCCCTCGCTGGCCTGCTCCTCCTGCAGGGC 161 CTGTGAGCTGCTCACAACTGGGTCAACGCTTTAGGCTGAGTCACTCCTCGGGTCTCTCCATAATTCAGCCCAACAATGCT 241 TGGTTTATTTCAATCAGCTCTGACACTTGTTTAGACGATTGGCCATTCTAAAGTTGGTGAGTTTGTCAAGCAACTATCGA 321 CTTGATCAGTTCAGCCAAGCAACTGACAAATCAAAAACCCACTTGTCAGTTCAGTAAAATAATTTGGTCAAACAACAGTC 401 TATTGCATTGATTTATAAATAGTTGTCAGTTCACATAGCAATTTAATCAAGTAATCATTAATTAGTTACCCCCTATATAT 481 AAATATATGTAATCAATTTCTTCAAATAGCTTGCTTACATGATAATCAATTAGCCAACCATGAGTCATTTAGAATAGTGA 561 TAAATAGAATACACAGAATAGTGATGAAATTCAATTTAAAAAATCACGTTAGCCTCCAAACCATTTAATTCAAATGAACC 641 CATCAACTGGATGCCAACTCTGGCGAATGTAGGACCTCTGAGTGGCTGTATAATTGTTAATTCAAATGAAATTCATTTAA 721 ACAGTTGACAAACTGTCATTCAACAATTAGCTCCAGGAAATAACAGTTATTTCATCATAAAACAGTCCCTTCAAACACAC 801 AATTGTTCTGCTGAAGAGTTGTCATCAACAATCCAATGCTCACCTATTCAGTTGCTCTGTGGTCAGTGTGGCTGCATAAC 881 AGTGGATTCCATGAAAGGAGTCATTTTAGTGATGAGCTGCCAGTCCATTCCCAGGCCAGGCTGTCGCTGGCCATCCATTC 961 AGTCGATTCAGTCATAGGCGAATCTGTTCTGCCCGAGGCTTGTGGTCAAGCAAAAATTCAGCCCTGAAATCAGGCACATC 1041 TGTTCGTTGGACTAAACCCACAGGTTAGTTCAGTCAAAGCAGGCAACCCCCTTGTGGGCACTGACCCTGCCACTGGGGTC 1121 ATGGCGGTTGTGGCAGCTGGGGAGGTTTGGCCCCAACAGCCCTCCTGTGCCTGCTTCCCTGTGTGTCGGGGTCCTCCAGG 1201 GAGCTGACCCAGAGGTGGAGGCCACGGAGGCAGGGTCTCTGGGGACTGTCGGGGGGTACAGAGGGAGAAGGCTCTGCAAG 1281 AGCTCCCTGGCAATACCCCCTTGTGTAATTGCTTTGTGTGCGACAGGGAGGAAGTTTCAATAAAGCAGCAACAAGCTTCT 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 | BC-1 | ||||||
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 GSM796037. RNA binding protein: AGO2. Condition:4-Thiouridine
PAR-CLIP data was present in GSM796038. RNA binding protein: AGO2. Condition:4-Thiouridine
... - Gottwein E; Corcoran DL; Mukherjee N; et al., 2011, Cell host & microbe. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Gottwein E; Corcoran DL; Mukherjee N; et al. - Cell host & microbe, 2011
Primary effusion lymphoma (PEL) is caused by Kaposi's sarcoma-associated herpesvirus (KSHV) and frequently also harbors Epstein-Barr virus (EBV). The expression of KSHV- and EBV-encoded microRNAs (miRNAs) in PELs suggests a role for these miRNAs in latency and lymphomagenesis. Using PAR-CLIP, a technology which allows the direct and transcriptome-wide identification of miRNA targets, we delineate the target sites for all viral and cellular miRNAs expressed in PEL cell lines. The resulting data set revealed that KSHV miRNAs directly target more than 2000 cellular mRNAs, including many involved in pathways relevant to KSHV pathogenesis. Moreover, 58% of these mRNAs are also targeted by EBV miRNAs, via distinct binding sites. In addition to a known viral analog of cellular miR-155, we show that KSHV encodes a viral miRNA that mimics cellular miR-142-3p function. In summary, this study identifies an extensive list of KSHV miRNA targets, which are likely to influence viral replication and pathogenesis.
LinkOut: [PMID: 22100165]
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CLIP-seq Support 1 for dataset GSM796037 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | BC-1 / 4-Thiouridine |
Location of target site | ENST00000294507.3 | 3UTR | UCAAGCAAAAAUUCAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 22100165 / GSE32109 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM796038 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | BC-1 / 4-Thiouridine |
Location of target site | ENST00000294507.3 | 3UTR | UCAAGCAAAAAUUCAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 22100165 / GSE32109 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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48 hsa-miR-4656 Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT135536 | RAB5B | RAB5B, member RAS oncogene family | 2 | 2 | ||||||||
MIRT168127 | SOX4 | SRY-box 4 | 2 | 2 | ||||||||
MIRT301229 | SH3BP4 | SH3 domain binding protein 4 | 2 | 2 | ||||||||
MIRT444362 | TIMM8B | translocase of inner mitochondrial membrane 8 homolog B | 2 | 2 | ||||||||
MIRT445909 | SLC10A3 | solute carrier family 10 member 3 | 2 | 2 | ||||||||
MIRT447283 | LAPTM5 | lysosomal protein transmembrane 5 | 2 | 2 | ||||||||
MIRT453797 | KBTBD12 | kelch repeat and BTB domain containing 12 | 2 | 2 | ||||||||
MIRT456777 | MTHFSD | methenyltetrahydrofolate synthetase domain containing | 2 | 2 | ||||||||
MIRT459647 | PCSK9 | proprotein convertase subtilisin/kexin type 9 | 2 | 2 | ||||||||
MIRT462333 | BCL7B | BCL tumor suppressor 7B | 2 | 2 | ||||||||
MIRT463535 | ZBTB7A | zinc finger and BTB domain containing 7A | 2 | 2 | ||||||||
MIRT465799 | TMEM91 | transmembrane protein 91 | 2 | 2 | ||||||||
MIRT470647 | POM121C | POM121 transmembrane nucleoporin C | 2 | 2 | ||||||||
MIRT470837 | PLXND1 | plexin D1 | 2 | 2 | ||||||||
MIRT471129 | PHF19 | PHD finger protein 19 | 2 | 2 | ||||||||
MIRT483310 | SLC35C2 | solute carrier family 35 member C2 | 2 | 2 | ||||||||
MIRT487264 | CCNF | cyclin F | 2 | 2 | ||||||||
MIRT491731 | SEMA3F | semaphorin 3F | 2 | 2 | ||||||||
MIRT497195 | DRP2 | dystrophin related protein 2 | 2 | 2 | ||||||||
MIRT508384 | SPTBN2 | spectrin beta, non-erythrocytic 2 | 2 | 4 | ||||||||
MIRT530496 | FADS6 | fatty acid desaturase 6 | 2 | 2 | ||||||||
MIRT546995 | PPP2CA | protein phosphatase 2 catalytic subunit alpha | 2 | 2 | ||||||||
MIRT549790 | KIAA0391 | KIAA0391 | 2 | 2 | ||||||||
MIRT560368 | TAF8 | TATA-box binding protein associated factor 8 | 2 | 2 | ||||||||
MIRT566000 | RNF4 | ring finger protein 4 | 2 | 2 | ||||||||
MIRT574035 | PEX26 | peroxisomal biogenesis factor 26 | 2 | 2 | ||||||||
MIRT574231 | DMRT2 | doublesex and mab-3 related transcription factor 2 | 2 | 2 | ||||||||
MIRT576139 | Hmox1 | heme oxygenase 1 | 2 | 2 | ||||||||
MIRT576640 | Mill2 | MHC I like leukocyte 2 | 1 | 1 | ||||||||
MIRT609875 | RAD54L2 | RAD54 like 2 | 2 | 4 | ||||||||
MIRT622651 | POU2F3 | POU class 2 homeobox 3 | 2 | 4 | ||||||||
MIRT628848 | FAM151B | family with sequence similarity 151 member B | 2 | 2 | ||||||||
MIRT634252 | TIAL1 | TIA1 cytotoxic granule associated RNA binding protein like 1 | 2 | 2 | ||||||||
MIRT634672 | GDE1 | glycerophosphodiester phosphodiesterase 1 | 2 | 2 | ||||||||
MIRT649087 | FBXO25 | F-box protein 25 | 2 | 2 | ||||||||
MIRT665019 | ELK1 | ELK1, ETS transcription factor | 2 | 2 | ||||||||
MIRT666939 | PMEPA1 | prostate transmembrane protein, androgen induced 1 | 2 | 2 | ||||||||
MIRT668960 | CNBP | CCHC-type zinc finger nucleic acid binding protein | 2 | 2 | ||||||||
MIRT675802 | MED28 | mediator complex subunit 28 | 2 | 2 | ||||||||
MIRT684022 | FOLR1 | folate receptor 1 | 2 | 2 | ||||||||
MIRT696480 | COX6B1 | cytochrome c oxidase subunit 6B1 | 2 | 2 | ||||||||
MIRT705894 | ADCY9 | adenylate cyclase 9 | 2 | 2 | ||||||||
MIRT709434 | ZSCAN25 | zinc finger and SCAN domain containing 25 | 2 | 2 | ||||||||
MIRT713572 | SLC2A8 | solute carrier family 2 member 8 | 2 | 2 | ||||||||
MIRT716697 | HLA-B | major histocompatibility complex, class I, B | 2 | 2 | ||||||||
MIRT719735 | SLC39A11 | solute carrier family 39 member 11 | 2 | 2 | ||||||||
MIRT724907 | DAO | D-amino acid oxidase | 2 | 2 | ||||||||
MIRT725321 | NFASC | neurofascin | 2 | 2 |
miRNA-Drug Associations | ||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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