pre-miRNA Information | |
---|---|
pre-miRNA | hsa-mir-514b |
Genomic Coordinates | chrX: 147250151 - 147250230 |
Description | Homo sapiens miR-514b stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
Mature miRNA | hsa-miR-514b-5p | |||||||||
Sequence | 13| UUCUCAAGAGGGAGGCAAUCAU |34 | |||||||||
Evidence | Experimental | |||||||||
Experiments | Illumina | |||||||||
SNPs in miRNA |
|
|||||||||
Putative Targets |
miRNA Expression profile | |
---|---|
Human miRNA Tissue Atlas | |
Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene Symbol | PHF12 | ||||||||||||||||||||
Synonyms | PF1 | ||||||||||||||||||||
Description | PHD finger protein 12 | ||||||||||||||||||||
Transcript | NM_001033561 | ||||||||||||||||||||
Other Transcripts | NM_020889 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on PHF12 | |||||||||||||||||||||
3'UTR of PHF12 (miRNA target sites are highlighted) |
>PHF12|NM_001033561|3'UTR 1 GACTGGCGGCTACCCCGCCACTGGCCTGTACACCCACCCAAGACTCCTGCAATGCAAAAATGTACACAAACCAAGCCCGG 81 GTGTTTTCTATACTCTACCAGAAACCCTTCAACTACAATCTTTGCATGAAATGAAGAAAACCTTTTGACTGTTTTTTAAA 161 AATCCTTTTTCTTTTCTCAAGTTCTAGGGGGCATTTGCACATATATTTGTACTCAACATTTCATGGGAAAGCGGCAGACC 241 TGAGCTGAGGAACAGCGTGGGCAGGGAGGGAAAGACCCAGGGTCTGGACACTTCCTCCAACACAAAACCCTTCCCCACCC 321 ACCTCCTGCTCCCTCCCCCTCGCCCACCATTGTAAAATAATCAGAAACTTGTTCTATTTTGTGGCAGTGACAATAGTTTT 401 ATATTAAAAGAAAAAATACAGTTTTCATACAGCAAAATCTATACAATATCATTGTTTTATTTAATATAAAGATCGCTACC 481 CACCTTCCTTCCATGGTTCCCACCCTCCACGTTATTTTCCCTTTCTGCAGCGGTTGCACTACAGGTAGCTACTGTGTATT 561 ATGGACAAATGAGAAATGAATTCTTTTTCTGGCTGTCCATCTATTTTATTTCAAATAAGGAAAAGTGTATTTGGATTTTG 641 TGTAAATACATCTAGTGATGACATTTTTTCAATGTTTTTAAAAACCGTGTACAGTACTACATGTGGTAGAGCGTTTTCTC 721 AAATTGTCTATTGTAGCAAAAATGTTTTTGTCGTAAACCTGTTTTGTCTCCTTTTTTTGTTCTCTTGCCACTTCTCTCCT 801 CTTCCTCCTGCCCCTGGTTCCCTCCTCTCCTCCCACCCCCACAACCAGTACCAATGTACATAGTAATTGTAATGTTTTAG 881 ACTTTACAGAAACTTTCCTGTATTCTGTATATAAAAAACAAAAATACTTC Target sites
Provided by authors
Predicted by miRanda
DRVs
SNPs
DRVs & SNPs
|
||||||||||||||||||||
miRNA-target interactions (Predicted by miRanda) |
|
||||||||||||||||||||
DRVs in gene 3'UTRs | |||||||||||||||||||||
SNPs in gene 3'UTRs |
Experimental Support 1 for Functional miRNA-Target Interaction | |
---|---|
miRNA:Target | ---- |
Validation Method |
|
Conditions | LCL35 |
Disease | MIMAT0015087 |
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 GSM1020022. RNA binding protein: AGO2. Condition:EBV B95-8-infected
... - Skalsky RL; Corcoran DL; Gottwein E; Frank et al., 2012, PLoS pathogens. |
Article |
- Skalsky RL; Corcoran DL; Gottwein E; Frank et al. - PLoS pathogens, 2012
Epstein-Barr virus (EBV) is a ubiquitous human herpesvirus linked to a number of B cell cancers and lymphoproliferative disorders. During latent infection, EBV expresses 25 viral pre-microRNAs (miRNAs) and induces the expression of specific host miRNAs, such as miR-155 and miR-21, which potentially play a role in viral oncogenesis. To date, only a limited number of EBV miRNA targets have been identified; thus, the role of EBV miRNAs in viral pathogenesis and/or lymphomagenesis is not well defined. Here, we used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) combined with deep sequencing and computational analysis to comprehensively examine the viral and cellular miRNA targetome in EBV strain B95-8-infected lymphoblastoid cell lines (LCLs). We identified 7,827 miRNA-interaction sites in 3,492 cellular 3'UTRs. 531 of these sites contained seed matches to viral miRNAs. 24 PAR-CLIP-identified miRNA:3'UTR interactions were confirmed by reporter assays. Our results reveal that EBV miRNAs predominantly target cellular transcripts during latent infection, thereby manipulating the host environment. Furthermore, targets of EBV miRNAs are involved in multiple cellular processes that are directly relevant to viral infection, including innate immunity, cell survival, and cell proliferation. Finally, we present evidence that myc-regulated host miRNAs from the miR-17/92 cluster can regulate latent viral gene expression. This comprehensive survey of the miRNA targetome in EBV-infected B cells represents a key step towards defining the functions of EBV-encoded miRNAs, and potentially, identifying novel therapeutic targets for EBV-associated malignancies.
LinkOut: [PMID: 22291592]
|
CLIP-seq Support 1 for dataset GSM1020022 | |
---|---|
Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | LCL35 / EBV B95-8-infected, 4-thiouridine, RNase T1 |
Location of target site | ENST00000577226.1 | 3UTR | UCAAGUUCAAGUUGAGA |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 22291592 / GSE41437 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
---|---|---|---|---|---|---|---|
|
MiRNA-Target Expression Profile (TCGA) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
101 hsa-miR-514b-5p Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT106072 | YTHDF3 | YTH N6-methyladenosine RNA binding protein 3 | 2 | 2 | ||||||||
MIRT169586 | PNRC1 | proline rich nuclear receptor coactivator 1 | 2 | 2 | ||||||||
MIRT259395 | SLC6A8 | solute carrier family 6 member 8 | 2 | 4 | ||||||||
MIRT271675 | SDE2 | SDE2 telomere maintenance homolog | 2 | 2 | ||||||||
MIRT286339 | PHF12 | PHD finger protein 12 | 2 | 2 | ||||||||
MIRT334478 | RPL27A | ribosomal protein L27a | 2 | 4 | ||||||||
MIRT336467 | SRP9 | signal recognition particle 9 | 2 | 2 | ||||||||
MIRT442118 | KCNH5 | potassium voltage-gated channel subfamily H member 5 | 2 | 2 | ||||||||
MIRT462291 | PPM1H | protein phosphatase, Mg2+/Mn2+ dependent 1H | 2 | 2 | ||||||||
MIRT474679 | KLF10 | Kruppel like factor 10 | 2 | 2 | ||||||||
MIRT475557 | HNRNPF | heterogeneous nuclear ribonucleoprotein F | 2 | 2 | ||||||||
MIRT479222 | CKS2 | CDC28 protein kinase regulatory subunit 2 | 2 | 2 | ||||||||
MIRT496187 | TECPR1 | tectonin beta-propeller repeat containing 1 | 2 | 2 | ||||||||
MIRT496811 | CHRNB2 | cholinergic receptor nicotinic beta 2 subunit | 2 | 2 | ||||||||
MIRT506493 | MSANTD4 | Myb/SANT DNA binding domain containing 4 with coiled-coils | 2 | 4 | ||||||||
MIRT509595 | PEX26 | peroxisomal biogenesis factor 26 | 2 | 4 | ||||||||
MIRT512411 | KIAA0391 | KIAA0391 | 2 | 2 | ||||||||
MIRT512439 | SFTPB | surfactant protein B | 2 | 2 | ||||||||
MIRT512581 | ZNF223 | zinc finger protein 223 | 2 | 2 | ||||||||
MIRT525990 | MAGEL2 | MAGE family member L2 | 2 | 2 | ||||||||
MIRT526427 | PARP15 | poly(ADP-ribose) polymerase family member 15 | 2 | 4 | ||||||||
MIRT526772 | DNTTIP2 | deoxynucleotidyltransferase terminal interacting protein 2 | 2 | 2 | ||||||||
MIRT528090 | UCHL3 | ubiquitin C-terminal hydrolase L3 | 2 | 2 | ||||||||
MIRT530438 | SULT1B1 | sulfotransferase family 1B member 1 | 2 | 2 | ||||||||
MIRT532572 | GSS | glutathione synthetase | 2 | 2 | ||||||||
MIRT533990 | SUZ12 | SUZ12 polycomb repressive complex 2 subunit | 2 | 2 | ||||||||
MIRT534782 | RAD23B | RAD23 homolog B, nucleotide excision repair protein | 2 | 2 | ||||||||
MIRT536246 | LPP | LIM domain containing preferred translocation partner in lipoma | 2 | 2 | ||||||||
MIRT536471 | KIAA1549L | KIAA1549 like | 2 | 2 | ||||||||
MIRT538428 | COL19A1 | collagen type XIX alpha 1 chain | 2 | 2 | ||||||||
MIRT538839 | BTG3 | BTG anti-proliferation factor 3 | 2 | 2 | ||||||||
MIRT539323 | AHSA2 | activator of HSP90 ATPase homolog 2 | 2 | 4 | ||||||||
MIRT547012 | PPP1R15B | protein phosphatase 1 regulatory subunit 15B | 2 | 2 | ||||||||
MIRT551817 | TMEM138 | transmembrane protein 138 | 2 | 2 | ||||||||
MIRT552910 | VPS37A | VPS37A, ESCRT-I subunit | 2 | 2 | ||||||||
MIRT553169 | UBE2G1 | ubiquitin conjugating enzyme E2 G1 | 2 | 2 | ||||||||
MIRT553462 | TNRC6A | trinucleotide repeat containing 6A | 2 | 2 | ||||||||
MIRT553551 | TMEM161B | transmembrane protein 161B | 2 | 2 | ||||||||
MIRT556253 | MAPRE2 | microtubule associated protein RP/EB family member 2 | 2 | 2 | ||||||||
MIRT556874 | ITGA2 | integrin subunit alpha 2 | 2 | 2 | ||||||||
MIRT558152 | ELAVL2 | ELAV like RNA binding protein 2 | 2 | 2 | ||||||||
MIRT560320 | DCAF17 | DDB1 and CUL4 associated factor 17 | 2 | 2 | ||||||||
MIRT564022 | CEBPB | CCAAT/enhancer binding protein beta | 2 | 2 | ||||||||
MIRT566386 | PLEKHA1 | pleckstrin homology domain containing A1 | 2 | 2 | ||||||||
MIRT569339 | EFHC1 | EF-hand domain containing 1 | 2 | 2 | ||||||||
MIRT572595 | PAPLN | papilin, proteoglycan like sulfated glycoprotein | 2 | 2 | ||||||||
MIRT574178 | TMPO | thymopoietin | 2 | 2 | ||||||||
MIRT610592 | NUS1 | NUS1 dehydrodolichyl diphosphate synthase subunit | 2 | 2 | ||||||||
MIRT615803 | COQ7 | coenzyme Q7, hydroxylase | 2 | 2 | ||||||||
MIRT616714 | FEM1B | fem-1 homolog B | 2 | 2 | ||||||||
MIRT617931 | EBNA1BP2 | EBNA1 binding protein 2 | 2 | 2 | ||||||||
MIRT620333 | SPAST | spastin | 2 | 2 | ||||||||
MIRT620669 | BBS5 | Bardet-Biedl syndrome 5 | 2 | 2 | ||||||||
MIRT620711 | ASB16 | ankyrin repeat and SOCS box containing 16 | 2 | 2 | ||||||||
MIRT622709 | PLEKHA2 | pleckstrin homology domain containing A2 | 2 | 2 | ||||||||
MIRT623780 | GOSR1 | golgi SNAP receptor complex member 1 | 2 | 2 | ||||||||
MIRT624111 | DNAH10OS | dynein axonemal heavy chain 10 opposite strand | 2 | 2 | ||||||||
MIRT626537 | EMCN | endomucin | 2 | 2 | ||||||||
MIRT630145 | ZDHHC9 | zinc finger DHHC-type containing 9 | 2 | 4 | ||||||||
MIRT631638 | WDR91 | WD repeat domain 91 | 2 | 4 | ||||||||
MIRT635122 | RAD51 | RAD51 recombinase | 2 | 2 | ||||||||
MIRT637461 | DEFB105B | defensin beta 105B | 2 | 4 | ||||||||
MIRT637493 | DEFB105A | defensin beta 105A | 2 | 4 | ||||||||
MIRT641197 | TRIB1 | tribbles pseudokinase 1 | 2 | 4 | ||||||||
MIRT643396 | PROM1 | prominin 1 | 2 | 2 | ||||||||
MIRT644889 | ZBED1 | zinc finger BED-type containing 1 | 2 | 2 | ||||||||
MIRT647244 | PTGDR2 | prostaglandin D2 receptor 2 | 2 | 2 | ||||||||
MIRT647528 | CCDC121 | coiled-coil domain containing 121 | 2 | 2 | ||||||||
MIRT648395 | WRN | Werner syndrome RecQ like helicase | 2 | 2 | ||||||||
MIRT650121 | G6PC | glucose-6-phosphatase catalytic subunit | 2 | 2 | ||||||||
MIRT652355 | TMEM92 | transmembrane protein 92 | 2 | 2 | ||||||||
MIRT653817 | SIM2 | single-minded family bHLH transcription factor 2 | 2 | 2 | ||||||||
MIRT653943 | SEPSECS | Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase | 2 | 2 | ||||||||
MIRT657290 | HOXB5 | homeobox B5 | 2 | 2 | ||||||||
MIRT657826 | GJD3 | gap junction protein delta 3 | 2 | 2 | ||||||||
MIRT658706 | EMB | embigin | 2 | 2 | ||||||||
MIRT658739 | ELAVL4 | ELAV like RNA binding protein 4 | 2 | 2 | ||||||||
MIRT660175 | BNC2 | basonuclin 2 | 2 | 2 | ||||||||
MIRT661323 | TBC1D15 | TBC1 domain family member 15 | 2 | 2 | ||||||||
MIRT662205 | PLA2G4E | phospholipase A2 group IVE | 2 | 2 | ||||||||
MIRT662965 | ZSWIM1 | zinc finger SWIM-type containing 1 | 2 | 2 | ||||||||
MIRT663876 | CCDC65 | coiled-coil domain containing 65 | 2 | 2 | ||||||||
MIRT671779 | RGS17 | regulator of G protein signaling 17 | 2 | 2 | ||||||||
MIRT673644 | CYCS | cytochrome c, somatic | 2 | 2 | ||||||||
MIRT675531 | RPL37 | ribosomal protein L37 | 2 | 2 | ||||||||
MIRT676349 | KLF8 | Kruppel like factor 8 | 2 | 2 | ||||||||
MIRT678427 | PDE4C | phosphodiesterase 4C | 2 | 2 | ||||||||
MIRT678484 | ARHGEF39 | Rho guanine nucleotide exchange factor 39 | 2 | 2 | ||||||||
MIRT690846 | PVR | poliovirus receptor | 2 | 2 | ||||||||
MIRT691991 | SGTB | small glutamine rich tetratricopeptide repeat containing beta | 2 | 2 | ||||||||
MIRT698392 | TMED10 | transmembrane p24 trafficking protein 10 | 2 | 2 | ||||||||
MIRT701264 | NUP210 | nucleoporin 210 | 2 | 2 | ||||||||
MIRT703553 | FKBP14 | FK506 binding protein 14 | 2 | 2 | ||||||||
MIRT711984 | EXTL3 | exostosin like glycosyltransferase 3 | 2 | 2 | ||||||||
MIRT712653 | PGAP3 | post-GPI attachment to proteins 3 | 2 | 2 | ||||||||
MIRT716759 | TRABD2A | TraB domain containing 2A | 2 | 2 | ||||||||
MIRT717931 | ZFP64 | ZFP64 zinc finger protein | 2 | 2 | ||||||||
MIRT718027 | FAM163A | family with sequence similarity 163 member A | 2 | 2 | ||||||||
MIRT718972 | SPTSSA | serine palmitoyltransferase small subunit A | 2 | 2 | ||||||||
MIRT721650 | RPL34 | ribosomal protein L34 | 2 | 2 | ||||||||
MIRT724860 | RIMBP2 | RIMS binding protein 2 | 2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|