pre-miRNA Information | |
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pre-miRNA | hsa-mir-4707 |
Genomic Coordinates | chr14: 22956950 - 22957029 |
Description | Homo sapiens miR-4707 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | ||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-4707-3p | |||||||||||||||||||||||||||
Sequence | 52| AGCCCGCCCCAGCCGAGGUUCU |73 | |||||||||||||||||||||||||||
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 | RNF40 | ||||||||||||||||||||
Synonyms | BRE1B, RBP95, STARING | ||||||||||||||||||||
Description | ring finger protein 40 | ||||||||||||||||||||
Transcript | NM_014771 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on RNF40 | |||||||||||||||||||||
3'UTR of RNF40 (miRNA target sites are highlighted) |
>RNF40|NM_014771|3'UTR 1 ACCTGAAACTCAGGGGACTCTGGAACACCATGGACCCTGGGGGCTGTGCCCCCATCTCCTCCCCACCCCAGGTCTAGTGG 81 CCCCACCCTCCATTCCGGACCCCATGGGCCCAGCCCCTGCCCATCTAGTTGGTTTGGGGACCCTGGTGCATGCTAGTGGG 161 CATGGGATCAGCCAAGCTTCGTTCCATCTTTTCCTAAAGGTCAGAGCTGCAGCCTAGGGGGCACTGCCCTACAGAAAAGG 241 TCTGCCTGAGAGGCCTGAGGAGCCCAGAGCACTTGACTGAGCTTCCCGGAAACTGGCCCTAACCTGTCTGTCTCCGTGGA 321 TGCATCCTAACCCTAAGGAAAATTCCCCAGGCTGTGATCTACCCTAGAGAAGGCTCGCTCCCTGCCTACTGGCTCACAAA 401 TGAGGACCAGTGAGCCATGTCCTTGTTCCTTGTTTGAGACTGGGCTGCAGGCCCCAGGAAGACTTTCCTTCACCCACCAT 481 CCCCCTAACCTCGGCAGGGCTTCTGTCCTGTGGAGTTCCCTGGACACCTTGGTCTGGCTCTTGTGCCAAGGGCTGAAGGA 561 GGTACCCTCTTGGCAGATGGGGGCATCACTTGCTTCCTTTGGGAAGCTCTAAGGTTGCTGCAGTCACCTTCCTCATCTTG 641 CAGGTGCTGAACCAACATCATCAGTTTCTATTCTAATCAGGCCCCTTCCCAATCTCCATTTCTCTGCCAAGCCCATTTAC 721 CCCCACCTCATGCATCCCAAGGCTCTACTGGGTCCCTGGACCTAACCCTGCTTTCATCCTGGTGGCCTTAACTACAGTGG 801 AGGTGGAACTTCCCAGGAGGGGAAGGGACAGACCAGCCCCAGCCGCTGGGCCAACTTCCAATCATTCCAGCTAGAAGAGC 881 TTCCCCCTGACACCCTGTGACTGAGCCTGTGTCCTGTCTGCCTGCCCAGCCATGCTCCATCGGCTGTGAGGGCAGTGCCC 961 GGAGAGGCCAGAGGGTTGGAGCTGCAGGGACCCGTTTGGACCCACAGCCTCTGTTCTAGAGATGCTTGTATAGGCTGTTA 1041 ATTGTGATGAATAAACGTTCAACCCTCGGCCTGCAGCCAGAGTAGCCAGGCCGCGCACCCCAAATGTAGTCCCCCGATTT 1121 TAGCTGCAGCAGCTGAGCAGCACTTTGCTGGCTTGGTGTGAGCCTGGGAGGGCTCAGACTTAACGGCCGGCAGGGATCCC 1201 GGACTGGGCCTGAAGGGGAGAGCGTGGTGGTCGTCGCGGAGCCGCCTGTCCTGCTCCCACCGACCCCGGTCTGACCACGT 1281 CCTTGGCTGTCATGGCCGGGGGATGCCGGGACTCCTCGGGCTGCATCCTGGGAAGTGTAGTTCCTGGTCCGCACATGGTT 1361 AGGAGGTTCTCGGAGAGAGAGCTAGTTTCCCGGTTGCGCTGGCCAAAGGCCGGCCTGAACTGGATCCTGCGGACCGCTTC 1441 TCAGCGGCTTCACCCCCACACCACTCGAATGCACAGATCGGGACACCTCAGCTGGGTGACTTCCCTCGTTGCAATCGGCC 1521 TCGGGAGCGGTGCGGCGTGTACCGAGCGGCGCCCCTGGGCTCAGCGCGCTGCAGGCGCCCCGGGCGGATCCTTCACCGAG 1601 GCAGGACTGGGGCTGGCGCCAGAGCCGGTGCGGAGCGGTGTTGGTTCAGGCGCTGGCGACAGTGCTATGGCCACGGCAGG 1681 GGCCGCGTGCGTCTCAGCGGTGGCGCCTTCGGACCCTATTGGCGCCCGGGACTTAAGCGGGGCCGCCGCTGCTGGACCAG 1761 GACGAACTGGAGAAGGAGACGCGGGCCGCCACGGTGACCTCGGGCGTAGGGCCGGCGGCGGCGGGCACGCTGGTGGAAGC 1841 GCGGGCCGCGGCAGGGGAGGACATCGGGCCGCAGAGAAAGTGCCGATGGCCTGGGGCAGCGGTGCGAGGGTGGGAAAAAC 1921 GCAGGATATTGCATCATAGAGACGCGGCCACCTTCGCCCCTGGAGAGCGCCAGTCTCAGGAGCGCCGCACCGGTCACGGG 2001 TGGAGGTCAGCCAGGCCTCCGTAAGCGCGGTCCCCTTCCAGGAGTAGCCTTCGCCTGGGCTCTTGAGTAGATGCCAAGTA 2081 ATTCCGCATCGTCTCTCTAGATATCTGCGCTAAAGGCCACCCGGTCTCCTTATCAGAGGGGCAAAACTCTCCTCGTGGGT 2161 CTTCATACCTAATAAAAGTCGGCATCAAACCACAAA 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 | HeLa | ||||||
Location of target site | 3'UTR | ||||||
Tools used in this research | TargetScan , miRTarCLIP , Piranha | ||||||
Original Description (Extracted from the article) |
...
HITS-CLIP data was present in Chi_ControlB_2A8_130_50. RNA binding protein: AGO. Condition:HeLa cell Control B
... - Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Chi SW; Zang JB; Mele A; Darnell RB - Nature, 2009
MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
LinkOut: [PMID: 19536157]
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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/HeLa | ||||||
Location of target site | 3'UTR | ||||||
Tools used in this research | TargetScan , miRTarCLIP , Piranha | ||||||
Original Description (Extracted from the article) |
...
HITS-CLIP data was present in GSM1067869. RNA binding protein: AGO2. Condition:Ago2 IP-seq (asynchronous cells)
... - Kishore S; Gruber AR; Jedlinski DJ; Syed et al., 2013, Genome biology. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Kishore S; Gruber AR; Jedlinski DJ; Syed et al. - Genome biology, 2013
BACKGROUND: In recent years, a variety of small RNAs derived from other RNAs with well-known functions such as tRNAs and snoRNAs, have been identified. The functional relevance of these RNAs is largely unknown. To gain insight into the complexity of snoRNA processing and the functional relevance of snoRNA-derived small RNAs, we sequence long and short RNAs, small RNAs that co-precipitate with the Argonaute 2 protein and RNA fragments obtained in photoreactive nucleotide-enhanced crosslinking and immunoprecipitation (PAR-CLIP) of core snoRNA-associated proteins. RESULTS: Analysis of these data sets reveals that many loci in the human genome reproducibly give rise to C/D box-like snoRNAs, whose expression and evolutionary conservation are typically less pronounced relative to the snoRNAs that are currently cataloged. We further find that virtually all C/D box snoRNAs are specifically processed inside the regions of terminal complementarity, retaining in the mature form only 4-5 nucleotides upstream of the C box and 2-5 nucleotides downstream of the D box. Sequencing of the total and Argonaute 2-associated populations of small RNAs reveals that despite their cellular abundance, C/D box-derived small RNAs are not efficiently incorporated into the Ago2 protein. CONCLUSIONS: We conclude that the human genome encodes a large number of snoRNAs that are processed along the canonical pathway and expressed at relatively low levels. Generation of snoRNA-derived processing products with alternative, particularly miRNA-like, functions appears to be uncommon.
LinkOut: [PMID: 23706177]
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CLIP-seq Support 1 for dataset Chi_ControlB_2A8_130_50 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | HeLa / HeLa cell Control B |
Location of target site | ENST00000324685.6 | 3UTR | UAGGGCCGGCGGCGGC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 19536157 / Chi_HITSCLIP |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM1067869 | |
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Method / RBP | HITS-CLIP / AGO2 |
Cell line / Condition | HEK293/HeLa / Ago2 IP-seq (asynchronous cells) |
Location of target site | ENST00000324685.6 | 3UTR | CGUAGGGCCGGCGGCGGCGGGCACG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23706177 / GSE43666 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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91 hsa-miR-4707-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT442514 | SYT7 | synaptotagmin 7 | ![]() |
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2 | 4 | ||||||
MIRT457799 | NQO2 | N-ribosyldihydronicotinamide:quinone reductase 2 | ![]() |
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2 | 2 | ||||||
MIRT466318 | THRA | thyroid hormone receptor, alpha | ![]() |
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2 | 2 | ||||||
MIRT486129 | TRAF3 | TNF receptor associated factor 3 | ![]() |
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2 | 2 | ||||||
MIRT492341 | SEPT8 | septin 8 | ![]() |
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2 | 2 | ||||||
MIRT495690 | KCNC3 | potassium voltage-gated channel subfamily C member 3 | ![]() |
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2 | 2 | ||||||
MIRT496928 | DPYSL5 | dihydropyrimidinase like 5 | ![]() |
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2 | 2 | ||||||
MIRT499518 | MAFK | MAF bZIP transcription factor K | ![]() |
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2 | 2 | ||||||
MIRT501367 | REXO1 | RNA exonuclease 1 homolog | ![]() |
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2 | 4 | ||||||
MIRT501636 | PIAS4 | protein inhibitor of activated STAT 4 | ![]() |
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2 | 4 | ||||||
MIRT521071 | SLC25A16 | solute carrier family 25 member 16 | ![]() |
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2 | 2 | ||||||
MIRT525700 | PCYT2 | phosphate cytidylyltransferase 2, ethanolamine | ![]() |
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2 | 2 | ||||||
MIRT532722 | DDTL | D-dopachrome tautomerase like | ![]() |
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2 | 2 | ||||||
MIRT533137 | WWC1 | WW and C2 domain containing 1 | ![]() |
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2 | 4 | ||||||
MIRT537288 | G3BP1 | G3BP stress granule assembly factor 1 | ![]() |
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2 | 4 | ||||||
MIRT570555 | PHF21B | PHD finger protein 21B | ![]() |
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2 | 2 | ||||||
MIRT573469 | MTRNR2L9 | MT-RNR2-like 9 | ![]() |
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2 | 2 | ||||||
MIRT576750 | Tmem127 | transmembrane protein 127 | ![]() |
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2 | 2 | ||||||
MIRT609342 | DAAM2 | dishevelled associated activator of morphogenesis 2 | ![]() |
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2 | 2 | ||||||
MIRT610638 | PIGM | phosphatidylinositol glycan anchor biosynthesis class M | ![]() |
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2 | 2 | ||||||
MIRT612591 | RANGAP1 | Ran GTPase activating protein 1 | ![]() |
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2 | 2 | ||||||
MIRT614237 | WDR53 | WD repeat domain 53 | ![]() |
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2 | 4 | ||||||
MIRT622784 | PGK1 | phosphoglycerate kinase 1 | ![]() |
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2 | 2 | ||||||
MIRT628880 | MED16 | mediator complex subunit 16 | ![]() |
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2 | 2 | ||||||
MIRT629550 | SPN | sialophorin | ![]() |
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2 | 2 | ||||||
MIRT634714 | DDX19B | DEAD-box helicase 19B | ![]() |
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2 | 2 | ||||||
MIRT634932 | GTF2H2C | GTF2H2 family member C | ![]() |
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2 | 4 | ||||||
MIRT635341 | RBL1 | RB transcriptional corepressor like 1 | ![]() |
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2 | 2 | ||||||
MIRT637838 | CPT1A | carnitine palmitoyltransferase 1A | ![]() |
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2 | 2 | ||||||
MIRT644311 | NFKBID | NFKB inhibitor delta | ![]() |
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2 | 2 | ||||||
MIRT649206 | KIAA1715 | lunapark, ER junction formation factor | ![]() |
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2 | 2 | ||||||
MIRT657262 | HSPA4L | heat shock protein family A (Hsp70) member 4 like | ![]() |
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2 | 2 | ||||||
MIRT658919 | DPY19L4 | dpy-19 like 4 | ![]() |
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2 | 2 | ||||||
MIRT663608 | SEC23B | Sec23 homolog B, coat complex II component | ![]() |
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2 | 2 | ||||||
MIRT667425 | MFAP2 | microfibril associated protein 2 | ![]() |
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2 | 2 | ||||||
MIRT667667 | KREMEN1 | kringle containing transmembrane protein 1 | ![]() |
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2 | 2 | ||||||
MIRT668144 | GDPD1 | glycerophosphodiester phosphodiesterase domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT668540 | ERGIC1 | endoplasmic reticulum-golgi intermediate compartment 1 | ![]() |
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2 | 2 | ||||||
MIRT670039 | NFRKB | nuclear factor related to kappaB binding protein | ![]() |
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2 | 2 | ||||||
MIRT670875 | RAB10 | RAB10, member RAS oncogene family | ![]() |
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2 | 2 | ||||||
MIRT672694 | ZNF677 | zinc finger protein 677 | ![]() |
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2 | 2 | ||||||
MIRT673107 | MFSD2A | major facilitator superfamily domain containing 2A | ![]() |
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2 | 2 | ||||||
MIRT673508 | TNFAIP8L1 | TNF alpha induced protein 8 like 1 | ![]() |
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2 | 4 | ||||||
MIRT674244 | NUP62 | nucleoporin 62 | ![]() |
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2 | 4 | ||||||
MIRT676541 | IRGQ | immunity related GTPase Q | ![]() |
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2 | 2 | ||||||
MIRT676787 | CXorf38 | chromosome X open reading frame 38 | ![]() |
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2 | 4 | ||||||
MIRT677600 | PRKX | protein kinase, X-linked | ![]() |
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2 | 2 | ||||||
MIRT678607 | MRPL17 | mitochondrial ribosomal protein L17 | ![]() |
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2 | 2 | ||||||
MIRT678940 | MYADM | myeloid associated differentiation marker | ![]() |
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2 | 2 | ||||||
MIRT679104 | CD99 | CD99 molecule (Xg blood group) | ![]() |
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2 | 2 | ||||||
MIRT679196 | WNT2B | Wnt family member 2B | ![]() |
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2 | 2 | ||||||
MIRT679325 | ZMYM4 | zinc finger MYM-type containing 4 | ![]() |
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2 | 2 | ||||||
MIRT679634 | BRMS1L | breast cancer metastasis-suppressor 1 like | ![]() |
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2 | 2 | ||||||
MIRT679819 | TMEM106B | transmembrane protein 106B | ![]() |
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2 | 2 | ||||||
MIRT679898 | FBXO48 | F-box protein 48 | ![]() |
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2 | 2 | ||||||
MIRT680579 | ZNF784 | zinc finger protein 784 | ![]() |
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2 | 2 | ||||||
MIRT680600 | SZT2 | SZT2, KICSTOR complex subunit | ![]() |
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2 | 2 | ||||||
MIRT682991 | RNF40 | ring finger protein 40 | ![]() |
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2 | 4 | ||||||
MIRT683483 | ZNF7 | zinc finger protein 7 | ![]() |
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2 | 2 | ||||||
MIRT683681 | MICA | MHC class I polypeptide-related sequence A | ![]() |
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2 | 2 | ||||||
MIRT684122 | CEP104 | centrosomal protein 104 | ![]() |
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2 | 2 | ||||||
MIRT684774 | MYO1F | myosin IF | ![]() |
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2 | 2 | ||||||
MIRT685698 | BHMT2 | betaine--homocysteine S-methyltransferase 2 | ![]() |
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2 | 2 | ||||||
MIRT686471 | LINC00598 | long intergenic non-protein coding RNA 598 | ![]() |
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2 | 2 | ||||||
MIRT687940 | HMGB1 | high mobility group box 1 | ![]() |
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2 | 2 | ||||||
MIRT688627 | CRISPLD2 | cysteine rich secretory protein LCCL domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT689110 | ZBTB25 | zinc finger and BTB domain containing 25 | ![]() |
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2 | 2 | ||||||
MIRT690063 | MBD1 | methyl-CpG binding domain protein 1 | ![]() |
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2 | 2 | ||||||
MIRT691067 | NUGGC | nuclear GTPase, germinal center associated | ![]() |
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2 | 2 | ||||||
MIRT691317 | KIAA1841 | KIAA1841 | ![]() |
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2 | 2 | ||||||
MIRT692778 | SYNPO2L | synaptopodin 2 like | ![]() |
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2 | 2 | ||||||
MIRT694087 | KIAA0930 | KIAA0930 | ![]() |
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2 | 2 | ||||||
MIRT696148 | WDR59 | WD repeat domain 59 | ![]() |
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2 | 2 | ||||||
MIRT696176 | GNB5 | G protein subunit beta 5 | ![]() |
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2 | 2 | ||||||
MIRT696434 | SUGP1 | SURP and G-patch domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT697974 | TSPAN6 | tetraspanin 6 | ![]() |
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2 | 2 | ||||||
MIRT698917 | SPEM1 | spermatid maturation 1 | ![]() |
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2 | 2 | ||||||
MIRT699312 | SLC35F5 | solute carrier family 35 member F5 | ![]() |
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2 | 4 | ||||||
MIRT700500 | PTPN4 | protein tyrosine phosphatase, non-receptor type 4 | ![]() |
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2 | 2 | ||||||
MIRT700557 | PTBP1 | polypyrimidine tract binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT701817 | MRPL37 | mitochondrial ribosomal protein L37 | ![]() |
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2 | 2 | ||||||
MIRT702045 | METTL21A | methyltransferase like 21A | ![]() |
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2 | 2 | ||||||
MIRT702215 | LPCAT1 | lysophosphatidylcholine acyltransferase 1 | ![]() |
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2 | 2 | ||||||
MIRT702337 | KLHL7 | kelch like family member 7 | ![]() |
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2 | 2 | ||||||
MIRT704139 | DNAL1 | dynein axonemal light chain 1 | ![]() |
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2 | 2 | ||||||
MIRT704189 | LDHD | lactate dehydrogenase D | ![]() |
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2 | 2 | ||||||
MIRT705344 | ATP1B3 | ATPase Na+/K+ transporting subunit beta 3 | ![]() |
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2 | 2 | ||||||
MIRT706097 | ENTPD4 | ectonucleoside triphosphate diphosphohydrolase 4 | ![]() |
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2 | 2 | ||||||
MIRT709068 | FAHD1 | fumarylacetoacetate hydrolase domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT717579 | VTA1 | vesicle trafficking 1 | ![]() |
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2 | 2 | ||||||
MIRT722440 | ZBTB7B | zinc finger and BTB domain containing 7B | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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