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Copy pathRNA-RNA.json
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194 lines (185 loc) · 9.34 KB
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[{
"version": "RIFv1.0",
"ID": "76ahgas-8as8a",
"class": "RNA-RNA-Protein",
"type": "basepairing",
"evidence": [
{
"type": "experimental",
"method": "gel shift assay",
"data": {
"URI": "https://journals.asm.org/doi/full/10.1128/JB.183.6.1997-2005.2001",
"note": "Hfq and DsrA interact in vivo"
}
},
{
"type": "experimental",
"method": "protein binding assay",
"data": {
"URI": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370368/"
}
}
],
"partners": [
{
"name": "Hfq",
"symbol": "Hfq",
"type": "polypeptide",
"sequence_type": "protein",
"genomic_coordinates": "NC_000913.3:+:4400288-4400596",
"organism_name": "Escherichia coli K-12 MG1655",
"organism_acc": "NC_000913.3",
"local_sites": {
"dsrA": [[60,78],[45,55]],
"rpoS": [[10,40]]
},
"info": {
"description": "RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations.",
"sequence": "MAKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHSNNAGGGTSSNYHHGSSAQNTSAQQDSEETE",
"note": "https://www.ebi.ac.uk/pdbe/entry/pdb/5I21"
}
},
{
"name": "dsrA",
"symbol": "dsrA",
"type": "small_regulatory_ncRNA",
"sequence_type": "rna",
"genomic_coordinates": "NC_000913.3:-:2025223-2025313",
"organism_name": "Escherichia coli K-12 MG1655",
"organism_acc": "NC_000913.3",
"local_sites": {
"Hfq": [[12,30],[80,90]],
"rpoS": [[50,70]]
},
"info": {
"description": "DsrA small regulatory RNA; riboregulator of RpoS and H-NS production",
"sequence": "AACGCATCGGATTTCCCGGTGTAACGAATTTTCAAGTGCTTCTTGCATTAGCAAGTTTGATCCCGACTCCTGCGAGTCGGGATTT",
"structure": "...(((((((.....)))))))..(((((((...(((((.....)))))...)))))))((((((((((....)))))))))).."
},
"custom": {}
},
{
"name": "rpoS",
"symbol": "rpoS",
"type": "mRNA",
"sequence_type": "rna",
"genomic_coordinates": "NC_000913.3:-:2866559-2867551",
"organism_name": "Escherichia coli K-12 MG1655",
"organism_acc": "NC_000913.3",
"local_sites": {
"Hfq": [[200,230]],
"dsrA": [[587,607]]
},
"info": {
"description": "RNA polymerase, sigma S (sigma 38) factor",
"sequence": "TGAGTCAGAATACGCTGAAAGTTCATGATTTAAATGAAGATGCGGAATTTGATGAGAACGGAGTTGAGGTTTTTGACGAAAAGGCCTTAGTAGAACAGGAACCCAGTGATAACGATTTGGCCGAAGAGGAACTGTTATCGCAGGGAGCCACACAGCGTGTGTTGGACGCGACTCAGCTTTACCTTGGTGAGATTGGTTATTCACCACTGTTAACGGCCGAAGAAGAAGTTTATTTTGCGCGTCGCGCACTGCGTGGAGATGTCGCCTCTCGCCGCCGGATGATCGAGAGTAACTTGCGTCTGGTGGTAAAAATTGCCCGCCGTTATGGCAATCGTGGTCTGGCGTTGCTGGACCTTATCGAAGAGGGCAACCTGGGGCTGATCCGCGCGGTAGAGAAGTTTGACCCGGAACGTGGTTTCCGCTTCTCAACATACGCAACCTGGTGGATTCGCCAGACGATTGAACGGGCGATTATGAACCAAACCCGTACTATTCGTTTGCCGATTCACATCGTAAAGGAGCTGAACGTTTACCTGCGAACCGCACGTGAGTTGTCCCATAAGCTGGACCATGAACCAAGTGCGGAAGAGATCGCAGAGCAACTGGATAAGCCAGTTGATGACGTCAGCCGTATGCTTCGTCTTAACGAGCGCATACCTCGGTAGACACCCCGCTGGGTGGTGATTCCGAAAAAGCGTTGCTGGACATCCTGGCCGATGAAAAAGAGAACGGTCCGGAAGATACCACGCAAGATGACGATATGAAGCAGAGCATCGTCAAATGGCTGTTCGAGCTGAACGCCAAACAGCGTGAAGTGCTGGCACGTCGATTCGGTTTGCTGGGGTACGAAGCGGCAACACTGGAAGATGTAGGTCGTGAAATTGGCCTCACCCGTGAACGTGTTCGCCAGATTCAGGTTGAAGGCCTGCGCCGTTTGCGCGAAATCCTGCAAACGCAGGGGCTGAATATCGAAGCGCTGTTCCGCGAGTAA",
"structure": "(((((((((((.........)))).))))))).........(((((((..((((.((((((..(((((((((((.....))))))))))).......((..(((.(((((((((......((.....))...))))))))).)))..)).....(((((((((.((((((....((((((..((((((..(((((((.....))))..)))....))).)))..)))))).......))))))....((((((((((....(((((((..(((((((((((..((((.....))))))))))))))).....(((((((((.....)))..(((.((((((((...))))))))....)))...))))))...))))).)))))))))))).(((((((..((((((...)).))))...))))))))))))))))...((((((....))))))((((....(((((...............))))).....))))...))).))).))))........(((((.((((...((((((.((((((.((.(((((((........))))....))))).))))))......))))))..(((((((....)))))))..))))))))).(((((((((((....))))).)))))).((((....((((((....)).))))...))))...(((((((((((...(((.(((((.............))))).))).....))).)))......((((((..(((......((((((((((((.((((.....))))(((...((((.((((...((((((((((..((((((((((((..........)))))).)))))).)))))((((((......))))))(((........)))...))))).)))).))))..)))....)))))))).))))..((((((....)))))))))..))))))..))))))))))))......"
},
"custom": {}
}
]
},
{
"version": "RIFv1.0",
"ID": "76ahad87abb",
"class": "RNA-RNA",
"type": "basepairing",
"evidence": [{
"type": "Data-driven",
"method": "Direct Duplex Detection",
"command": "RNAnue -minfraglen 18 -minlen 36 -sitelenratio 0.3",
"data": {
"complementarity": {
"unit": "gcs",
"value": 0.8
},
"energy": {
"unit": "ges (ddG)",
"value": -12.6
},
"significance": {
"unit": "p-value",
"value": 1.415e-6
},
"reads": {
"unit": "counts",
"value": 43
}
}
},
{
"type": "prediction",
"method" : "CopraRNA",
"command": "CopraRNA2.pl -srnaseq sRNAs.fa -ntup 200 -ntdown 100 -region 5utr -enrich 200 -topcount 200",
"data": {
"energy": {
"unit": "ddG",
"value": -21.69
},
"significance":{
"unit": "p-value",
"value": 2.411e-07
}
}
},
{
"type":"prediction",
"method": "RNAcofold",
"command": "RNAcofold --shapeMethod Z --maxBPspan 10 --dangles 4",
"data": {
"energy": {
"unit": "ddG",
"value" : -17.21
}
}
},
{
"type":"knockout experiments",
"method": "qPCR",
"data": {
"fold_change": {
"unit": "ddCt",
"value": 3
}
}
}
],
"partners": [
{
"name": "micF",
"symbol": "micF",
"type": "small_regulatory_ncRNA",
"sequence_type": "rna",
"genomic_coordinates": "NC_000913.3:+:2313084-2313176",
"organism_name": "Escherichia coli K-12 MG1655",
"organism_acc": "NC_000913.3",
"local_sites": {
"lrp": [[25,32],[55,64]]
},
"info": {
"description": "The micF RNA is a non-coding RNA stress response gene found in Escherichia coli and related bacteria that post-transcriptionally controls expression of the outer membrane porin gene ompF",
"sequence": "AACGCATCGGATTTCCCGGTGTAACGAATTTTCAAGTGCTTCTTGCATTAGCAAGTTTGATCCCGACTCCTGCGAGTCGGGATTT",
"structure": "...(((((((.....)))))))..(((((((...(((((.....)))))...)))))))((((((((((....)))))))))).."
},
"custom": {}
},
{
"name": "lrp",
"symbol": "lrp",
"type": "mRNA",
"sequence_type": "rna",
"genomic_coordinates": "NC_000913.3:+:932595-933089",
"organism_name": "Escherichia coli K-12 MG1655",
"organisms_acc": "NC_000913.3",
"local_sites": {
"micF": [[100,107],[158,167]]
},
"info": {
"description": "leucine-responsive global transcriptional regulator",
"sequence": "TGGTAGATAGCAAGAAGCGCCCTGGCAAAGATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGTCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGTTTGAACAATTCAATACCGCTGTACAAAAACTTGAAGAAATTCAGGAGTGTCATTTAGTATCCGGTGATTTCGACTACCTGTTGAAAACACGCGTGCCGGATATGTCAGCCTACCGTAAGTTGCTGGGGGAAACCCTGCTGCGTCTGCCTGGCGTCAATGACACACGGACATACGTTGTTATGGAAGAAGTCAAGCAGAGTAATCGTCTGGTTATTAAGACGCGCTAA",
"structure": ".(((((((((((.......((((((((((((.((((((.((...((((((..(((((((..((.....)).))))))).))).)))....))))))))...)))..(((.(((((.((((((((.(((((((((.....))))).)))).))..))))))....(((((....(((.(((....))).)))...))))).....((((((.(((.(((((((.((((.((.....)).))))..)))..)))).)))))))))(((.(((((...)))))...)))((.(((....((((((....))))))..)))))....((((((((((.(((((((.....))))))).))......)))))))).....))))))))...))))))))).......))))..)))))))..(((((((((((...(((((.(((.(((((.(((......)))))))).)))...)))))))))))..)))))....."
},
"custom": {}
}
]
}]