User:M2bioinfo-Orsay/sandbox/team1
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| Teg 147 family | |
|---|---|
 Predicted secondary structure and sequence conservation of Teg 147 using LocARNA[1] | |
| Identifiers | |
| Symbol | Teg 147 |
| Alt. Symbols | sRNA85, srn_0960, SAOUHSCs103 |
| Other data | |
| RNA type | Gene; |
| Domain(s) | Firmicutes |
| PDB structures | PDBe |
Firmicutes cis-acting regulatory element (CRE)
[edit]
Firmicutes cis-acting regulatory element (CRE) is a CRE recoverded from a RNAseq of S. aureus N315 strain [2].
The SEED is composed of a 60 nucleotides sequence, corresponding to Teg147 also named sRNA85 or SAOUHSCs103. Its structure is quite conserved among the specie. The final Rfam family is composed of 17 homologous sequences, which all belong the Firmicutes phylum. Frequently among the family, the corresponding sequence was found in the 5' region of the gene labA at a distance of approximately, 20 nucleotides. The protein LabA regulates KaiC which is implicated in the circadian circle regulation among the Cyanobacteria phylum
[3].
S. aureus has a GC content of 33%, which is low among the Firmicutes. Local variation within the genome of this percentage could show a possible DNA acquisition by horizontal transfer. Indeed, Teg147 has a GC content above 40%. [4]
| ID | Organism strain | Strand | Position in the genome | Distance between the Firmicutes CRE and the gene (in nucleotides) | Gene ID | Gene annotation |
|---|---|---|---|---|---|---|
| CP000253.1 | S.aureus subsp. aureus NCTC 8325 | antisense |
|
241 | SAOUHSC_01956 | Hypothetical protein[5] |
| JMJF01000005.1 | S.chromogenes MU 970 SCHR_MU970 | antisense |
|
31 | SCHR-07570 | Hypothetical protein (authentic frame-shift mutation)[5] |
| GG694019.1 | Granulicatella adiacens ATCC 49175 | sense | 83180-83240
|
20 |
|
LabA Uncharacterized conserved protein, LabA/DUF88 family [Function unknown][5] |
| FR889308.1 | Clostridium sp. CAG:352 | sense |
|
22 | BN621_00979 | LabA Uncharacterized conserved protein, LabA/DUF88 family [Function unknown][5] |
| FR889121.1 | Eubacterium sp. CAG:251 | sense | 78580-78640
|
18 | CDC32186.1 | LabA Uncharacterized conserved protein, LabA/DUF88 family [Function unknown][5] |
| FR882256.1 | Lachnospiraceae bacterium CAG:215 | antisense | 14036-13976 | 19 | CDB01384.1 | LabA Uncharacterized conserved protein, LabA/DUF88 family [Function unknown][5] |
| NFIF01000003.1 | Blautia sp. An46 | sense | 27535-27595 | 42 | B5G00_03530 | NYN domain-containing protein[5] |
| KI535286.1 | Eubacterium brachy ATCC 33089 | antisense | 254894-254834 | 20 | ESE29873.1 | NYN domain limkain-b1-type[5] |
| JH414699.1 | Subdoligranulum sp. 4_3_54A2FAA | antisense | 193622-193562 | 22 | EHL72285.1 | LabA Uncharacterized conserved protein, LabA/DUF88 family [Function unknown][5] |
| HF991807.1 | Clostridium sp. CAG:678 | sense | 3955-4015 | 16 | CCY66959.1 | LabA Uncharacterized conserved protein, LabA/DUF88 family [Function unknown][5] |
| JH590863.1 | Lachnospiraceae bacterium ACC2 | sense | 470853-470914 | 833 | EH016010.1 | Predicted nuclease of the RNAse H fold, HicB family |
| JH590863.1 | Lachnospiraceae bacterium ACC2 | antisense | 16453-16394 | 25 | EH016446.1 | LabA Uncharacterized conserved protein, LabA/DUF88 family [Function unknown][5] |
| HF995344.1 | Firmicutes bacterium CAG:646 | sense | 9468-9528 | 22 | CCZ34610.1 | LabA Uncharacterized conserved protein, LabA/DUF88 family [Function unknown][5] |
| FR885222.1 | Phascolarctobacterium sp. CAG:207 | sense | 16452-16513 | 38 | CDB45685.1 | LabA Uncharacterized conserved protein, LabA/DUF88 family [Function unknown][5] |
| CP001859.1 | CP001859.1 | antisense | 1843461-1843400 | 28 | Acfer_1667 | Hypothetical protein[5] |
References
[edit]- ^ a b c "LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs". RNA. 18 (5): 900–914. 2012. doi:10.1261/rna.029041.111. PMC 3334699. PMID 22450757.
{{cite journal}}: Unknown parameter|authors=ignored (help)CS1 maint: PMC format (link) - ^ "Cartography of Methicillin-Resistant S. Aureus Transcripts: Detection, Orientation and Temporal Expression During Growth Phase and Stress Conditions". PLoS One. 5 (5): e10725. May 20, 2010. doi:10.1371/journal.pone.0010725. PMC 2873960. PMID 20505759.
{{cite journal}}: Unknown parameter|authors=ignored (help)CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link) - ^ "labA: A Novel Gene Required for Negative Feedback Regulation of the Cyanobacterial Circadian Clock Protein KaiC". Gene Dev. 21 (1): 60–70. Jan 1, 2007. doi:10.1101/gad.1488107. PMC 1759901. PMID 17210789.
{{cite journal}}: Unknown parameter|authors=ignored (help)CS1 maint: PMC format (link) - ^ "Horizontal Gene Transfer in Bacterial and Archaeal Complete Genomes". Genome Research. 10 (11): 1719–25. Nov 2000. doi:10.1101/gr.130000. PMC 310969. PMID 11076857.
{{cite journal}}: Unknown parameter|authors=ignored (help)CS1 maint: PMC format (link) - ^ a b c d e f g h i j k l m n Information, National Center for Biotechnology; Pike, U. S. National Library of Medicine 8600 Rockville. "National Center for Biotechnology Information". www.ncbi.nlm.nih.gov. Retrieved 2019-12-12.
{{cite web}}: CS1 maint: numeric names: authors list (link)