3HOXD

Complete rna polymerase ii elongation complex v
Total Genus 47
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
47
sequence length
219
structure length
178
Chain Sequence
VSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKTREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY
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The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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molecule tags Transcription,transferase/dna/rna hybrid
molecule keywords DNA-directed RNA polymerase II subunit RPB1
publication title Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.
pubmed doi rcsb
total genus 47
structure length 178
sequence length 219
ec nomenclature
pdb deposition date 2009-06-03

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
D PF03874 RNA_pol_Rpb4 RNA polymerase Rpb4
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.20.1250.40 Mainly Alpha Up-down Bundle Growth Hormone; Chain: A; Growth Hormone; Chain: A; 3hoxD02
4A3BD 5IYDD 3PO2D 1Y1VD 4A3DD 2C35A 5C3ED 3H3VE 5IYCD 3HOYD 4BBSD 4A3FD 2R7ZD 3I4ND 2VUMD 4BY7D 3HOUD 5C44D 2JA8D 1Y14A 4BBRD 4A3ID 1WCMD 5C4XD 2R92D 2JA7D 1Y1WD 2R93D 3HOZD 5IP9D 5IYBD 5IP7D 2JA6D 4A93D 3HOVD 3HOWD 4A3GD 2JA5D 4A3MD 5FLMD 3AYHA 4A3ED 3H0GD 4BY1D 4A3LD 3HOXD 4A3JD 4A3KD 4A3CD 2B63D 3FKID 4BXXD 3I4MD 3PO3D
chains in the Genus database with same CATH superfamily
3QAZA 4A3DD 3NCFA 1AXIA 3G6DA 3HOUD 3SE3B 1F45B 5D72A 1INRA 2R93D 1IL6A 5IP9D 3VA2A 3EJJA 1ITFA 3UF5A 2B63D 4WRLB 4NN5A 1Z92A 5IYDD 1BGCA 3DGCL 4BBSD 4U4VA 3PIWA 2L3OA 4OAAA 2VUMD 5EQIA 1IARA 4APSA 5EQHA 1PGRA 4DKEA 4GBYA 3H0GD 1B5LA 3D85C 2XQBA 1HIJA 3HOYD 3QT2C 2E9WC 1BBNA 4I77Z 3BPLA 4BBRD 1HGUA 2ERJD 2O6IA 5TS9A 3L5XA 5IP7D 1Y6KL 4U4WA 4BY1D 4A3JD 4Z5RD 3WDOA 2LAGA 4O6KA 4EXNA 4LRLA 1V7MV 1ETEA 3LB6B 2B91A 1PY2A 4IKVA 3HOZD 2D9QA 4A3GD 1CN4C 1HZIA 4YBQA 1N1FA 1AU1A 2O27A 1YKBA 3PO2D 2C35A 1M48A 5E4EA 1M47A 5A2OA 1EMRA 3DUHC 4DOHA 4NKQC 4ZYRA 1PV7A 3EW3A 5IYBD 5C7XA 1D9GA 2HYMB 1BGEA 1SCFA 1HULA 1NBPA 3PO3D 2CYKA 3DI2A 5C3ED 3NCEA 4A3FD 5FUCA 1BP3A 1AX8A 3HHCA 1M49A 4IKXA 2JA8D 5D71A 4GS7A 4YPGC 1M4BA 4UVMA 3TGXB 3HOWD 1M4RA 4U4TA 2V8NA 4JREA 4A3KD 2B8ZA 4IKYA 1PW4A 4JR9A 3BPOA 3L5WI 2O26A 4LEPA 1P9MB 5D70A 2Y5YA 4BY7D 3HHRA 1FG9A 2Q98A 3HMXB 2Q14A 3IRHA 4NI7A 3HOVD 3Q1SI 2B8YA 5D6KA 4ZWCA 4TPHA 4MHLA 1PW6A 1ITLA 5C65A 4DKDA 1IJZA 4A3CD 1EERA 4NN7A 2XUTA 1EXZA 3UX9A 4NI9A 5C44D 3NPZA 5C4XD 3BPNA 3QB1A 5KNHI 1HWHA 4PS4A 1I1RB 3UEZE 3WCYI 2Q7NB 3INKC 4GC0A 4GBZA 3O7QA 1GNCA 2B8XA 3SE4B 4ZF7A 4XNJA 1ITMA 2PSMA 3QWRB 3PIVA 1LKIA 1ALUA 1ILKA 1CD9A 4A93D 1BUYA 1GA3A 4A3MD 4RS1A 4PYPA 1JLIA 3NCCA 3D87A 1KF9A 5GXBA 4O9HA 4ZW9A 4IU8A 4D2BA 1IRLA 2D48A 3DLQI 1HUWA 5EQGA 2Z3RA 1VLKA 3N0PA 3MZGA 3OG4A 4YQXA 2JA5D 2CFQA 3QB7A 1HWGA 5FHXA 4XNIA 4DKFA 3DI3A 2R92D 1BCNA 4DKCA 2JA6D 4D2CA 1EVSA 4Q65A 4LDSA 3AYHA 4ZS7A 4A3LD 1RCBA 4IKZA 1ITIA 3I4MD 2R7ZD 3OQ3A 3S9DA 3O7PA 3I4ND 2H24A 2IL6A 1M4AA 1F6FA 5D22A 5D58A 3OG6A 1CNT1 4J4LC 1Y1VD 4GRWA 1CYLA 4CNIC 1PVHB 1V7NV 1Y1WD 4NEMA 1QVNA 4FA8E 4A3BD 3B5KA 4X51A 4ZWBA 4EXPA 4J05A 4TPJA 2GMFA 3LB6A 4TPGA 1A22A 4NN6A 1HIKA 1Y6ML 1WCMD 2B90A 1RW5A 3UF2A 4W6VA 3D48P 2INTA 2KZ1A 1WU3I 5A2NA 4IU9A 3BESL 5L6YC 2Z3QA 1J7VL 4NEJA 2B8UA 3FKID 3NCBA 4QIQA 3G9VB 5D59A 2CFPA 5IYCD 1Y6NL 2OQPA 1EKUA 1Y14A 2JA7D 1CSGA 3N06A 4IKWA 4D2DA 4YB9D 1D9CA 1LQSL 4A3ED 1IK0A 3HOXD 2LMSA 1FYHA 4BXXD 5D28B 2L3YA 1RHGA 3H3VE 2B5IA 1M4CA 4A3ID 1BGDA 4YDYI 5LQBA 1RFBA 1LK3A 4YUEC 4OH3A 5FLMD 2ILKA 1Z7CA 1A7MA 1PV6A 4JA3A
chains in the Genus database with same CATH topology
1CNT1 2O27A 4J4LC 1YKBA 3QAZA 3PO2D 1Y1VD 4A3DD 2C35A 1IK0A 1M48A 5E4EA 2B8XA 4GRWA 3SE4B 1M47A 3NCFA 4ZF7A 1CYLA 1AXIA 1EMRA 3DUHC 4CNIC 3G6DA 4DOHA 4NKQC 1ITMA 3SE3B 1PVHB 2PSMA 3HOUD 3QWRB 1F45B 3PIVA 1LKIA 1ALUA 1V7NV 5D72A 1INRA 1Y1WD 2R93D 1ILKA 3EW3A 1IL6A 5IP9D 5C7XA 5IYBD 1CD9A 4A93D 1BUYA 4NEMA 1GA3A 3VA2A 1D9GA 3EJJA 4RS1A 4A3MD 1JLIA 1ITFA 3NCCA 2HYMB 3UF5A 1BGEA 1QVNA 1SCFA 1HULA 3D87A 4WRLB 2B63D 1NBPA 4NN5A 3PO3D 1KF9A 4FA8E 3B5KA 4A3BD 1Z92A 5IYDD 2CYKA 1BGCA 4O9HA 3DI2A 3DGCL 4X51A 5C3ED 3NCEA 4EXPA 4BBSD 4A3FD 1IRLA 2D48A 3DLQI 5FUCA 1BP3A 1HUWA 1AX8A 2L3OA 3PIWA 2VUMD 3HHCA 2GMFA 3LB6A 1M49A 2JA8D 1A22A 4NN6A 1HIKA 1Y6ML 1WCMD 1IARA 4GS7A 5D71A 4YPGC 2B90A 1M4BA 1PGRA 1RW5A 3TGXB 2Z3RA 3UF2A 1VLKA 3D48P 3HOWD 3N0PA 3MZGA 3OG4A 4YQXA 2JA5D 2INTA 1M4RA 2KZ1A 1WU3I 4DKEA 3QB7A 3BESL 3H0GD 5L6YC 2Z3QA 1B5LA 1J7VL 3D85C 4A3KD 4NEJA 2B8UA 3FKID 2B8ZA 3NCBA 2XQBA 1HIJA 3BPOA 1HWGA 3G9VB 5FHXA 3L5WI 5IYCD 1Y6NL 3HOYD 2OQPA 3QT2C 2E9WC 2O26A 5D70A 1BBNA 1P9MB 4I77Z 3BPLA 3HHRA 4DKFA 4BY7D 1FG9A 1EKUA 3DI3A 1Y14A 4BBRD 1HGUA 2Q98A 3HMXB 2R92D 2ERJD 1CSGA 2O6IA 5TS9A 3N06A 2JA7D 1BCNA 4DKCA 3L5XA 2Q14A 5IP7D 2JA6D 3IRHA 1D9CA 1Y6KL 4NI7A 3HOVD 3Q1SI 2B8YA 1EVSA 1LQSL 4MHLA 3AYHA 4A3ED 4BY1D 1PW6A 1ITLA 4ZS7A 3HOXD 2LMSA 1RCBA 4DKDA 4A3JD 4A3LD 4Z5RD 1FYHA 1IJZA 4A3CD 1ITIA 1EERA 4NN7A 3I4MD 2R7ZD 5D28B 4BXXD 2LAGA 2L3YA 4O6KA 1RHGA 4LRLA 4EXNA 3H3VE 1EXZA 3OQ3A 1A7MA 3UX9A 3S9DA 4NI9A 2B5IA 1V7MV 3I4ND 1ETEA 1M4CA 2H24A 3LB6B 5C44D 2B91A 3NPZA 4A3ID 1BGDA 5C4XD 2IL6A 3BPNA 1PY2A 3QB1A 3HOZD 5KNHI 4YDYI 1M4AA 1F6FA 5D22A 1HWHA 1RFBA 4PS4A 2D9QA 1I1RB 5LQBA 1LK3A 4YUEC 4A3GD 3UEZE 3WCYI 2Q7NB 5FLMD 2ILKA 3INKC 1CN4C 1HZIA 1N1FA 1Z7CA 3OG6A 1GNCA 1AU1A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4A3B D;  5IYD D;  3PO2 D;  1Y1V D;  4A3D D;  2C35 A;  5C3E D;  3H3V E;  5IYC D;  3HOY D;  4BBS D;  4A3F D;  2R7Z D;  3I4N D;  2VUM D;  4BY7 D;  3HOU D;  5C44 D;  2JA8 D;  1Y14 A;  4BBR D;  4A3I D;  1WCM D;  5C4X D;  2R92 D;  2JA7 D;  1Y1W D;  2R93 D;  3HOZ D;  5IP9 D;  5IYB D;  5IP7 D;  2JA6 D;  4A93 D;  3HOV D;  3HOW D;  4A3G D;  2JA5 D;  4A3M D;  5FLM D;  3AYH A;  4A3E D;  3H0G D;  4BY1 D;  4A3L D;  3HOX D;  4A3J D;  4A3K D;  4A3C D;  2B63 D;  3FKI D;  4BXX D;  3I4M D;  3PO3 D; 
#chains in the Genus database with same CATH topology
 3QAZ A;  4A3D D;  3NCF A;  1AXI A;  3G6D A;  3HOU D;  3SE3 B;  1F45 B;  5D72 A;  1INR A;  2R93 D;  1IL6 A;  5IP9 D;  3VA2 A;  3EJJ A;  1ITF A;  3UF5 A;  2B63 D;  4WRL B;  4NN5 A;  1Z92 A;  5IYD D;  1BGC A;  3DGC L;  4BBS D;  4U4V A;  3PIW A;  2L3O A;  4OAA A;  2VUM D;  5EQI A;  1IAR A;  4APS A;  5EQH A;  1PGR A;  4DKE A;  4GBY A;  3H0G D;  1B5L A;  3D85 C;  2XQB A;  1HIJ A;  3HOY D;  3QT2 C;  2E9W C;  1BBN A;  4I77 Z;  3BPL A;  4BBR D;  1HGU A;  2ERJ D;  2O6I A;  5TS9 A;  3L5X A;  5IP7 D;  1Y6K L;  4U4W A;  4BY1 D;  4A3J D;  4Z5R D;  3WDO A;  2LAG A;  4O6K A;  4EXN A;  4LRL A;  1V7M V;  1ETE A;  3LB6 B;  2B91 A;  1PY2 A;  4IKV A;  3HOZ D;  2D9Q A;  4A3G D;  1CN4 C;  1HZI A;  4YBQ A;  1N1F A;  1AU1 A;  2O27 A;  1YKB A;  3PO2 D;  2C35 A;  1M48 A;  5E4E A;  1M47 A;  5A2O A;  1EMR A;  3DUH C;  4DOH A;  4NKQ C;  4ZYR A;  1PV7 A;  3EW3 A;  5IYB D;  5C7X A;  1D9G A;  2HYM B;  1BGE A;  1SCF A;  1HUL A;  1NBP A;  3PO3 D;  2CYK A;  3DI2 A;  5C3E D;  3NCE A;  4A3F D;  5FUC A;  1BP3 A;  1AX8 A;  3HHC A;  1M49 A;  4IKX A;  2JA8 D;  5D71 A;  4GS7 A;  4YPG C;  1M4B A;  4UVM A;  3TGX B;  3HOW D;  1M4R A;  4U4T A;  2V8N A;  4JRE A;  4A3K D;  2B8Z A;  4IKY A;  1PW4 A;  4JR9 A;  3BPO A;  3L5W I;  2O26 A;  4LEP A;  1P9M B;  5D70 A;  2Y5Y A;  4BY7 D;  3HHR A;  1FG9 A;  2Q98 A;  3HMX B;  2Q14 A;  3IRH A;  4NI7 A;  3HOV D;  3Q1S I;  2B8Y A;  5D6K A;  4ZWC A;  4TPH A;  4MHL A;  1PW6 A;  1ITL A;  5C65 A;  4DKD A;  1IJZ A;  4A3C D;  1EER A;  4NN7 A;  2XUT A;  1EXZ A;  3UX9 A;  4NI9 A;  5C44 D;  3NPZ A;  5C4X D;  3BPN A;  3QB1 A;  5KNH I;  1HWH A;  4PS4 A;  1I1R B;  3UEZ E;  3WCY I;  2Q7N B;  3INK C;  4GC0 A;  4GBZ A;  3O7Q A;  1GNC A;  2B8X A;  3SE4 B;  4ZF7 A;  4XNJ A;  1ITM A;  2PSM A;  3QWR B;  3PIV A;  1LKI A;  1ALU A;  1ILK A;  1CD9 A;  4A93 D;  1BUY A;  1GA3 A;  4A3M D;  4RS1 A;  4PYP A;  1JLI A;  3NCC A;  3D87 A;  1KF9 A;  5GXB A;  4O9H A;  4ZW9 A;  4IU8 A;  4D2B A;  1IRL A;  2D48 A;  3DLQ I;  1HUW A;  5EQG A;  2Z3R A;  1VLK A;  3N0P A;  3MZG A;  3OG4 A;  4YQX A;  2JA5 D;  2CFQ A;  3QB7 A;  1HWG A;  5FHX A;  4XNI A;  4DKF A;  3DI3 A;  2R92 D;  1BCN A;  4DKC A;  2JA6 D;  4D2C A;  1EVS A;  4Q65 A;  4LDS A;  3AYH A;  4ZS7 A;  4A3L D;  1RCB A;  4IKZ A;  1ITI A;  3I4M D;  2R7Z D;  3OQ3 A;  3S9D A;  3O7P A;  3I4N D;  2H24 A;  2IL6 A;  1M4A A;  1F6F A;  5D22 A;  5D58 A;  3OG6 A;  1CNT 1;  4J4L C;  1Y1V D;  4GRW A;  1CYL A;  4CNI C;  1PVH B;  1V7N V;  1Y1W D;  4NEM A;  1QVN A;  4FA8 E;  4A3B D;  3B5K A;  4X51 A;  4ZWB A;  4EXP A;  4J05 A;  4TPJ A;  2GMF A;  3LB6 A;  4TPG A;  1A22 A;  4NN6 A;  1HIK A;  1Y6M L;  1WCM D;  2B90 A;  1RW5 A;  3UF2 A;  4W6V A;  3D48 P;  2INT A;  2KZ1 A;  1WU3 I;  5A2N A;  4IU9 A;  3BES L;  5L6Y C;  2Z3Q A;  1J7V L;  4NEJ A;  2B8U A;  3FKI D;  3NCB A;  4QIQ A;  3G9V B;  5D59 A;  2CFP A;  5IYC D;  1Y6N L;  2OQP A;  1EKU A;  1Y14 A;  2JA7 D;  1CSG A;  3N06 A;  4IKW A;  4D2D A;  4YB9 D;  1D9C A;  1LQS L;  4A3E D;  1IK0 A;  3HOX D;  2LMS A;  1FYH A;  4BXX D;  5D28 B;  2L3Y A;  1RHG A;  3H3V E;  2B5I A;  1M4C A;  4A3I D;  1BGD A;  4YDY I;  5LQB A;  1RFB A;  1LK3 A;  4YUE C;  4OH3 A;  5FLM D;  2ILK A;  1Z7C A;  1A7M A;  1PV6 A;  4JA3 A; 
#chains in the Genus database with same CATH homology
 1CNT 1;  2O27 A;  4J4L C;  1YKB A;  3QAZ A;  3PO2 D;  1Y1V D;  4A3D D;  2C35 A;  1IK0 A;  1M48 A;  5E4E A;  2B8X A;  4GRW A;  3SE4 B;  1M47 A;  3NCF A;  4ZF7 A;  1CYL A;  1AXI A;  1EMR A;  3DUH C;  4CNI C;  3G6D A;  4DOH A;  4NKQ C;  1ITM A;  3SE3 B;  1PVH B;  2PSM A;  3HOU D;  3QWR B;  1F45 B;  3PIV A;  1LKI A;  1ALU A;  1V7N V;  5D72 A;  1INR A;  1Y1W D;  2R93 D;  1ILK A;  3EW3 A;  1IL6 A;  5IP9 D;  5C7X A;  5IYB D;  1CD9 A;  4A93 D;  1BUY A;  4NEM A;  1GA3 A;  3VA2 A;  1D9G A;  3EJJ A;  4RS1 A;  4A3M D;  1JLI A;  1ITF A;  3NCC A;  2HYM B;  3UF5 A;  1BGE A;  1QVN A;  1SCF A;  1HUL A;  3D87 A;  4WRL B;  2B63 D;  1NBP A;  4NN5 A;  3PO3 D;  1KF9 A;  4FA8 E;  3B5K A;  4A3B D;  1Z92 A;  5IYD D;  2CYK A;  1BGC A;  4O9H A;  3DI2 A;  3DGC L;  4X51 A;  5C3E D;  3NCE A;  4EXP A;  4BBS D;  4A3F D;  1IRL A;  2D48 A;  3DLQ I;  5FUC A;  1BP3 A;  1HUW A;  1AX8 A;  2L3O A;  3PIW A;  2VUM D;  3HHC A;  2GMF A;  3LB6 A;  1M49 A;  2JA8 D;  1A22 A;  4NN6 A;  1HIK A;  1Y6M L;  1WCM D;  1IAR A;  4GS7 A;  5D71 A;  4YPG C;  2B90 A;  1M4B A;  1PGR A;  1RW5 A;  3TGX B;  2Z3R A;  3UF2 A;  1VLK A;  3D48 P;  3HOW D;  3N0P A;  3MZG A;  3OG4 A;  4YQX A;  2JA5 D;  2INT A;  1M4R A;  2KZ1 A;  1WU3 I;  4DKE A;  3QB7 A;  3BES L;  3H0G D;  5L6Y C;  2Z3Q A;  1B5L A;  1J7V L;  3D85 C;  4A3K D;  4NEJ A;  2B8U A;  3FKI D;  2B8Z A;  3NCB A;  2XQB A;  1HIJ A;  3BPO A;  1HWG A;  3G9V B;  5FHX A;  3L5W I;  5IYC D;  1Y6N L;  3HOY D;  2OQP A;  3QT2 C;  2E9W C;  2O26 A;  5D70 A;  1BBN A;  1P9M B;  4I77 Z;  3BPL A;  3HHR A;  4DKF A;  4BY7 D;  1FG9 A;  1EKU A;  3DI3 A;  1Y14 A;  4BBR D;  1HGU A;  2Q98 A;  3HMX B;  2R92 D;  2ERJ D;  1CSG A;  2O6I A;  5TS9 A;  3N06 A;  2JA7 D;  1BCN A;  4DKC A;  3L5X A;  2Q14 A;  5IP7 D;  2JA6 D;  3IRH A;  1D9C A;  1Y6K L;  4NI7 A;  3HOV D;  3Q1S I;  2B8Y A;  1EVS A;  1LQS L;  4MHL A;  3AYH A;  4A3E D;  4BY1 D;  1PW6 A;  1ITL A;  4ZS7 A;  3HOX D;  2LMS A;  1RCB A;  4DKD A;  4A3J D;  4A3L D;  4Z5R D;  1FYH A;  1IJZ A;  4A3C D;  1ITI A;  1EER A;  4NN7 A;  3I4M D;  2R7Z D;  5D28 B;  4BXX D;  2LAG A;  2L3Y A;  4O6K A;  1RHG A;  4LRL A;  4EXN A;  3H3V E;  1EXZ A;  3OQ3 A;  1A7M A;  3UX9 A;  3S9D A;  4NI9 A;  2B5I A;  1V7M V;  3I4N D;  1ETE A;  1M4C A;  2H24 A;  3LB6 B;  5C44 D;  2B91 A;  3NPZ A;  4A3I D;  1BGD A;  5C4X D;  2IL6 A;  3BPN A;  1PY2 A;  3QB1 A;  3HOZ D;  5KNH I;  4YDY I;  1M4A A;  1F6F A;  5D22 A;  1HWH A;  1RFB A;  4PS4 A;  2D9Q A;  1I1R B;  5LQB A;  1LK3 A;  4YUE C;  4A3G D;  3UEZ E;  3WCY I;  2Q7N B;  5FLM D;  2ILK A;  3INK C;  1CN4 C;  1HZI A;  1N1F A;  1Z7C A;  3OG6 A;  1GNC A;  1AU1 A; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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