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


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