5C44D

Crystal structure of a transcribing rna polymerase ii complex reveals a complete transcription bubble
Total Genus 39
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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
39
sequence length
218
structure length
178
Chain Sequence
STSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY
Loading diagram...

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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publication title Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.
pubmed doi rcsb
molecule keywords DNA-directed RNA polymerase II subunit RPB1
molecule tags Transferase/dna/rna
source organism Saccharomyces cerevisiae (strain atcc 204508 / s288c)
total genus 39
structure length 178
sequence length 218
ec nomenclature
pdb deposition date 2015-06-17

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; 5c44D02
4A3LD 3HOYD 3FKID 4A3BD 3HOXD 5C44D 4BBRD 5FLMD 4BY1D 2JA6D 3H3VE 4A3GD 4A3DD 2C35A 3PO2D 4A3CD 3H0GD 4A3ID 4A3ED 5IYBD 1Y1WD 2JA7D 3HOUD 2R93D 5IYCD 4A3MD 3AYHA 3PO3D 5IP7D 1WCMD 4BBSD 2JA5D 2JA8D 5C3ED 2R92D 3I4ND 2B63D 5C4XD 3HOVD 5IP9D 4A3FD 4BXXD 4A3JD 3HOZD 1Y14A 4BY7D 3HOWD 4A3KD 1Y1VD 2VUMD 4A93D 3I4MD 5IYDD 2R7ZD
chains in the Genus database with same CATH superfamily
1INRA 1V7NV 5FHXA 3QT2C 1EVSA 3PO2D 1EXZA 5A2NA 3HOUD 3DI3A 2B8UA 3AYHA 4NEMA 3HOWD 1WU3I 4X51A 5FUCA 2HYMB 1HGUA 4LRLA 5D71A 5E4EA 1Y1WD 2R93D 5EQHA 1EERA 1EKUA 1LKIA 4A3FD 4ZW9A 4W6VA 1Y6ML 1PV6A 3N0PA 2XUTA 3SE3B 1M4AA 1BP3A 4NI9A 4A3GD 1F45B 2JA7D 1RFBA 4XNIA 4ZF7A 3HMXB 4LDSA 1CYLA 4ZWCA 3MZGA 2D9QA 4MHLA 2LAGA 4YBQA 5A2OA 3HOXD 2CFPA 3NCFA 4QIQA 5IYBD 3B5KA 1HUWA 2Q7NB 1RHGA 2CYKA 1BGDA 1WCMD 1YKBA 2Q98A 3I4ND 4FA8E 4GRWA 4CNIC 4O9HA 4IKZA 4A93D 2GMFA 1B5LA 4D2BA 1ITLA 1Y6KL 2B90A 2O27A 4J4LC 1ITIA 5EQGA 2KZ1A 5KNHI 3PO3D 1FYHA 5D59A 1D9CA 1LQSL 4JA3A 3QB7A 4IU9A 1QVNA 1PW4A 3HOYD 3BPNA 1GNCA 4OH3A 4YB9D 1ETEA 1KF9A 1J7VL 4DKDA 3UF5A 1M4RA 1Z7CA 3TGXB 1RCBA 4BBSD 1A22A 3D87A 1HZIA 2B8ZA 1VLKA 3EJJA 4NI7A 4TPGA 4YQXA 2XQBA 4WRLB 4PS4A 3LB6A 1Z92A 3LB6B 4ZWBA 1V7MV 1HWHA 1D9GA 2H24A 2R7ZD 1CSGA 1BGCA 1CNT1 4ZS7A 1FG9A 3D48P 4EXPA 4A3CD 4IU8A 4IKXA 4D2DA 4DKEA 1HIJA 4Z5RD 5IP9D 1CD9A 1BBNA 1PV7A 4GS7A 2B91A 4U4VA 3I4MD 3NPZA 4APSA 3DGCL 3EW3A 5D22A 2CFQA 3IRHA 4Q65A 1JLIA 4DOHA 4A3ID 1AU1A 1LK3A 1I1RB 4NN7A 4JR9A 3WDOA 2INTA 3BPOA 3UX9A 4GC0A 2Y5YA 4BXXD 4OAAA 4IKWA 3DLQI 4A3KD 1GA3A 1SCFA 2Z3QA 1M4CA 2JA6D 3H3VE 4NEJA 4LEPA 3H0GD 4EXNA 3PIWA 3BPLA 5D70A 5C4XD 1F6FA 5TS9A 2D48A 4J05A 3PIVA 1ILKA 1BGEA 1ITFA 3OQ3A 1IARA 2E9WC 3NCCA 3O7PA 5EQIA 4A3LD 3HHCA 2V8NA 2ERJD 5D72A 4DKFA 2Z3RA 3D85C 3L5XA 3UEZE 3OG6A 3OG4A 5GXBA 3QAZA 1PY2A 2IL6A 1AXIA 1HIKA 1M49A 1N1FA 4IKVA 2B63D 3HOVD 4O6KA 4A3JD 1Y14A 1PW6A 4UVMA 4YDYI 3UF2A 4TPJA 2PSMA 1NBPA 4A3BD 4BBRD 3N06A 1A7MA 4GBZA 4BY1D 4YPGC 4A3DD 2B5IA 5IYCD 2L3YA 4IKYA 4PYPA 5C3ED 3NCEA 2R92D 3QB1A 5LQBA 1Y1VD 1AX8A 1M48A 1HULA 1BCNA 5D28B 4GBYA 2B8YA 1M4BA 4U4TA 3INKC 5C44D 1IK0A 1IL6A 5FLMD 1ITMA 2LMSA 3DUHC 1M47A 2C35A 3Q1SI 2L3OA 3DI2A 2JA8D 3HOZD 4BY7D 4NKQC 4JREA 1ALUA 5D6KA 1CN4C 3NCBA 1Y6NL 3G9VB 5D58A 5IP7D 1IJZA 2JA5D 3HHRA 4D2CA 4ZYRA 2Q14A 2O26A 1BUYA 2O6IA 2OQPA 1RW5A 1HWGA 4RS1A 4YUEC 4U4WA 1PVHB 3G6DA 5C65A 4TPHA 3SE4B 4I77Z 4A3MD 3S9DA 4NN5A 3QWRB 2B8XA 4NN6A 3VA2A 5C7XA 4DKCA 2VUMD 3O7QA 1IRLA 3FKID 1P9MB 2ILKA 3WCYI 3BESL 4A3ED 1PGRA 4XNJA 1EMRA 3L5WI 5L6YC 5IYDD
chains in the Genus database with same CATH topology
3NPZA 1M4BA 3DGCL 1INRA 1ITLA 1V7NV 3INKC 5C44D 1Y6KL 1IK0A 2B90A 3EW3A 5D22A 1IL6A 3IRHA 5FHXA 5FLMD 1ITMA 2LMSA 3DUHC 1EVSA 1M47A 3QT2C 2C35A 1EXZA 1JLIA 4DOHA 1AU1A 2O27A 3Q1SI 4A3ID 3HOUD 3PO2D 4J4LC 1ITIA 1LK3A 2L3OA 3DI3A 1I1RB 2KZ1A 4NN7A 5KNHI 2B8UA 3DI2A 3AYHA 3PO3D 1FYHA 2INTA 3BPOA 3UX9A 1D9CA 1LQSL 2JA8D 3QB7A 4BXXD 4NEMA 3HOZD 4BY7D 1QVNA 3HOWD 4A93D 1WU3I 4NKQC 3DLQI 4X51A 4A3KD 1ALUA 1GA3A 1SCFA 2Z3QA 3HOYD 5FUCA 2HYMB 1M4CA 3BPNA 1HGUA 4LRLA 5D71A 2JA6D 1CN4C 3H3VE 3NCBA 4NEJA 3H0GD 5E4EA 1Y1WD 1GNCA 1Y6NL 2R93D 3G9VB 1ETEA 4EXNA 5IP7D 1IJZA 3PIWA 1EERA 2JA5D 3BPLA 3HHRA 1KF9A 5D70A 1J7VL 5C4XD 1EKUA 1F6FA 1LKIA 5TS9A 4DKDA 2Q14A 4A3FD 2D48A 2O26A 1BUYA 2O6IA 3PIVA 3UF5A 1ILKA 1BGEA 1M4RA 1RW5A 1Y6ML 2OQPA 1ITFA 3OQ3A 1IARA 2E9WC 3N0PA 1Z7CA 3NCCA 3TGXB 1RCBA 4BBSD 4A3LD 1HWGA 3HHCA 3SE3B 2ERJD 4RS1A 1A22A 4YUEC 5D72A 4DKFA 1BCNA 1PVHB 2Z3RA 3D85C 1M4AA 3L5XA 3D87A 1BP3A 1HZIA 3UEZE 3OG6A 4NI9A 4A3GD 3OG4A 3G6DA 1F45B 2B8ZA 3QAZA 2JA7D 1VLKA 3EJJA 3SE4B 1PY2A 2IL6A 1AXIA 4NI7A 4I77Z 1HIKA 1RFBA 1M49A 3S9DA 4A3MD 4YQXA 4ZF7A 2XQBA 1N1FA 3HMXB 4WRLB 4PS4A 3LB6A 2B63D 1Z92A 3HOVD 1CYLA 4O6KA 3MZGA 4A3JD 1Y14A 4NN5A 3LB6B 1PW6A 5L6YC 3QWRB 2B8XA 2D9QA 4NN6A 3VA2A 4YDYI 1V7MV 5C7XA 4MHLA 4DKCA 2VUMD 3UF2A 1HWHA 1D9GA 1IRLA 2H24A 2LAGA 1CSGA 2R7ZD 2PSMA 1NBPA 3FKID 1P9MB 4A3BD 3HOXD 1BGCA 1CNT1 3N06A 4BBRD 2ILKA 4ZS7A 4BY1D 1A7MA 3WCYI 3NCFA 1FG9A 3D48P 3BESL 4YPGC 4EXPA 4A3CD 4A3DD 4A3ED 5IYBD 3B5KA 2B5IA 5IYCD 1HUWA 1PGRA 1RHGA 2Q7NB 1HIJA 4DKEA 2L3YA 2CYKA 1BGDA 1WCMD 1YKBA 4Z5RD 3NCEA 2Q98A 5C3ED 2R92D 3I4ND 5IP9D 4FA8E 1CD9A 4GRWA 3QB1A 1EMRA 1BBNA 1Y1VD 3L5WI 1AX8A 4GS7A 1M48A 1HULA 4O9HA 2B91A 4CNIC 5LQBA 3I4MD 5D28B 5IYDD 2GMFA 1B5LA 2B8YA
chains in the Genus database with same CATH homology


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