3HOUD

Complete rna polymerase ii elongation complex i with a t-u mismatch
Total Genus 50
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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
50
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 50
structure length 178
sequence length 219
chains with identical sequence P
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; 3houD02
3HOWD 4A3MD 4A93D 4A3LD 4A3ED 2JA5D 5C4XD 2R7ZD 4A3KD 4A3JD 3PO2D 3HOXD 5IYBD 3I4MD 4BY7D 5IP9D 1Y1WD 4A3ID 1Y1VD 2JA6D 3HOYD 3HOZD 4A3DD 5C3ED 5C44D 4A3FD 4BXXD 4A3CD 3HOVD 2VUMD 2JA7D 2JA8D 3HOUD 3FKID 1WCMD 4A3GD 5IP7D 4BY1D 3H3VE 3H0GD 2C35A 3AYHA 4A3BD 3PO3D 3I4ND 4BBRD 2R93D 2R92D 2B63D 1Y14A 5IYDD 5IYCD 4BBSD 5FLMD
chains in the Genus database with same CATH superfamily
3SE4B 4IKZA 2CFPA 3O7QA 1P9MB 4DOHA 4PS4A 1A22A 3NPZA 5D70A 1BP3A 4YBQA 2ILKA 3OG6A 2Q7NB 4D2BA 4ZYRA 1JLIA 1M48A 1I1RB 2ERJD 4IKXA 1M4CA 1ITMA 5D71A 4I77Z 4FA8E 3INKC 1V7MV 1IK0A 1D9GA 3LB6A 1VLKA 4GBZA 5KNHI 2CFQA 3OG4A 4YPGC 5C4XD 2R7ZD 1LK3A 3HOXD 3N0PA 4O6KA 4D2CA 4ZWBA 4CNIC 4PYPA 1Z7CA 2B91A 4NN7A 1Y6ML 2R93D 4Z5RD 2Y5YA 3Q1SI 3HOZD 5C44D 2O6IA 1HIKA 5A2OA 1Y6NL 1ITLA 4OH3A 5EQHA 5TS9A 4U4TA 2V8NA 1M47A 4ZF7A 5IYDD 4LEPA 1RW5A 1J7VL 4U4WA 1INRA 1ETEA 1M4AA 4NI7A 4DKFA 1ITFA 1EVSA 4QIQA 4BY7D 1CN4C 5C3ED 4GBYA 4A3CD 1EERA 1M49A 1CD9A 4NEJA 3QB7A 1ILKA 3EJJA 2L3OA 1HGUA 5IP7D 4YB9D 5C65A 2Z3RA 3NCFA 1Y14A 4BBSD 2B90A 2LAGA 1BCNA 5C7XA 5D59A 4A3LD 4A3KD 1EKUA 1BUYA 2KZ1A 4ZWCA 4JR9A 1FYHA 3VA2A 1N1FA 1KF9A 2GMFA 4DKEA 4EXNA 3BPOA 3H3VE 3AYHA 4LDSA 3HHCA 4DKDA 1D9CA 4IKVA 2R92D 2D48A 5E4EA 3LB6B 4A93D 3QT2C 1Y1WD 5EQGA 3G6DA 5LQBA 3PIVA 1PVHB 3BPNA 4XNIA 5A2NA 3D48P 5L6YC 2C35A 4A3BD 4RS1A 4APSA 4IU9A 1Z92A 1LKIA 3NCCA 4NKQC 1GA3A 5FHXA 1PV7A 1ALUA 1LQSL 3DI2A 4A3JD 3TGXB 4OAAA 1A7MA 3L5WI 2B8YA 2B8UA 5EQIA 1M4RA 1YKBA 3HOYD 1AU1A 4A3MD 3QAZA 3OQ3A 5GXBA 4XNJA 1HWHA 2JA7D 2JA8D 4NN6A 3HOUD 3DGCL 1RHGA 3PO3D 2O26A 4BBRD 3QWRB 4O9HA 5D22A 4D2DA 3D87A 4J05A 3I4MD 5D72A 1FG9A 2E9WC 3S9DA 2INTA 2VUMD 3IRHA 2Q98A 3FKID 2HYMB 4JREA 1AX8A 1M4BA 3BESL 4MHLA 4WRLB 1NBPA 4GC0A 3SE3B 2L3YA 4YDYI 2D9QA 3HOWD 4A3ED 4J4LC 3PO2D 4ZW9A 4A3DD 1CYLA 1IL6A 4DKCA 1HIJA 3N06A 4TPGA 4UVMA 3DLQI 4BY1D 1RFBA 3H0GD 3HHRA 3DUHC 3WCYI 1BGDA 2OQPA 4GRWA 1AXIA 2B63D 5IYCD 3NCEA 1SCFA 1BGEA 1BBNA 2CYKA 5IP9D 4IU8A 1Y1VD 5FUCA 3UF2A 1IARA 3O7PA 4YUEC 4TPJA 4JA3A 3QB1A 2Q14A 1F6FA 3G9VB 4Q65A 1QVNA 1B5LA 1V7NV 1HWGA 2XQBA 5D58A 1CSGA 3MZGA 1HZIA 5D28B 4W6VA 1Y6KL 1PGRA 4BXXD 1EMRA 2B8ZA 4A3FD 3L5XA 3EW3A 4IKWA 1HULA 1PW4A 3PIWA 2B5IA 3UF5A 4TPHA 1PV6A 1GNCA 4YQXA 4A3GD 4NI9A 4ZS7A 5D6KA 3WDOA 5IYBD 4LRLA 1BGCA 1IRLA 2O27A 2XUTA 4U4VA 1WCMD 2H24A 2LMSA 4NEMA 1RCBA 3UEZE 5FLMD 3D85C 1ITIA 2JA6D 4A3ID 2Z3QA 4GS7A 3DI3A 1EXZA 1PY2A 4IKYA 3B5KA 3I4ND 4EXPA 1F45B 2JA5D 2IL6A 2B8XA 3UX9A 2PSMA 3HOVD 1HUWA 1PW6A 4NN5A 3NCBA 1IJZA 4X51A 1CNT1 1WU3I 3BPLA 3HMXB
chains in the Genus database with same CATH topology
3MZGA 1HZIA 3SE4B 1AU1A 1J7VL 1RW5A 1INRA 1ETEA 1M4AA 3QAZA 5D28B 4NI7A 4DKFA 1EVSA 1Y6KL 1PGRA 4BY7D 1CN4C 1P9MB 4BXXD 1EMRA 2B8ZA 4PS4A 4DOHA 5C3ED 3L5XA 3OQ3A 4A3FD 1A22A 3EW3A 4A3CD 1EERA 1M49A 3NPZA 1HULA 1CD9A 1HWHA 1BP3A 4NEJA 5D70A 2JA7D 2JA8D 3PIWA 3QB7A 4NN6A 3HOUD 2ILKA 1ILKA 3DGCL 3OG6A 3EJJA 2L3OA 2B5IA 1RHGA 1HGUA 5IP7D 1YKBA 3UF5A 2Q7NB 3PO3D 2O26A 4BBRD 3QWRB 5IYDD 1GNCA 4O9HA 4YQXA 2Z3RA 3NCFA 1JLIA 1M48A 1I1RB 1Y14A 5D22A 4BBSD 2B90A 2LAGA 4A3GD 1BCNA 5C7XA 4A3LD 1IK0A 4NI9A 4ZS7A 4A3KD 1EKUA 3D87A 2ERJD 5IYBD 3I4MD 1BUYA 2KZ1A 5D72A 1FG9A 2E9WC 1FYHA 3S9DA 4LRLA 1M4CA 1BGCA 3VA2A 1ITMA 5D71A 4I77Z 1IRLA 1N1FA 2INTA 2O27A 4FA8E 2VUMD 1KF9A 2GMFA 4DKEA 3IRHA 2Q98A 3INKC 3FKID 2HYMB 1WCMD 1V7MV 1AX8A 2H24A 1M4BA 2LMSA 3BESL 3BPOA 1D9GA 3LB6A 4MHLA 4EXNA 4NEMA 3AYHA 1VLKA 3H3VE 1RCBA 4WRLB 1ITFA 1NBPA 3HHCA 4DKDA 5KNHI 1D9CA 3UEZE 3SE3B 4A3MD 2R92D 2D48A 2L3YA 4YDYI 5E4EA 3D85C 2D9QA 3LB6B 3OG4A 5FLMD 3HOWD 4YPGC 4A93D 4A3ED 5C4XD 2R7ZD 1LK3A 3QT2C 4J4LC 1ITIA 3PO2D 3HOXD 1Y1WD 4A3ID 2JA6D 3G6DA 3HOYD 2Z3QA 4A3DD 4GS7A 1CYLA 3N0PA 4O6KA 3DI3A 1IL6A 4DKCA 1HIJA 3PIVA 5LQBA 1PVHB 3BPNA 3N06A 1EXZA 3D48P 1PY2A 4CNIC 3DLQI 3B5KA 1Z7CA 5L6YC 4BY1D 2B91A 1RFBA 2C35A 3H0GD 3HHRA 4A3BD 3DUHC 4NN7A 1BGDA 2OQPA 4GRWA 3WCYI 3I4ND 1Y6ML 4RS1A 2R93D 1Z92A 1AXIA 4Z5RD 2B63D 1LKIA 3NCCA 3NCEA 4EXPA 5IYCD 1F45B 4NKQC 1GA3A 1SCFA 5FHXA 1BGEA 2JA5D 3Q1SI 1ALUA 1LQSL 3DI2A 4A3JD 3TGXB 2IL6A 1BBNA 2CYKA 5IP9D 3HOZD 1Y1VD 5FUCA 3UF2A 1IARA 2B8XA 5C44D 1A7MA 3L5WI 4YUEC 2O6IA 2B8YA 3UX9A 2PSMA 3HOVD 1HUWA 1HIKA 3QB1A 1PW6A 1Y6NL 1ITLA 2Q14A 1F6FA 5TS9A 3G9VB 2B8UA 1QVNA 1B5LA 4NN5A 3NCBA 1IJZA 4X51A 1M47A 1HWGA 1V7NV 2XQBA 1CNT1 4ZF7A 1WU3I 3BPLA 1M4RA 3HMXB 1CSGA
chains in the Genus database with same CATH homology


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