2JA8D

Cpd lesion containing rna polymerase ii elongation complex d
Total Genus 40
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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
40
sequence length
218
structure length
177
Chain Sequence
STSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKTREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY
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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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publication title Cpd Damage Recognition by Transcribing RNA Polymerase II.
pubmed doi rcsb
molecule keywords DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT
molecule tags Transferase
total genus 40
structure length 177
sequence length 218
ec nomenclature
pdb deposition date 2006-11-23

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; 2ja8D02
4A3ID 5IP9D 2JA5D 4A3KD 3HOVD 3HOUD 3I4MD 3PO3D 5C4XD 3HOYD 4A3DD 3FKID 2R92D 4BBRD 4A3CD 2JA6D 2B63D 4A3FD 4A3LD 4A3GD 3HOXD 4A93D 4A3BD 4BBSD 5IYCD 5FLMD 2JA8D 4A3MD 3HOWD 4BXXD 4A3JD 5C44D 5IP7D 4A3ED 1Y14A 2R7ZD 5C3ED 3H3VE 2R93D 3HOZD 1WCMD 1Y1VD 4BY1D 4BY7D 3H0GD 3I4ND 5IYBD 2JA7D 3PO2D 5IYDD 2VUMD 3AYHA 1Y1WD 2C35A
chains in the Genus database with same CATH superfamily
1ALUA 4D2DA 1P9MB 2KZ1A 2B91A 4BBRD 4A3BD 1F6FA 4GS7A 3N06A 4PS4A 1KF9A 1F45B 4NN5A 4GRWA 1BGDA 4JA3A 1Y6KL 2VUMD 1HWHA 1BGEA 3BPNA 4X51A 3DUHC 1CN4C 4YDYI 4A3DD 3S9DA 1FYHA 1HGUA 1V7NV 1LKIA 4BY7D 4MHLA 4NEJA 1IL6A 1M48A 4TPHA 3PIWA 3Q1SI 4Q65A 1LK3A 3D87A 4DKDA 1BGCA 2R92D 4EXNA 1EVSA 4YQXA 1M47A 1A22A 4NI9A 5A2NA 1IJZA 2L3YA 5C44D 5IP7D 4LRLA 4DKEA 4RS1A 3NCFA 1QVNA 2XQBA 1ETEA 5L6YC 3D48P 2O27A 3DGCL 4A93D 2O26A 2H24A 4YPGC 4IU8A 3INKC 4U4WA 4O9HA 5C3ED 3H3VE 1D9CA 2V8NA 5KNHI 4NI7A 4LDSA 4DOHA 3LB6B 1HZIA 3NCBA 3QT2C 1GNCA 1BUYA 5C7XA 1M4RA 3G9VB 3O7QA 4FA8E 4PYPA 1M4BA 4APSA 4GC0A 5D28B 4BBSD 4BXXD 4JR9A 4IKXA 5E4EA 5GXBA 1Y1VD 1ITFA 1CNT1 1M4AA 1ILKA 3PO3D 3EW3A 1HUWA 5D70A 5D59A 2JA8D 4OAAA 1IRLA 1Y14A 1PW4A 4YBQA 1SCFA 3L5XA 1Y6ML 5FUCA 3B5KA 3DLQI 3D85C 1D9GA 4NKQC 3WCYI 4JREA 2GMFA 1RW5A 2CFQA 2JA6D 1Z92A 2INTA 1PW6A 3PIVA 3EJJA 1PVHB 1I1RB 4TPGA 4Z5RD 4XNJA 3DI3A 5D6KA 3HOZD 1WCMD 1FG9A 3QB7A 4ZS7A 4IKZA 3QB1A 3N0PA 4ZW9A 1BCNA 1JLIA 3UEZE 3HOYD 3SE4B 3LB6A 5FLMD 4CNIC 2R7ZD 1HIJA 5LQBA 5TS9A 1HULA 1PGRA 2Q14A 2JA7D 5IYDD 1ITLA 1YKBA 1LQSL 2Y5YA 4YUEC 2C35A 4A3KD 3MZGA 3FKID 2O6IA 5EQIA 4DKFA 4A3GD 3NCCA 1WU3I 3NCEA 5EQHA 1PY2A 1PV7A 3O7PA 5D72A 5A2OA 4WRLB 2HYMB 3BPLA 4O6KA 4ZYRA 3HOUD 3BPOA 2B90A 2Q98A 1EKUA 2OQPA 5EQGA 3HOWD 1GA3A 3NPZA 4ZWBA 3QWRB 2LAGA 3AYHA 3OQ3A 4DKCA 3OG6A 5IP9D 3L5WI 3HOVD 2L3OA 4NEMA 3HHRA 4A3CD 1PV6A 4A3FD 3HHCA 1N1FA 3QAZA 3OG4A 4A3JD 3SE3B 1A7MA 1RFBA 2LMSA 2R93D 1CSGA 1IK0A 5C65A 1AX8A 1ITIA 2D48A 4IKVA 2CFPA 1CD9A 4NN6A 1Y6NL 4UVMA 1EMRA 1M4CA 4YB9D 3I4MD 2B63D 1BBNA 4A3LD 4J05A 4IU9A 5IYCD 4A3MD 2Z3QA 1M49A 3UF2A 4XNIA 5IYBD 1NBPA 3PO2D 1EERA 1Z7CA 1BP3A 2B8XA 4U4TA 4D2BA 4A3ID 2B8ZA 3UX9A 2CYKA 4U4VA 2D9QA 1B5LA 2PSMA 1HWGA 4ZF7A 4GBYA 2Z3RA 4A3ED 4GBZA 1J7VL 4IKYA 1CYLA 1RHGA 2B8UA 2Q7NB 5FHXA 4W6VA 2B5IA 4IKWA 4TPJA 3TGXB 5D71A 3IRHA 4ZWCA 1EXZA 5D22A 3VA2A 1RCBA 1IARA 2ILKA 2ERJD 3DI2A 4EXPA 4BY1D 4OH3A 3H0GD 3UF5A 1ITMA 1HIKA 4J4LC 4NN7A 4I77Z 2IL6A 3G6DA 1Y1WD 1V7MV 2E9WC 2JA5D 3HMXB 5C4XD 3HOXD 4LEPA 4QIQA 4D2CA 1INRA 3I4ND 1AU1A 5D58A 3WDOA 1VLKA 1AXIA 2XUTA 3BESL 2B8YA
chains in the Genus database with same CATH topology
4NI7A 1BCNA 1Y6NL 1ALUA 1EMRA 1M4CA 3I4MD 4DOHA 1JLIA 1P9MB 2KZ1A 3UEZE 3HOYD 3LB6B 2B91A 3SE4B 4BBRD 2B63D 1BBNA 1HZIA 4A3LD 3NCBA 3QT2C 3LB6A 4A3BD 1F6FA 5IYCD 5FLMD 4A3MD 4GS7A 2Z3QA 4CNIC 3N06A 4PS4A 1GNCA 1KF9A 1F45B 4NN5A 4GRWA 1M49A 2R7ZD 1BGDA 1BUYA 3UF2A 5C7XA 1HIJA 5LQBA 1M4RA 5TS9A 1HULA 3G9VB 1PGRA 5IYBD 1NBPA 2Q14A 4FA8E 2JA7D 1EERA 1Z7CA 1ITLA 1Y6KL 1YKBA 1LQSL 5IYDD 1BP3A 1HWHA 1M4BA 2B8XA 4YUEC 2VUMD 2C35A 1BGEA 3BPNA 4A3ID 4A3KD 2B8ZA 3UX9A 4X51A 3DUHC 1CN4C 2CYKA 3MZGA 3PO2D 2D9QA 4YDYI 4A3DD 1B5LA 2O6IA 2PSMA 3FKID 4DKFA 4A3GD 3NCCA 1WU3I 5D28B 1HWGA 4BBSD 3S9DA 4BXXD 4ZF7A 1FYHA 1HGUA 2Z3RA 4A3ED 3NCEA 1PY2A 1V7NV 1LKIA 5E4EA 5D72A 1Y1VD 4MHLA 4BY7D 1J7VL 1ITFA 1CYLA 4NEJA 1IL6A 1M48A 1RHGA 2B8UA 3PIWA 4WRLB 2HYMB 1CNT1 3BPLA 4O6KA 2Q7NB 3Q1SI 5FHXA 1LK3A 1ILKA 1M4AA 3D87A 4DKDA 3HOUD 3PO3D 1BGCA 2B5IA 3BPOA 3EW3A 2B90A 2R92D 1EVSA 1HUWA 2Q98A 4YQXA 5D70A 1EKUA 5D71A 3TGXB 3IRHA 4EXNA 1M47A 1A22A 4NI9A 1EXZA 2OQPA 5D22A 3VA2A 1IRLA 1RCBA 2JA8D 1IARA 1IJZA 3HOWD 2L3YA 1GA3A 5C44D 2ILKA 5IP7D 2ERJD 4LRLA 1Y14A 3DI2A 3NPZA 4DKEA 4EXPA 4BY1D 3H0GD 3QWRB 3UF5A 4RS1A 1ITMA 1SCFA 3L5XA 1HIKA 1Y6ML 4J4LC 4NN7A 2LAGA 5FUCA 4I77Z 3B5KA 2IL6A 3NCFA 3AYHA 3G6DA 1Y1WD 3OQ3A 4DKCA 3OG6A 3DLQI 1QVNA 1V7MV 2E9WC 2JA5D 5IP9D 2XQBA 3L5WI 3HOVD 1ETEA 2L3OA 1D9GA 3D85C 3HMXB 3HHRA 4NEMA 4NKQC 3WCYI 5L6YC 5C4XD 2GMFA 4A3CD 3D48P 1RW5A 2JA6D 4A3FD 2O27A 1Z92A 3DGCL 3HHCA 3HOXD 4A93D 2O26A 2H24A 4YPGC 1N1FA 3QAZA 3OG4A 2INTA 1PW6A 4A3JD 3INKC 3PIVA 3EJJA 1PVHB 3SE3B 1A7MA 1I1RB 4Z5RD 4O9HA 1RFBA 2LMSA 5C3ED 1INRA 3H3VE 3DI3A 2R93D 3HOZD 1CSGA 1WCMD 1IK0A 1AX8A 1FG9A 3I4ND 3QB7A 1AU1A 1ITIA 2D48A 1VLKA 1AXIA 3BESL 1CD9A 4NN6A 4ZS7A 3QB1A 2B8YA 3N0PA 1D9CA 5KNHI
chains in the Genus database with same CATH homology


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