4A3BD

Rna polymerase ii initial transcribing complex with a 4nt dna-rna hybrid
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
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 initial RNA polymerase II transcription.
pubmed doi rcsb
molecule tags Transcription
total genus 50
structure length 178
sequence length 219
ec nomenclature
pdb deposition date 2011-09-30

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; 4a3bD02
3AYHA 5FLMD 3FKID 4A3ID 3HOUD 4A93D 2JA6D 2R92D 5IYCD 3PO2D 5IP9D 4A3GD 1Y14A 5C44D 4A3FD 2C35A 3HOVD 3PO3D 3H0GD 2VUMD 3HOYD 4BXXD 3H3VE 1WCMD 2R93D 4A3MD 1Y1WD 4BY1D 3I4MD 5IYDD 4BY7D 3HOXD 2JA7D 5IYBD 2R7ZD 2B63D 3HOWD 4BBRD 4A3CD 4A3JD 1Y1VD 4BBSD 5C4XD 2JA5D 5IP7D 4A3DD 4A3KD 3HOZD 3I4ND 2JA8D 4A3ED 4A3BD 5C3ED 4A3LD
chains in the Genus database with same CATH superfamily
4ZS7A 4A3ID 1I1RB 1CSGA 3OQ3A 4NN5A 1CYLA 1ITMA 1SCFA 1RFBA 4YBQA 1RW5A 3H0GD 2ERJD 3L5WI 4Z5RD 1AU1A 2JA7D 1CNT1 1EVSA 1N1FA 3HOZD 3BPOA 4GBYA 4A3ED 1Z92A 3QB7A 3LB6A 4EXPA 1A7MA 5FHXA 2D9QA 1HWHA 5C44D 2XUTA 4A3FD 1PGRA 4OAAA 1HGUA 1ILKA 2R7ZD 1PV7A 4IKYA 1PV6A 3LB6B 1M4AA 4NI9A 1M49A 1NBPA 3UX9A 2HYMB 4GBZA 5L6YC 3UF5A 3HOVD 4JREA 1J7VL 2B8XA 5EQHA 1CD9A 3DI3A 1AX8A 1WU3I 2JA8D 1LK3A 4NI7A 3D48P 1F6FA 4IKVA 2R92D 3O7QA 2Z3QA 3PO3D 1BGDA 4JA3A 3DI2A 3MZGA 2L3YA 5D28B 3Q1SI 4YPGC 2B90A 3HOXD 4A3JD 2B8ZA 5C7XA 4GC0A 4DKCA 4A3LD 2Q14A 5D58A 1IK0A 4IKZA 1BP3A 2H24A 2Q7NB 4D2CA 1AXIA 4JR9A 1GNCA 2B8YA 1IJZA 4XNIA 4PYPA 2ILKA 1ITLA 3G6DA 3HOWD 2O26A 1HWGA 3NCFA 3NPZA 4NKQC 3FKID 1QVNA 4YB9D 3N06A 1PW4A 4APSA 4NEJA 1RHGA 2VUMD 5LQBA 2R93D 1V7MV 5TS9A 1EMRA 2KZ1A 3TGXB 5C3ED 4O6KA 2IL6A 1VLKA 4ZWBA 4CNIC 4O9HA 1BGEA 1FYHA 3QAZA 4QIQA 1M4RA 3H3VE 1IL6A 2V8NA 4NN7A 4Q65A 3N0PA 1BUYA 3NCCA 3INKC 1IARA 2GMFA 4TPGA 4FA8E 2LAGA 1LQSL 3NCEA 3SE3B 4TPJA 3O7PA 4A3MD 2LMSA 3I4MD 3BPNA 2B63D 1P9MB 3UEZE 3HMXB 4ZF7A 1FG9A 5D71A 1LKIA 2Q98A 3QWRB 4D2DA 4YDYI 3G9VB 1M48A 5FUCA 1M4BA 2L3OA 5C4XD 4GRWA 4A3DD 1KF9A 4J05A 1ETEA 4RS1A 2INTA 4X51A 4DKDA 4XNJA 3PO2D 2XQBA 1HULA 1WCMD 3BESL 5EQGA 1B5LA 1Y6KL 5IYBD 3OG6A 4A3CD 4BBSD 1M47A 5D22A 4GS7A 2D48A 1IRLA 1GA3A 4U4TA 1EXZA 5D6KA 3DGCL 5GXBA 3QB1A 4ZW9A 4YQXA 1HIKA 1HUWA 4PS4A 4A3BD 4TPHA 1A22A 4DKFA 4MHLA 3OG4A 1Y6NL 4A93D 1ITFA 1EKUA 1F45B 4IU8A 4NN6A 4IU9A 3HHCA 5IYCD 3IRHA 1HIJA 2B5IA 4WRLB 4NEMA 4IKXA 3UF2A 1ITIA 4BY7D 3NCBA 1JLIA 5D72A 4I77Z 1Y1VD 2OQPA 2JA5D 2CFQA 1BCNA 1PVHB 5FLMD 3BPLA 4J4LC 5IP9D 4A3GD 3WCYI 3HOYD 4DKEA 5C65A 5IYDD 2B91A 4ZWCA 2CFPA 4BBRD 3VA2A 5IP7D 1D9GA 3PIVA 2E9WC 1YKBA 3S9DA 4ZYRA 5KNHI 3D87A 3HOUD 4U4WA 4IKWA 4LRLA 5EQIA 1D9CA 3B5KA 1CN4C 1PW6A 2C35A 5D59A 1BGCA 1Z7CA 4EXNA 2PSMA 1RCBA 1HZIA 2O27A 4W6VA 3HHRA 5A2OA 2Z3RA 1V7NV 4UVMA 5A2NA 2O6IA 1M4CA 3SE4B 3DUHC 3EW3A 3WDOA 4BXXD 3DLQI 1Y1WD 4LDSA 1Y6ML 3I4ND 4YUEC 2Y5YA 1INRA 3AYHA 4DOHA 5D70A 2JA6D 3QT2C 1BBNA 3L5XA 3PIWA 1Y14A 1EERA 1PY2A 4D2BA 5E4EA 4BY1D 1ALUA 3D85C 2B8UA 4LEPA 3EJJA 4U4VA 4A3KD 4OH3A 2CYKA
chains in the Genus database with same CATH topology
2Q14A 1PVHB 4ZS7A 5FLMD 3BPLA 4J4LC 4A3ID 1IK0A 2Q98A 1I1RB 3QWRB 1BP3A 1CSGA 3OQ3A 2H24A 2Q7NB 4NN5A 5IP9D 1ITMA 4A3GD 1CYLA 1AXIA 1SCFA 1GNCA 1RFBA 3WCYI 2B8YA 1RW5A 1ITIA 3H0GD 1IJZA 2ERJD 3G9VB 4YDYI 3L5WI 3HOYD 1M48A 5FUCA 4DKEA 4Z5RD 5IYDD 2B91A 1AU1A 2JA7D 1M4BA 1CNT1 2ILKA 1ITLA 2L3OA 3G6DA 4BBRD 3HOWD 3VA2A 4GRWA 5C4XD 1EVSA 5IP7D 4A3DD 1D9GA 1KF9A 1N1FA 3PIVA 2E9WC 1YKBA 3HOZD 2O26A 3BPOA 3S9DA 1ETEA 1HWGA 3NCFA 4A3ED 1Z92A 5KNHI 3NPZA 4RS1A 4NKQC 2INTA 3FKID 1BCNA 3D87A 3QB7A 3LB6A 4X51A 3HOUD 1QVNA 4EXPA 4DKDA 3N06A 4LRLA 1A7MA 5FHXA 2D9QA 1HWHA 2XQBA 4NEJA 3PO2D 1RHGA 1D9CA 3B5KA 5C44D 4A3FD 1CN4C 1PW6A 1PGRA 2C35A 1HULA 2VUMD 1BGCA 5LQBA 1WCMD 1Z7CA 3BESL 4EXNA 2R93D 1HGUA 1B5LA 2PSMA 1V7MV 1ILKA 1Y6KL 5TS9A 1EMRA 1RCBA 1HZIA 5IYBD 3OG6A 2KZ1A 2O27A 2R7ZD 4A3CD 3HHRA 4BBSD 1M47A 2Z3RA 5D22A 4GS7A 3LB6B 3TGXB 1M4AA 1V7NV 5C3ED 1M49A 4NI9A 4O6KA 1NBPA 2IL6A 1VLKA 2D48A 2O6IA 4CNIC 1IRLA 1M4CA 3SE4B 3UX9A 4O9HA 2HYMB 5L6YC 1BGEA 1GA3A 3DUHC 1EXZA 1FYHA 3EW3A 3UF5A 3QAZA 3HOVD 3DGCL 1M4RA 3DLQI 4BXXD 3H3VE 3QB1A 1Y1WD 1J7VL 2B8XA 1Y6ML 4YQXA 1CD9A 3DI3A 1IL6A 1HIKA 4NN7A 1HUWA 3N0PA 1AX8A 1WU3I 3I4ND 4PS4A 1BUYA 4YUEC 2JA8D 4A3BD 1LK3A 1A22A 3NCCA 1INRA 3D48P 4NI7A 4DKFA 3AYHA 3INKC 4MHLA 1IARA 2GMFA 1Y6NL 1F6FA 3OG4A 5D70A 4DOHA 4A93D 1ITFA 1EKUA 1F45B 2JA6D 4NN6A 2R92D 4BY7D 3QT2C 1BBNA 2Z3QA 3HHCA 3L5XA 3PIWA 4FA8E 5IYCD 1Y14A 3IRHA 4A3LD 1HIJA 2B5IA 2LAGA 1EERA 1LQSL 4WRLB 3PO3D 3NCEA 1PY2A 4NEMA 1BGDA 3SE3B 3UF2A 3DI2A 3MZGA 5E4EA 2L3YA 5D28B 4A3MD 3Q1SI 2LMSA 1ALUA 3NCBA 1JLIA 2B90A 5D72A 4YPGC 3HOXD 4BY1D 3I4MD 3BPNA 3D85C 2B8UA 2B63D 4I77Z 1P9MB 4A3JD 1Y1VD 2OQPA 2JA5D 3EJJA 3UEZE 3HMXB 4ZF7A 2B8ZA 4A3KD 1FG9A 5C7XA 4DKCA 5D71A 1LKIA 2CYKA
chains in the Genus database with same CATH homology


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