2JA5D

Cpd lesion containing rna polymerase ii elongation complex a
Total Genus 38
204060801001201401600510152025303540
Genus TraceResidueGenus

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
38
sequence length
218
structure length
177
Chain Sequence
STSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKTREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY

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
EMPTYO2 (9-11)O5 (19-21)TIV1 (24-27)TI1 (30-33)S2 (44-46)TI2 (39-42)TIV3 (31-34)AH1 (54-69)TIV5 (69-72)TI3 (71-74)TIV7 (72-75)AH4 (158-168)O3 (14-16)S1 (36-38)AH2 (120-133)TIV9 (135-138)AH3 (139-151)TIV11 (168-171)TIV4 (51-54)Updating...
connected with : NaN
publication title Cpd Damage Recognition by Transcribing RNA Polymerase II
pubmed doi rcsb
molecule keywords DNA-directed RNA polymerase II subunit RPB1
molecule tags Transferase
total genus 38
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; 2ja5D02
4BY7D 1Y1VD 2R7ZD 3HOUD 4A3MD 5FLMD 5IYBD 5C44D 4A3KD 1Y1WD 4A3FD 4BY1D 4A93D 4A3CD 3PO2D 4A3DD 2R92D 4BXXD 4BBSD 4A3LD 2B63D 3AYHA 2R93D 3H0GD 4A3GD 5C3ED 5IYCD 2JA8D 1Y14A 2C35A 3HOYD 5IYDD 3HOXD 3HOVD 3I4ND 3PO3D 4BBRD 3H3VE 2JA5D 4A3JD 5C4XD 3HOZD 1WCMD 2VUMD 4A3BD 3HOWD 4A3ED 3FKID 3I4MD 2JA7D 2JA6D 5IP9D 5IP7D 4A3ID
chains in the Genus database with same CATH superfamily
3G9VB 1ITMA 2B8YA 3BESL 5FUCA 3VA2A 4D2BA 4IKZA 4LEPA 4A3LD 2Q14A 4J05A 3UEZE 5A2OA 2Q98A 4ZWBA 3D87A 1GA3A 1BGCA 1M47A 3Q1SI 2B8ZA 1PW4A 1IARA 4MHLA 5D6KA 4IU8A 1HIJA 4TPHA 3H0GD 2PSMA 4NN7A 1YKBA 1PW6A 4PYPA 1PY2A 5D70A 1WCMD 4NI7A 4W6VA 3QT2C 1SCFA 4BY1D 3LB6A 3PO2D 3L5XA 3NCBA 1BP3A 1ITFA 5LQBA 4PS4A 4NN5A 3HOVD 3HHRA 3PO3D 4I77Z 4QIQA 4FA8E 1BGEA 4NKQC 4A3ED 5D59A 1LQSL 4U4VA 1EKUA 1QVNA 1EVSA 4A3MD 4NEMA 4IKWA 1PV6A 2B91A 2L3OA 3DI3A 3HHCA 1BCNA 2ILKA 1HIKA 1EMRA 2VUMD 1CD9A 4OAAA 3SE4B 4NI9A 4Q65A 5IP7D 1EXZA 1HGUA 4ZS7A 3EJJA 4A3FD 4BBSD 3AYHA 4IKYA 2B5IA 2XUTA 2JA8D 1Z7CA 2V8NA 1CSGA 5D72A 4DKEA 4IU9A 1HZIA 2B8UA 4RS1A 1Z92A 3I4MD 4EXPA 4OH3A 4JREA 2Y5YA 3L5WI 4A3KD 4GRWA 2CFPA 4ZF7A 4A3DD 3UF5A 4YUEC 2IL6A 4EXNA 1RHGA 4LRLA 1ITIA 2O6IA 1Y6NL 5C65A 3PIWA 5FLMD 3O7QA 4D2DA 5GXBA 5E4EA 4LDSA 3QB1A 5C3ED 1I1RB 2B90A 3NCEA 1PGRA 1V7MV 4YPGC 1RW5A 4GS7A 3MZGA 4BY7D 2LAGA 4GC0A 3D48P 4U4TA 5EQIA 3S9DA 2R93D 2Q7NB 2C35A 1PVHB 2B8XA 1D9GA 4A3JD 1J7VL 1FYHA 5EQGA 4A3BD 3WCYI 1GNCA 2R7ZD 4BXXD 4WRLB 4APSA 2O26A 4NN6A 1LK3A 3INKC 3N0PA 2D9QA 3FKID 3OG4A 1IK0A 2O27A 4TPGA 2JA6D 1HWGA 2Z3QA 3SE3B 3HMXB 4A93D 1BGDA 5FHXA 1ITLA 3I4ND 1KF9A 4ZW9A 1IL6A 3LB6B 4J4LC 4XNJA 1BUYA 1M4AA 2HYMB 1Y1WD 4NEJA 5C7XA 1CYLA 1M48A 4X51A 1V7NV 5D22A 2B63D 3QWRB 1ETEA 4A3GD 5IYCD 3IRHA 1Y14A 3HOYD 2CFQA 4O9HA 1VLKA 3NCFA 1M4BA 1P9MB 3DGCL 3BPOA 2XQBA 2JA7D 4ZYRA 1Y1VD 3UX9A 1RFBA 5IYBD 5KNHI 1M49A 1ILKA 4A3CD 3DLQI 3NPZA 4JA3A 5TS9A 4BBRD 3H3VE 3NCCA 1CN4C 5C4XD 2GMFA 5EQHA 3O7PA 3BPLA 1IJZA 1HULA 4YB9D 1AX8A 3HOUD 1HUWA 2E9WC 2LMSA 1HWHA 4JR9A 4IKXA 1CNT1 3D85C 2H24A 3OQ3A 4XNIA 4D2CA 5L6YC 1A22A 1INRA 1AXIA 4UVMA 2OQPA 2INTA 5IP9D 1BBNA 3EW3A 5C44D 3B5KA 4IKVA 4YDYI 2ERJD 1B5LA 1A7MA 2D48A 1AU1A 5D71A 3N06A 4GBYA 3HOXD 2KZ1A 4Z5RD 4CNIC 1JLIA 3BPNA 1IRLA 1PV7A 3HOZD 3QAZA 1FG9A 1LKIA 1WU3I 4DOHA 1ALUA 1N1FA 4O6KA 4YBQA 5D28B 2R92D 3OG6A 1NBPA 2L3YA 4YQXA 1Y6KL 4GBZA 3G6DA 4DKDA 5A2NA 1F6FA 3TGXB 5IYDD 5D58A 1M4CA 3HOWD 1F45B 4ZWCA 4DKFA 2Z3RA 3WDOA 1EERA 1RCBA 1M4RA 4DKCA 1D9CA 4TPJA 3DUHC 4U4WA 2JA5D 1Y6ML 3QB7A 3UF2A 2CYKA 3DI2A 3PIVA 4A3ID
chains in the Genus database with same CATH topology
3G9VB 1HGUA 3BPLA 1IJZA 4ZS7A 1HULA 3EJJA 1ITMA 2B8YA 2R7ZD 1AX8A 3HOUD 3BESL 1HUWA 2E9WC 5FUCA 3VA2A 4A3FD 2LMSA 1HWHA 4BXXD 4WRLB 4BBSD 1CNT1 3D85C 2H24A 3OQ3A 4A3LD 2Q14A 3AYHA 4A3ID 2B5IA 5L6YC 2JA8D 2O26A 1A22A 1Z7CA 1INRA 3UEZE 1AXIA 2Q98A 4NN6A 1CSGA 3D87A 1LK3A 2OQPA 3INKC 5D72A 2INTA 3N0PA 4DKEA 1HZIA 1GA3A 1BGCA 1M47A 2B8UA 3Q1SI 4RS1A 2D9QA 3FKID 1Z92A 3OG4A 2O27A 2JA6D 5IP9D 3I4MD 4EXPA 1IK0A 1BBNA 1HWGA 2B8ZA 2Z3QA 3SE3B 3EW3A 5C44D 3L5WI 3HMXB 4A3KD 3B5KA 4GRWA 4A93D 4ZF7A 4YDYI 1BGDA 1IARA 4MHLA 2ERJD 5C3ED 3I4ND 4A3DD 5FHXA 1B5LA 1BCNA 1A7MA 2D48A 1AU1A 1HIJA 5D71A 3H0GD 3N06A 4YUEC 2PSMA 1CYLA 2IL6A 1ITLA 4NN7A 4EXNA 3HOXD 1RHGA 1YKBA 2KZ1A 4Z5RD 1PW6A 1JLIA 3BPNA 1KF9A 4LRLA 4CNIC 1IRLA 1ITIA 1PY2A 3HOZD 5D70A 1WCMD 1FG9A 3QAZA 2O6IA 1LKIA 1WU3I 1IL6A 1Y6NL 3LB6B 4NI7A 3QT2C 4J4LC 1SCFA 1BUYA 1M4AA 2HYMB 1ALUA 3PIWA 4DOHA 1N1FA 5FLMD 1Y1WD 4NEJA 5C7XA 4O6KA 4BY1D 3LB6A 3PO2D 1M48A 3L5XA 2R92D 5D28B 3NCBA 1BP3A 4X51A 5E4EA 1V7NV 1NBPA 3OG6A 5D22A 1ITFA 2L3YA 4YQXA 2B63D 5LQBA 1Y6KL 3QWRB 1ETEA 3QB1A 4A3GD 4PS4A 1I1RB 3G6DA 3IRHA 4DKDA 1Y14A 1F6FA 4NN5A 5IYCD 3TGXB 5IYDD 2B90A 3NCEA 1PGRA 3HHRA 4O9HA 3HOVD 3PO3D 1VLKA 4I77Z 1V7MV 4YPGC 3NCFA 4FA8E 1M4BA 1BGEA 1M4CA 4NKQC 3HOWD 4A3ED 1P9MB 1RW5A 3DGCL 3BPOA 1LQSL 4GS7A 2XQBA 1EKUA 1QVNA 2JA7D 3MZGA 1EVSA 4BY7D 1F45B 1Y1VD 3UX9A 2LAGA 1RFBA 4A3MD 5IYBD 3D48P 4NEMA 1M49A 1ILKA 5KNHI 4A3CD 3DLQI 4DKFA 2Z3RA 2B91A 2L3OA 3NPZA 1EERA 3S9DA 1RCBA 2R93D 1M4RA 3DI3A 2Q7NB 1D9CA 4DKCA 5IP7D 2C35A 1PVHB 3HHCA 3DUHC 5TS9A 3HOYD 4BBRD 2B8XA 3H3VE 2JA5D 1D9GA 1Y6ML 3QB7A 3NCCA 2ILKA 1CN4C 1HIKA 1J7VL 2CYKA 3UF2A 4A3JD 5C4XD 1EMRA 1FYHA 2GMFA 2VUMD 4A3BD 1CD9A 3DI2A 3SE4B 4NI9A 3PIVA 3WCYI 1GNCA 1EXZA 3UF5A
chains in the Genus database with same CATH homology


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

 
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#similar chains, but unknotted
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