3H3VE

Yeast rnap ii containing poly(a)-signal sequence in the active site
Total Genus 43
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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
43
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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molecule tags Transferase/dna/rna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
publication title Torpedo Nuclease Rat1 Is Insufficient to Terminate RNA Polymerase II in Vitro
pubmed doi rcsb
total genus 43
structure length 177
sequence length 218
ec nomenclature
pdb deposition date 2009-04-17

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
E 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; 3h3vE02
2C35A 1Y1VD 5IYDD 4A3KD 2JA8D 4BXXD 2JA5D 4A3GD 3H3VE 1WCMD 4BY1D 3PO3D 4A3JD 3HOVD 3HOZD 3AYHA 4A93D 3H0GD 2R93D 4BBSD 4A3LD 2R7ZD 3HOUD 4BY7D 3FKID 2JA6D 3I4ND 1Y14A 5C44D 4A3DD 5IYCD 5C4XD 3I4MD 4A3MD 5C3ED 4A3FD 5FLMD 2B63D 2JA7D 4BBRD 4A3ID 2R92D 3PO2D 3HOXD 4A3BD 5IP9D 5IYBD 2VUMD 3HOYD 3HOWD 1Y1WD 4A3CD 4A3ED 5IP7D
chains in the Genus database with same CATH superfamily
3NCCA 1RHGA 3H3VE 4D2BA 2CFQA 1HZIA 1CNT1 4IKXA 3NCBA 3HOZD 1EERA 3LB6A 4YQXA 4BY7D 2B8XA 4O6KA 4TPGA 4A3DD 5C3ED 2L3YA 5D28B 3DI3A 1M47A 4OAAA 1M4AA 1Y1WD 4DKDA 5A2NA 1EKUA 3DUHC 1ITLA 3O7PA 1BUYA 1ETEA 4O9HA 1IARA 1M4BA 4GC0A 1F6FA 1PGRA 2ERJD 2B63D 5IYBD 1Z7CA 2VUMD 5C7XA 1AX8A 1PVHB 1BBNA 2B8ZA 1RFBA 5IP7D 4EXPA 5IYDD 5KNHI 3EJJA 4YUEC 1WU3I 3B5KA 1V7MV 1EXZA 3HHRA 4NN5A 5LQBA 3NPZA 3INKC 3QB7A 4A3FD 4BBRD 2HYMB 1BGDA 1Y6KL 4U4TA 3OG6A 1M48A 1RW5A 4ZW9A 4IKYA 2H24A 4ZWCA 1HGUA 4A93D 1ITMA 5D71A 2D48A 1Y14A 4IU9A 2IL6A 1BCNA 3PO2D 3MZGA 3UF2A 4GBYA 4YB9D 3LB6B 3G9VB 4BXXD 1QVNA 4YDYI 5C4XD 4U4WA 4LRLA 4D2DA 4JA3A 1GA3A 1J7VL 2JA5D 5D59A 5E4EA 4JR9A 4NI7A 1EMRA 5IYCD 3OG4A 1M49A 4WRLB 2JA7D 1ITIA 1FYHA 5D72A 2CYKA 1INRA 3BPOA 4YPGC 1HULA 3PO3D 4RS1A 4QIQA 5EQGA 3FKID 1SCFA 3S9DA 1IL6A 5FLMD 3SE3B 1N1FA 3HOWD 1JLIA 4A3ED 5EQHA 1A7MA 1PV7A 4UVMA 4A3JD 4Z5RD 4ZWBA 3BPLA 3BESL 3DI2A 3QAZA 3HHCA 3NCEA 2E9WC 1F45B 5D6KA 1BGEA 3Q1SI 3L5WI 1EVSA 4APSA 1IK0A 4IKWA 5L6YC 3AYHA 4A3LD 4EXNA 2B5IA 4DKEA 3D87A 4NKQC 5EQIA 1NBPA 4A3MD 1P9MB 3D48P 3N0PA 3BPNA 4A3BD 5IP9D 2XQBA 4JREA 4XNJA 4PYPA 1Y1VD 1V7NV 3VA2A 1ALUA 1HWHA 2B90A 1WCMD 4CNIC 1FG9A 3NCFA 2B8UA 1BP3A 4U4VA 1YKBA 3UX9A 4IKVA 4TPHA 2B91A 1IJZA 1PW4A 2Q7NB 3I4MD 1AXIA 2R92D 4DOHA 1Y6ML 5D58A 1GNCA 4BY1D 2B8YA 2V8NA 2Q98A 4LDSA 1HWGA 1B5LA 2INTA 5A2OA 2OQPA 3WCYI 4XNIA 3QB1A 5C44D 4PS4A 4D2CA 5D22A 4NN7A 5D70A 3HOXD 4OH3A 3WDOA 1D9CA 3HOYD 1LKIA 4GS7A 4NEJA 3UF5A 2O26A 4W6VA 3HMXB 4TPJA 3H0GD 4IKZA 4IU8A 2D9QA 3I4ND 2O27A 1LK3A 1HIKA 5GXBA 1ITFA 2LMSA 2L3OA 4FA8E 2Q14A 1M4RA 5C65A 1PV6A 4A3KD 5FHXA 1HUWA 4NEMA 3L5XA 2ILKA 3HOUD 1CN4C 5TS9A 3EW3A 4I77Z 4Q65A 1PW6A 3QT2C 1IRLA 2JA8D 1CSGA 4MHLA 1VLKA 1KF9A 1BGCA 3DGCL 3G6DA 3D85C 4DKCA 1Z92A 1ILKA 4X51A 1HIJA 2CFPA 5FUCA 3TGXB 3N06A 4ZS7A 4NI9A 1RCBA 1M4CA 2LAGA 3DLQI 2PSMA 1Y6NL 4NN6A 1D9GA 4BBSD 1I1RB 3PIWA 3UEZE 4ZF7A 3QWRB 1A22A 3PIVA 4A3ID 4GBZA 1LQSL 4J4LC 2C35A 1CYLA 1AU1A 1PY2A 4A3GD 2O6IA 3HOVD 2Z3RA 2Y5YA 2R93D 3O7QA 4J05A 2R7ZD 1CD9A 2JA6D 3OQ3A 4YBQA 4GRWA 4DKFA 4LEPA 4ZYRA 3IRHA 3SE4B 4A3CD 2Z3QA 2KZ1A 2GMFA 2XUTA
chains in the Genus database with same CATH topology
3LB6B 4A3KD 5FHXA 3NCCA 3G9VB 4BXXD 1IK0A 1RHGA 3H3VE 1HZIA 1CNT1 3NCBA 3HOZD 5L6YC 1EERA 3AYHA 1HUWA 3LB6A 1QVNA 3L5XA 4NEMA 2ILKA 4YQXA 4YDYI 1CN4C 4EXNA 3HOUD 4A3LD 4BY7D 2B5IA 3UF2A 2B8XA 3D87A 3EW3A 4NKQC 5TS9A 4DKEA 4I77Z 4O6KA 1NBPA 4A3DD 1PW6A 5C4XD 4A3MD 5C3ED 2L3YA 1P9MB 3D48P 4LRLA 5D28B 3N0PA 3DI3A 1M47A 3BPNA 4A3BD 5IP9D 2XQBA 1M4AA 1Y1WD 4DKDA 3QT2C 1GA3A 1IRLA 1J7VL 1Y1VD 1EKUA 1V7NV 3DUHC 1ALUA 1HWHA 1CSGA 2B90A 3VA2A 2JA5D 2JA8D 1WCMD 4MHLA 1ITLA 4CNIC 1FG9A 1VLKA 1KF9A 5E4EA 3NCFA 1BGCA 2B8UA 1BP3A 3DGCL 3G6DA 3D85C 1BUYA 1ETEA 1Z92A 4DKCA 4O9HA 1IARA 1YKBA 4NI7A 3UX9A 1M4BA 1ILKA 1F6FA 1EMRA 4X51A 1HIJA 1PGRA 2ERJD 2B91A 1IJZA 5IYCD 2Q7NB 3I4MD 3OG4A 5FUCA 1M49A 1AXIA 4WRLB 2JA7D 2B63D 3TGXB 2R92D 1ITIA 4DOHA 1Y6ML 1Z7CA 5IYBD 2VUMD 5C7XA 1AX8A 3N06A 4ZS7A 1FYHA 1RCBA 4NI9A 1PVHB 1M4CA 2CYKA 2LAGA 1BBNA 1INRA 1RFBA 2B8ZA 5D72A 3BPOA 5IP7D 4EXPA 5IYDD 5KNHI 3EJJA 3L5WI 4YPGC 4YUEC 1GNCA 1HULA 4BY1D 3PO3D 2B8YA 3DLQI 1WU3I 2Q98A 1HWGA 2PSMA 1Y6NL 1B5LA 4RS1A 3B5KA 4NN6A 2INTA 1V7MV 1EXZA 1D9GA 3HHRA 4BBSD 1I1RB 2OQPA 3FKID 3PIWA 3UEZE 1SCFA 3WCYI 5C44D 3QB1A 4NN5A 4PS4A 4ZF7A 3NPZA 5LQBA 3S9DA 3INKC 3QWRB 5D22A 4NN7A 3QB7A 1IL6A 5FLMD 4A3FD 1A22A 3PIVA 4BBRD 5D70A 2HYMB 3SE3B 1N1FA 1BGDA 3HOXD 4A3ID 1Y6KL 1D9CA 3HOWD 1LQSL 3HOYD 3OG6A 1JLIA 4J4LC 4A3ED 1LKIA 1M48A 2C35A 1AU1A 4GS7A 1CYLA 1RW5A 1PY2A 4NEJA 1A7MA 4A3GD 3UF5A 2O26A 2O6IA 4A3JD 3HOVD 3HMXB 4Z5RD 2H24A 2KZ1A 1HGUA 4A93D 2Z3RA 1ITMA 3H0GD 2R93D 2R7ZD 3BPLA 1CD9A 3BESL 3DI2A 2D9QA 2D48A 3QAZA 5D71A 2JA6D 3I4ND 2O27A 1LK3A 1HIKA 1Y14A 3HHCA 1ITFA 3NCEA 2E9WC 1F45B 2LMSA 2IL6A 3OQ3A 1BCNA 1BGEA 2L3OA 4GRWA 3PO2D 4DKFA 4FA8E 3IRHA 3MZGA 3SE4B 2Q14A 3Q1SI 4A3CD 2Z3QA 1M4RA 1EVSA 2GMFA
chains in the Genus database with same CATH homology


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