5C4XD

Crystal structure of a transcribing rna polymerase ii complex reveals a complete transcription bubble
Total Genus 41
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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
41
sequence length
218
structure length
178
Chain Sequence
STSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY
Loading diagram...

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/rna/dna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
publication title Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.
pubmed doi rcsb
source organism Saccharomyces cerevisiae (strain atcc 204508 / s288c)
total genus 41
structure length 178
sequence length 218
ec nomenclature
pdb deposition date 2015-06-18

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; 5c4xD02
2B63D 3HOZD 4A3BD 4A3KD 3AYHA 3HOWD 5IYBD 3H3VE 4BY1D 4A3DD 4BY7D 3PO2D 1Y1VD 2JA5D 3HOYD 3I4ND 4A3ID 4A3GD 3PO3D 4A93D 2JA8D 2JA6D 4BXXD 1Y14A 1Y1WD 3FKID 4BBRD 5IYDD 5FLMD 4A3FD 2JA7D 3HOUD 2VUMD 3HOVD 4A3LD 5IP7D 5C44D 2R7ZD 1WCMD 2C35A 3HOXD 5C4XD 5IYCD 5C3ED 3H0GD 4A3MD 4A3ED 4A3JD 4BBSD 2R92D 5IP9D 4A3CD 2R93D 3I4MD
chains in the Genus database with same CATH superfamily
1IJZA 1GNCA 1EERA 1F6FA 1ILKA 3H3VE 4BY1D 5C7XA 1NBPA 2XUTA 3HOYD 3LB6A 1QVNA 1YKBA 4APSA 4NN6A 5E4EA 1BP3A 1IRLA 2V8NA 5FHXA 5IYCD 4J4LC 4IKWA 4A3JD 1CN4C 3SE4B 5IP9D 4TPGA 2B90A 3D87A 3OG6A 4O6KA 3NCBA 2H24A 4YPGC 3DI2A 5C44D 3OG4A 5C3ED 3IRHA 3UF5A 5D71A 4QIQA 1PV7A 4UVMA 2GMFA 3G9VB 3AYHA 5EQIA 3N0PA 3PO2D 3HMXB 3G6DA 2JA6D 1Y6ML 5LQBA 4NN7A 4DKCA 1PV6A 2Z3RA 5TS9A 3O7QA 3EJJA 3QB7A 5GXBA 4TPHA 3B5KA 1N1FA 1Y6KL 2LMSA 3DLQI 2KZ1A 5IYBD 2LAGA 5D70A 1AU1A 4O9HA 1PGRA 4BBRD 2L3OA 3HOVD 2VUMD 4JREA 4D2BA 4LRLA 1A7MA 4OH3A 4D2CA 3NCFA 5EQHA 3UX9A 1INRA 4A3KD 2OQPA 2Y5YA 2O26A 1FG9A 3L5XA 2E9WC 2R7ZD 2ILKA 1D9CA 3INKC 1IARA 4NI7A 3N06A 1M4BA 1KF9A 3L5WI 4NEMA 2B5IA 3PIVA 2Q7NB 1AX8A 3QB1A 3HOWD 4TPJA 4A3DD 1CNT1 1IK0A 3PO3D 1HIKA 4BXXD 1Z92A 4WRLB 1B5LA 2R92D 1J7VL 2ERJD 4FA8E 3D85C 1M48A 3HOZD 4LDSA 3BPLA 1HULA 4A3LD 2D9QA 1PY2A 4YQXA 3FKID 4ZF7A 1BBNA 2PSMA 1PW6A 4DKFA 4A3ED 2IL6A 1EMRA 4GS7A 3QT2C 1LK3A 4U4TA 1PW4A 5D72A 3VA2A 1ITLA 2Z3QA 5EQGA 4U4WA 3EW3A 5L6YC 4XNJA 1IL6A 4EXPA 2INTA 2CYKA 4A3MD 1FYHA 1M47A 1A22A 4U4VA 2Q14A 1EKUA 3D48P 4DOHA 4ZW9A 5FLMD 4A3FD 1HWHA 1BGEA 4IU9A 5D22A 4ZWBA 1Y6NL 2B91A 1ETEA 3BPOA 1HIJA 1M4AA 1M4CA 1CYLA 1Y1VD 2JA5D 3QAZA 3DUHC 3NCCA 2JA8D 4ZWCA 4YUEC 1RHGA 3O7PA 4DKEA 3TGXB 5A2NA 3NPZA 1EXZA 4DKDA 4YB9D 3DI3A 4BBSD 3UEZE 4YBQA 2O6IA 3I4MD 4NKQC 1ITIA 3UF2A 5A2OA 1Y14A 4PYPA 3WCYI 5C4XD 4GBYA 4I77Z 4IKYA 2Q98A 4CNIC 4Z5RD 4XNIA 1LQSL 5D28B 2O27A 4GC0A 1HGUA 4A3GD 1HUWA 1AXIA 1RFBA 3HOUD 2B8UA 1JLIA 1WCMD 3BPNA 1BGDA 4IU8A 2CFPA 4GBZA 4IKZA 4A3CD 4RS1A 5D58A 1WU3I 4NN5A 1Z7CA 2D48A 4BY7D 4NEJA 2CFQA 4A3ID 1RW5A 2B8ZA 4D2DA 3PIWA 1ITFA 3BESL 3HOXD 1V7NV 1ALUA 3HHCA 5D59A 5FUCA 3NCEA 2B8XA 4LEPA 4EXNA 1BGCA 5C65A 5D6KA 3QWRB 1EVSA 4PS4A 1Y1WD 2B8YA 2JA7D 4J05A 4YDYI 5IP7D 1I1RB 1RCBA 2L3YA 4X51A 1D9GA 2R93D 1GA3A 2B63D 4A3BD 1CD9A 4JA3A 1M4RA 3LB6B 4A93D 4IKVA 1CSGA 1VLKA 1V7MV 3OQ3A 1LKIA 2C35A 4NI9A 3H0GD 3Q1SI 1SCFA 3SE3B 3S9DA 4OAAA 1ITMA 4ZS7A 1PVHB 3HHRA 1BCNA 3I4ND 1HWGA 4GRWA 1M49A 2HYMB 1P9MB 2XQBA 5IYDD 4IKXA 3MZGA 1HZIA 1BUYA 4Q65A 4W6VA 4ZYRA 5KNHI 4MHLA 3DGCL 1F45B 4JR9A 3WDOA
chains in the Genus database with same CATH topology
1IJZA 4NN5A 1Z7CA 1GNCA 1EERA 1F6FA 1ILKA 3UX9A 1INRA 4A3KD 2D48A 2Q14A 2OQPA 3H3VE 1EKUA 4BY1D 5C7XA 4BY7D 3D48P 1NBPA 4NEJA 3HOYD 4DOHA 4A3ID 3LB6A 1RW5A 2B8ZA 1QVNA 2O26A 1FG9A 1YKBA 3L5XA 3PIWA 5FLMD 4A3FD 1ITFA 2E9WC 4NN6A 1HWHA 1BGEA 5D22A 5E4EA 1BP3A 3BESL 2R7ZD 2ILKA 1D9CA 3INKC 3HOXD 1IRLA 1IARA 5FHXA 4NI7A 5IYCD 3N06A 4J4LC 1M4BA 1KF9A 1V7NV 4A3JD 1Y6NL 1CN4C 3SE4B 3L5WI 1ALUA 4NEMA 5IP9D 2B91A 1ETEA 3HHCA 2B5IA 3BPOA 1HIJA 1M4AA 2B90A 3PIVA 3D87A 2Q7NB 5FUCA 1AX8A 1M4CA 3OG6A 3QB1A 3NCEA 2B8XA 3HOWD 4EXNA 4A3DD 1CYLA 1BGCA 1CNT1 1Y1VD 3NCBA 4O6KA 1HIKA 2JA5D 3QAZA 3PO3D 2H24A 3DUHC 3NCCA 2JA8D 3QWRB 4BXXD 1EVSA 4PS4A 1Z92A 4YUEC 1Y1WD 2B8YA 1RHGA 4YPGC 2JA7D 4DKEA 4WRLB 4YDYI 3DI2A 5IP7D 1I1RB 3OG4A 3TGXB 5C44D 1B5LA 5C3ED 3IRHA 3NPZA 1RCBA 1EXZA 3UF5A 4DKDA 3DI3A 4BBSD 2L3YA 5D71A 3UEZE 2R92D 4X51A 1J7VL 2ERJD 1D9GA 2O6IA 3I4MD 2R93D 4FA8E 1GA3A 2GMFA 1M48A 3D85C 3G9VB 4NKQC 3HOZD 2B63D 4A3BD 1ITIA 1CD9A 3BPLA 3AYHA 3UF2A 1HULA 1M4RA 4A3LD 3N0PA 3PO2D 3LB6B 3HMXB 2D9QA 1PY2A 4A93D 3G6DA 2JA6D 1Y6ML 1Y14A 4YQXA 5LQBA 4NN7A 3FKID 4DKCA 1CSGA 1VLKA 4ZF7A 1BBNA 1V7MV 2Z3RA 2PSMA 1PW6A 3OQ3A 3WCYI 1LKIA 5TS9A 2C35A 3EJJA 3QB7A 4DKFA 4NI9A 5C4XD 3B5KA 3H0GD 4I77Z 1IK0A 4A3ED 2IL6A 3Q1SI 1SCFA 3SE3B 3S9DA 1EMRA 2Q98A 3QT2C 4GS7A 1LK3A 1ITMA 1N1FA 1Y6KL 4CNIC 4ZS7A 2LMSA 3DLQI 4Z5RD 5D28B 1LQSL 1PVHB 2KZ1A 2O27A 3HHRA 1BCNA 5D72A 5IYBD 2LAGA 5D70A 3VA2A 1HGUA 1AU1A 1ITLA 1HWGA 4O9HA 3I4ND 4A3GD 1HUWA 4GRWA 2Z3QA 1AXIA 1M49A 1PGRA 2HYMB 1P9MB 2XQBA 2L3OA 4BBRD 5IYDD 3MZGA 1HZIA 1RFBA 3EW3A 5L6YC 2VUMD 3HOUD 3HOVD 1IL6A 1BUYA 2B8UA 4LRLA 4EXPA 1JLIA 1WCMD 2INTA 3BPNA 5KNHI 1A7MA 1BGDA 2CYKA 4MHLA 3DGCL 4A3MD 1F45B 1FYHA 1M47A 1A22A 3NCFA 4A3CD 4RS1A 1WU3I
chains in the Genus database with same CATH homology


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