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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcag

Basic information

species Oryza sativa
transcript LOC_Os11g43970.1
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 13
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcag
 ||||||||||| ||||||||||| |||||||| || |||||||||||||||||||||||||| ||||| || ||||||||||| |||||||| |||||||||| ||   | | |        | | ||||| |  ||         ||||  ||||||  ||||    || ||  | |||||||||
CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttgacctagcgggca-actgatgagattcact--------tgtg--tctcaagcctaaccagtggttcgtttactttcag

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G170037_T01 (Zea mays), 5'ss of exon 4
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcag
 ||| ||||||| ||||| ||||| |||||||| || |||||||||||| ||| ||| ||||| ||||| || ||||||||||| ||||||||||  ||||||| ||  || | || |     | | ||||| |  ||    |||| |      ||||| |||||    || ||| |  ||||||||
CGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATGTAAGgtattatttcacctaa-tgggcaactgatgagattcac----tactgt------ctcaaggctaaccagtggtttgttaactttcag

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 7
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcag
 ||||||||||| ||||| ||||| |||||||| || |||||||||||||||||||| ||||| ||||| || ||||||||||| ||||||||||||||||||| ||  || | || |     | | ||||| |  ||    |||| |      ||||| |||||    || ||| |  ||||||||
CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCGAAGgtattatttcacctaa-tgggcaactgatgagattcac----tactgt------ctcaaggctaaccagtggtttgttaactttcag

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G354532_T01 (Zea mays), 5'ss of exon 1
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggcatccaaattttgcattaatgaggtgtac-agtgtactatgtgattctcaaagctaaatgctgttttttctactttcag
 ||||||||||| ||||| ||||| |||||||| || |||||||||||||||||||| ||||| ||||| || ||||||||||| ||||||||||| ||||||| ||  || | ||       | | ||||| |  || | |||   | |                                      
CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtattatttcacctaatgggca-actgatgagattcactactgtctcaag--------------------------------------

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G435582_T01 (Zea mays), 5'ss of exon 2
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcag
 ||||||||||| ||||| ||||| |||||||| || |||||||||||||||||||| ||||| ||||| || ||||||||||| ||||||||||| ||||||| ||  || | || |     | | ||||| |  ||    |||| |      ||||| |||||    || ||| |  ||||||||
CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtattatttcacctaa-tgggcaactgatgagattcac----tactgt------ctcaaggctaaccagtggtttgttaactttcag

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 21
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctca-aagctaaatgctgttttttctactttcag
||| || ||||| || || ||||| |||||||| ||||| |||||||||||||| || || || ||||||||||| |||||||| |||||||| || ||||||| |  |  |  || ||     ||  || ||||||     |  ||||      | | |||  ||||   ||||| | |  || |||
TGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTTCAATGTCCAGCATTACTTCAAAGgtattaatgt-tgtaagttacttttttttgtggtgtatttccttgtatgcttcagtgacaagaaaaatatggttttgtttg-ttgcag

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GLYMA17G13850.1 (Glycine max), 5'ss of exon 20
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatgg----catccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcag
||| || ||||| ||||| ||||| |||||||| |||||| | || |||||||| |||||||||||||| ||||| || |||||||| || ||||| |||||   ||      |   | || | |  ||| ||      |  | |    |          |||  |    |  ||  | || |   |||||
TGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTTCTATGTCAAGTATCACATCTAAGgttaaatttgtctctctctaagtgtatattgatttcacctttattagtttgctgtgcatacaactcattttcttgcctctttttgcttcag

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 18
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatg---tgattctcaaagctaaatgctgtt-ttttctactttcag
||| || ||||| || || ||||| |||||||| ||||| || ||||||||||| || || || || |||||||| |||||||| ||||||||||| ||||||| |     |   || |||  | |  |  | | |||  |||| | |    | ||||   |||  | | | | || |||| |  || |||
TGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTTCAATGTCCAGCATTACATCCAAGgtatta----gttgcaaatttaaactgttttgctctactctgtattttcctttcattcattaagtgacaggatattgtttttttgttgcag

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GLYMA02G17410.1 (Glycine max), 5'ss of exon 17
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcag
||| || ||||| || || ||||| |||||||| ||||| |||||||||||||| || || || ||||||||||| |||||||| |||||||| || |||||||      ||   || ||    ||  ||  |||||     |  ||||      | | |   |||   || ||||  |  || |||
TGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTTCAATGTCCAGCATTACTTCAAAGgtat--caatattgtaaattactttttttgttgtgtatttccttgtatgcttcagttacaagaaaaacatggttttgtttgttgcag

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GLYMA10G02410.1 (Glycine max), 5'ss of exon 18
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaa------gctaaatgctgttttttctactttcag
||| |||||||| || || ||||| |||||||| ||||| |||||||||||||| || || || || |||||||| |||||||| |||||||| || |||||||  | |   | || ||   || |  ||   |     || |    | | ||||  ||       | || ||  ||||||||    || |||
TGGCCCTCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTTATTAACATTTCAATGTCCAGCATTACGTCCAAGgtat--tagttgcaaatttaaacagttttgctctactttgtatttcctttcattcataagtgacaggatagatattgtttttttg--ttgcag

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
lower sequence: AT1G62130.1 (Arabidopsis thaliana), 5'ss of exon 21
------------TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcag
            ||||||| |||| ||||| || ||||||||||| |||||||| ||||| ||||| ||||||||| |||| ||||| |||||||||||  | |||       |||  | | |   || ||   |  ||   |  | ||||  | |     ||    |||||  |   || | || |   || || |||
AATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGTCAATGTCAAGGgtaaca----gaatatccttgaa---aagttggactctaccaatttatacacggaatctcttg---ttcaaacttg--tgttcttctcaata-ttgcag

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 21
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgta----tgatggcatc-caaattttgcattaatgaggtgtac-agtg-tactatgtgattctcaaagctaaatgctgttttttctactttcag
|||||||||||||||||| || || ||||| || || |||||||||||||| || || || || ||||| || || |||||||| |||||||| |||||||||    | ||    |   |   ||| | || |||   | |   | || |  ||  |||   |  |  ||||||||| |               
TGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCTCAATGTCCAGCATTACTTCGAAGgtaactctcataaagtgatatgatttccttttatgctttcttttaatgattgtacttgaccatttacactaaatgctttgcag-----------

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
lower sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 21
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggca-tccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcag
|||||||||||| ||||| || ||||||||||| || ||||| ||||  ||||| | ||| |||||||| ||||| |||||||||||||| ||||| ||||||       | || |      |   ||  ||  |  |||  |    || |  || |||||  |   || | || ||  ||||  |||
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaactgaatactctatgaaaagttctaccgatttacacacgg---gatctttttttcaaacttg--tgttcttcttaatactg-cag

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgt-atgat-ggcatccaaattttgcattaa------tgaggtgtacagtgtactatg-----tgattctcaaagctaaatgctgttttttctactttcag
||| || ||||| || || || || |||||||||||||| || || |||||||| ||||| |||||||| || || |||||||||||||| ||||| ||||| || || |  |   |  || |   ||        |||  | || ||||   | |      |  || ||  ||||   | ||  | |||||  || |||
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 21
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatg-atg-gcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcag
||| |||||||| ||||| ||||| |||||||| ||||| || |||||||| |||||||| || || || |||||||||||||| || || || || ||||||   ||| ||||| ||||  || | ||   || | |    || |     || ||   |||  |      |  |  |  | ||| |||
TGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATATCAATGTCTAGTATCACTTCAAAGgtaaatatgtgcatcaaaatggtg-actatgcagctctcttttgcaagtcttgttttgaaaatatttgacatcctgatattgcttgcag

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
lower sequence: PP1S3_184V6.1 (Physcomitrella patens), 5'ss of exon 18
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgta-----tgatggcatccaaattt--tgcattaatgaggtgta--cagtgtac----tatgtgattctcaaagctaaatgctgttttttctactttcag
|||||| || ||||| ||||| || ||| | |||||||| || |||||||||||||| ||||||||||| ||||| || ||||| | |||| | || |||||      || |    || ||| ||  | |  |  ||| | |||  || ||| |     |||  ||| | | |  |  |  |  |||    | ||     
TGGACCACCAGGTACAGGGAAGACTATGTTAGCTAAGGCTGTTGCAACTGAAGCAGGGGCTAACTTCATAAACATTTCCATGTCTACCATTGCTTCCAAGgtgctttttggttttttcgaaagttgctacgatgttgaagagtagtcaatgttcaactcatgaaattataatatatgtagacattttcagttgctccaca

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
lower sequence: PP1S27_195V6.1 (Physcomitrella patens), 5'ss of exon 17
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgta----tgatggcatccaaattttgcatta-------atgaggtgtacagtgtac-tatgtgattctcaaagctaaatgctgttttttctactttcag-
|||||| || || || || || || ||||| ||||||||||| ||||| |||||||| |||||||| || || || || ||||| |  ||| | || |||||     | |   | ||    | || | |||       |||| |      ||| |    ||     ||||| |   |        ||   |  ||| || 
TGGACCACCAGGCACAGGCAAGACTATGCTAGCTAAGGCAGTCGCAACAGAAGCAGGGGCTAACTTTATAAATATTTCCATGTCCACTATTGCTTCCAAGgtgatcttcaattcttcttcctctttctttagccagtgatgatgaagctggtgaatacctgctgaactcaaggaatataataacgttagttgttttaagt

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|58684670|gb|CK073357.1|CK073357
EST:     AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAG                         TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
genomic: AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggc ... ctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
EST: gi|58687870|gb|CK076557.1|CK076557
EST:     AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAG                         TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
genomic: AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggc ... ctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
EST: gi|58692889|gb|CK081576.1|CK081576
EST:     AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAG                         TGGTTTGGCGAAGGAGAGAAATCATGTCAAAAGCTGTTTTCTCATTAGCAA
genomic: AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggc ... ctactttcagTGGTTTGGCGAAGGAGAGAAAT-ATGT-AAAAGCTGTTTTCTCATTAGCAA
EST: gi|58607816|gb|CK035849.1|CK035849
EST:     AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAG                         TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
genomic: AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggc ... ctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
EST: gi|163926070|gb|EG715026.1|EG715026
EST:     AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAG                         TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
genomic: AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggc ... ctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
EST: gi|66922707|gb|CX109555.1|CX109555
EST:     AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAG                         TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
genomic: AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggc ... ctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
EST: gi|86831749|gb|CI301599.1|CI301599
EST:     CTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAG                         TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
genomic: CTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggc ... ctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 72 (upstream exon), 60 (downstream exon)
Score: 24

TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggc ... ctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG




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