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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagaaaacactatcggaagtccaaacagttcaatatccgtgaagatcctttagttatttacaataaataatagtttacttgcccttaatcaggtgatgttaagtaactgttgtaatttatgcctttctcttttatagCTATACAAAATAATGAAAGAGCACAAAAATCCAAAGGTGCTTAGCGAGGGTATTCTTTGGATGGTTTCTGCCGTTGAGGACTTTGGGATCTCCAATTTAA

Basic information

species Oryza sativa
transcript LOC_Os01g60040.2
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 3
------------------------------------gtaagagaaaacac---tatcgga--agtccaaacagttcaatatccgtgaagatcctttagttatttacaataaataat----agtttacttgc--ccttaatc--------aggtg-atgttaagtaactgttgta-atttatgcctttctcttttatagCTATACAAAATAATGAAAGAGCACAAAAATCCAAAGGTGCTTAGCGAGGGTATTCTTTGGATGGTTTCTGCCGTTGAGGACTTTGGGATCTCCAATTTAA
                                      |||      |||   | |   |  |  ||||  || | | | |   ||  | |||   |   ||| | |||    | |    |   |  ||||    ||| |         || || |   |   ||  || |||| | |||||  |||   |||| ||||| |||||||||||||| |||||||| ||||| ||||| ||||| || ||||||||||||||||| ||||| || || ||||||||||||||||||||||
gtaagagataccattagattattattgtttttgttcaaaaggtcctccacatttgttcaatcaacccaattaggtgattttatatgctggtccgcaataaattcagaatgtgcactgtcgaacatctttgcaattttattttgtgctttagatgcacactgcttatatgatgtataattatgagttttaattttgtagCTTTACAAAATAATGAAGGAGCACAAGAATCCCAAGGTTCTTAGTGATGGTATTCTTTGGATGGTCTCTGCTGTGGAAGACTTTGGGATCTCCAATTTAA

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 21
gtaagagaaaacactatcggaagtccaaacagttcaatatccgtgaagatcctttagttatttacaataaataatagtttacttgcccttaatcaggtgatgttaagtaactgttgtaatttatgcctttctcttttatagCTATACAAAATAATGAAAGAGCACAAAAATCCAAAGGTGCTTAGCGAGGGTATTCTTTGGATGGTTTCTGCCGTTGAGGACTTTGGGATCTCCAATTTAA
                                      |     ||| ||| || | || | | |  |   | |  ||  ||    | |  | ||  |||||||    ||||  | || ||||||  |||   |||||||||| |||||||||||||| |||||||| ||||| ||||| ||||| |||||||||||||||||||| ||||| || || ||||||||||||||||||||||
-------------------------------------cactgtcgaacatctttcaattttattctgtgcttta-ggtgcacgctgcttccacca--tgatgtttgacaactactata-tttatgagttttatttttatagCTTTACAAAATAATGAAGGAGCACAAGAATCCCAAGGTTCTTAGTGAGGGTATTCTTTGGATGGTCTCTGCTGTGGAAGACTTTGGGATCTCCAATTTAA

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 23
gtaagagaaaacactatcggaagtccaaacagttcaatatccgtgaagatcctttagttatttacaataaataatagtttacttgcccttaatcaggtgatgttaagtaactgttgtaatttatgcctttctcttttatagCTATACAAAATAATGAAAGAGCACAAAAATCCAAAGGTGCTTAGCGAGGGTATTCTTTGGATGGTTTCTGCCGTTGAGGACTTTGGGATCTCCAATTTAA
                                |  || || |  |       | ||  | ||  |  || || ||| | |  |||    |  | | ||  | | || |||   ||| ||    ||  |||   |  | ||||| ||||| || ||||| ||||| || ||||| ||||| ||||| ||||| ||| | |||||||||||||| ||||| || |||||  ||||  || |||
--------------------------------tataaaatgcagg------ttgtatcttttggccgtatatcatattatttttgtttatctttatgtattatcaaataatgtttgaaaaccgtgaattt---tactgtagCTTTACAAGATCATGAAGGAGCATAAGAATCCCAAGGTTCTTAGTGAGGGAATTTTGTGGATGGTTTCTGCTGTTGAAGATTTTGGTGTCTCACATATAA

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 21
gtaagagaaaacactatcggaagtccaaacagttcaatatccgtgaagatcctttagttatttacaa-taaataatagtttacttgcccttaatcaggtgatgttaagtaactgttgtaatttatgcctttctcttttatagCTATACAAAATAATGAAAGAGCACAAAAATCCAAAGGTGCTTAGCGAGGGTATTCTTTGGATGGTTTCTGCCGTTGAGGACTTTGGGATCTCCAATTTAA
                                     |     | ||  ||   | ||   ||     |  |||||| |||  ||   ||| ||   ||  | | || |||   ||| ||   |  |     | |  | ||||| ||||| ||  |||| ||||| || ||||| ||||| ||||| ||||| ||| | |||||||||||||| ||||| || |||||  ||||  || |||
-------------------------------------ttcatataaaattcaggttgtaccttttggctgtataatatttttgtttatctttat---gtattatcaaataatgtttgaaaa--actctaaattttactgtagCTTTACAAGATCTTGAAGGAGCATAAGAATCCTAAGGTTCTTAGTGAGGGAATTTTGTGGATGGTTTCTGCTGTTGAAGATTTTGGTGTCTCACATATAA

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 21
lower sequence: AT2G35630.1 (Arabidopsis thaliana), 3'ss of exon 21
gtaagagaaaacactatcggaagtccaaacagttcaatatccgtgaagatcctttagttatttacaataaataatagtttacttgcccttaatcaggtgatgttaagtaactgttgtaatt-tatgcctttctcttttatagCTATACAAAATAATGAAAGAGCACAAAAATCCAAAGGTGCTTAGCGAGGGTATTCTTTGGATGGTTTCTGCCGTTGAGGACTTTGGGATCTCCAATTTAA
                                                                   ||  |  | |||   |   | ||  |    |    ||   |     |  ||||   ||     | |  ||| ||||| | |||||| |||||||||||||| ||||| ||||| ||||| || ||  |  | ||||||||||| || ||||| ||||||||  ||||   ||| |
------------------------------------------------------------------gtatgtgctggttcggtcaactttctttgactttcattttattctgatcataatgacatatggcttttgtttgtagCTTTTCAAAATCATGAAAGAGCACAAGAATCCCAAGGTTCTTAGTGAAGGCTTGTTATGGATGGTTTCGGCAGTTGATGACTTTGGTGTCTCACTTTTGA

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 21
lower sequence: Vv10s0116g00460.t01 (Vitis vinifera), 3'ss of exon 12
--------------------------------------gtaagagaaaacactatcggaagtccaaacagttcaatatccgtgaagatcctttagttatttacaataaataatagtttacttgcccttaat---caggtgatgttaagtaactgttgtaatt-tatgcct--ttctcttttatagCTATACAAAATAATGAAAGAGCACAAAAATCCAAAGGTGCTTAGCGAGGGTATTCTTTGGATGGTTTCTGCCGTTGAGGACTTTGGGATCTCCAATTTAA
                                         |          |||   || | |       | |||||   |  | |   | |   |||    ||   |||    | || | ||| ||  |      || || || | |   |  | |  || ||||  |  | || |||||||||| |||||||| |||||||||||||| ||||||||||| ||||| ||||| ||  | ||||||||||| || ||||| ||||||||  | ||  |||| |
gtaagtcaagtttctatcgggcttgaagcttctgtttctctatttggtttgatataaaaacttccttagaattaatatttttatatagattgtgtctatactgaa-gcatagatatctattggccattgttgtttcagtaatcttgacttggtcatatttttctatggatgatgcttttttatagCTTTACAAAATCATGAAAGAGCACAAGAATCCAAAGGTCCTTAGTGAGGGCATCTTGTGGATGGTTTCAGCAGTTGAAGACTTTGGTGTTTCACATTTGA

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|2309795|gb|C25950.1|C25950
EST:     GTCTCACTGCTTTTTGTGAGGCTGTTGGTCCGGGTTTTGTTTTTGAGAGG                         CTATACAAAATAATGANAGAGCACAAAANTCCAAAGGTGCTTAGCGAGGGT
genomic: GTCTCACTGCTTTTTGTGAGGCTGTTGGTCCGGGTTTTGTTTTTGAGAGGgtaagagaaa ... tcttttatagCTATACAAAATAATGAAAGAGCACAAAAATCCAAAGGTGCTTAGCGAGGGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttaatcaggtgatgttaagtaactgttgtaatttatgcctttctcttttatagCTATACAAAATAATGAAAGAGCACAAAAATCCAAAGGTGCTTAGCGAGGGTATTCTTTGGATGGTTTCTGCCGTTGAGGACTTTGGGATCTCCAATTTAA
                  aagtaac  putative branch site (score: 2)
                                 tttatgcctttctctt  putative PPT
                           ttgtaatttat  TA-rich tract