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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttattatatttatcaacttcttggtgatattatgcataagtagctaacatactttgcgtataatacaatctctgtaactgatcaatcagggcgaattatttcatattgtgcatacctatttctgatctggatgctattttggttttccttaactatatttctcttcaagTTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAG

Basic information

species Oryza sativa
transcript LOC_Os07g48200.1
intron # 4
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 4
--------------gtatcctta---ttatatttatcaacttcttggtgatattatgcataagtagctaacatactttgcgtataatacaatctctgtaactgatcaatcagggcgaattatt-tcatattgtgcatacctattt-------ctgatctggatgctattttggttttccttaactatatttctcttcaagTTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAG
              || ||| ||   ||  |  | | |||||| |||||| |||   |  |   |  ||   ||  ||    || |   |  ||||  ||  | ||| |  |    ||   || | ||||  ||||||  | | |       | ||| | | |  | ||||  | |||||| |||||||||   | |||||||||||||||| || || ||  |||| |||||||| || || || |||||||||||||||||||||||||||||||| |||||||| ||||| |||
gtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttag--taacttatacatca---aggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttctttta-tcttccttgactatattt---tgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG

upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G172621_T01 (Zea mays), 3'ss of exon 4
--------------gtatcctta---ttatatttatcaacttcttggtgatattatgcataagtagctaacatactttgcgtataatacaatctctgtaactgatcaatcagggcgaat-tatttcatattgtgcatac-ctatttctgatctggatgctattttggtttt-----ccttaactatatttctcttcaagTTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAG
              |  | | |    ||  | || |||||||| |||||| |||   | |    |  ||  |   | |   || ||  |    ||   ||  | ||| |  |    |   | | | ||||  ||||||   | ||| ||     |||||   ||| |||||     |||| |||||||||   |  ||||||||||||||| ||||| ||  ||||||||||||| || || || |||||||||||||||||||||||||||||||| |||||||| ||||| |||
gtatccttgataaggctttcatgcatttgaaattgtcaacttcctggtgacattgatctttgacatttagtaccttataaatacaaggc----tccagaagagctcattaggcttaagcctgtataatatgctgcataaattctttttgtaacagatgcaggttttgttttatcttccttgactatattt---tggaagTTCAAATTCCACGATTGTTCCATTGTTTGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCTGAG

upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G05840.1 (Glycine max), 3'ss of exon 6
gtatccttattatatttatcaacttcttggtgatattatgcataagtagctaacatactttgcgtataatacaatctctgtaactgatcaatcagggcgaattatttcatattgtgcatacctatttctgatctggatgctattttggttttccttaactatatttctcttcaagTTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAG
                                                               ||||  |  |   | | ||  || |      |  |  ||      ||| |   |     || |    |  ||| |  |    | |||| |||||| | |||         ||||  || |||||  | || ||  | |||||||||||  | || |||||||||||||| || || || || |||||||| |||||||||||||| |||
---------------------------------------------------------------gtatcctttatattttttatttggttgtcttgaacatat------ataatagactctgatagtataaagttggtttattcagtagtttcccttaa-tgtatgat------agTTTGAAATCCACTGTAGTGCCATTATTTGAGAAGGTGTTGAGTGCCAGTGATGCAGGTCGAATTGGCCGTCTTGTTCTCCCAAAAGCCTGTGCTGAG

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|58671720|gb|CK060406.1|CK060406
EST:     CGATATTGGCCTAGAATAACAGACCAAGAGCTACAGCAAATTTCTGGAGA                         TTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGA
genomic: CGATATTGGCCTAGAATAACAGACCAAGAGCTACAGCAAATTTCTGGAGAgtatccttat ... tctcttcaagTTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctatttctgatctggatgctattttggttttccttaactatatttctcttcaagTTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAG
 ttccttaac  putative branch site 
                                      ctatatttctcttc  putative PPT
                                  ttaactatatttct  TA-rich tract