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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctaaaccaaagtttcgttttcttttccgttttccattcgaagaaatgagattgcaagaagcatctcgttaggttacttctagtgcactaatcctctgtgtgcctaggatagCTCAAAGACAGATCGGGGAAACTTCTATGAATGAAGCGAGCTCCAGATCTCATCAGATACTCAGATTGGTTGGCCCTTGTATAGTACTGAATGATGTGCG

Basic information

species Zea mays
transcript GRMZM2G015395_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015395_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os09g35890.1 (Oryza sativa), 3'ss of exon 6
gtgctaaaccaaagtttcgttttcttttccgttttccattcgaagaaatgagattgcaagaagcatctcgttaggttact---tctagtgcactaatcctctgtgtgcctaggatagCTCAAAGACAGATCGGGGAAACTTCTATGAATGAAGCGAGCTCCAGATCTCATCAGATACTCAGATTGGTTGGCCCTTGTATAGTACTGAATGATGTGCG
|||   ||   || |||| || | | ||||    |  |   |  || ||   | |   || |||| ||| || | ||  |   ||| |||  |   |  | | ||    |  || ||||||||||||||| ||||||||| ||||||||||||| ||||||||||||||||| ||||||||  ||                                
gtgtggaaatgaattttctttctttcttcc-cagtgaacctg--gatatagcaataagagtagcagctcatttgtttcttcagtctggtgatcattttgtttttgcttgtgtgacagCTCAAAGACAGATTGGGGAAACTGCTATGAATGAAGCAAGCTCCAGATCTCATCAAATACTCAGGATG--------------------------------

upper sequence: GRMZM2G015395_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G07950.1 (Glycine max), 3'ss of exon 5
------------------------------------------gtgc-taaaccaaagtttcgttttctt-ttccgttttcca-ttcgaagaaatgagatt-gcaagaagcatctcgttaggttacttctagtgcactaatcctctgtgtgcctaggatagCTCAAAGACAGATCGGGGAAACTTCTATGAATGAAGCGAGCTCCAGATCTCATCAGATACTCAGATTGGTTGGCCCTTGTATAGTACTGAATGATGTGCG
                                           ||| || ||  ||  |   | || || ||   ||||||  ||  || ||||  |    || |||   | ||  ||||  | ||| | || ||   ||    ||  |   |     ||||||||| ||||| ||||| ||  |  |||||||||| ||||||||||||||||| || || ||| ||                                
gtaagggtaaggagggtttggatggttcttgtttcaatagagttgcctagactgaacatatatctttttgttatattttcctctttaaaaaaatttgtccagctagagctaactgcttag--tgcttatcgttca---attgattgcattttt---gcagCTCAAAGGCAGATAGGGGAGACAGCACTGAATGAAGCAAGCTCCAGATCTCATCAAATTCTAAGACTG--------------------------------

upper sequence: GRMZM2G015395_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G24250.1 (Glycine max), 3'ss of exon 5
---------------------------------------gtgctaaaccaaagtttcgttttcttttccgttttccattcgaagaaatgagattgcaagaagcatctcgttaggttacttctagtgcactaatcctc-------tgtgtgcctaggat-agCTCAAAGACAGATCGGGGAAACTTCTATGAATGAAGCGAGCTCCAGATCTCATCAGATACTCAGATTGGTTGGCCCTTGTATAGTACTGAATGATGTGCG
                                       | | || || | | || | || | | |    |||||  || |   || |    |    | ||   |   ||   | ||   ||       || |  ||       ||  ||| |    | ||||||||| ||||| ||||| ||| |  ||||||||| ||||||||||||||||||||| |||||| ||                                
gtagggactaaggataatttgaatgaccttgcttcaattgagttatac-agacttactttctttgtctatttttctttttgcttaattttcctcattacaaatcttctgtccagctagagctgactgcttagttatcataaaattgattgcattttttcagCTCAAAGGCAGATAGGGGAGACTGCCCTGAATGAAGTGAGCTCCAGATCTCATCAGATTCTCAGACTG--------------------------------

upper sequence: GRMZM2G015395_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G05650.1 (Glycine max), 3'ss of exon 5
gtgctaaaccaaagtttcgttttcttttccgttttccattcgaagaaatgagattgcaagaagcatctcgttaggttacttctagtgcactaatcctctgtgtgcctaggatagCTCAAAGACAGATCGGGGAAACTTCTATGAATGAAGCGAGCTCCAGATCTCATCAGATACTCAGATTGGTTGGCCCTTGTATAGTACTGAATGATGTGCG
  |  |   | |||  |  |||   |   |    | || | ||       |||||      |   |||   |   ||  |  |  |||  ||||  ||    |  ||     ||||||||| ||||| ||||| ||| || ||||||||| ||||||||||||||||||||| |||||| ||                                
--gtaaggactaaggataatttggatgaactcgcttcaattgagttgtacagattt-----actttctttgtctatttttctttttgc-ttaattttcctcattactt--tcagCTCAAAGGCAGATAGGGGAGACTGCTCTGAATGAAGTGAGCTCCAGATCTCATCAGATTCTCAGACTG--------------------------------

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|6587632|gb|AW244950.1|AW244950
EST:     AACTCTCAAGGACAAGGGCCATCTCTTGGAGCTCCTTGCAGTGTGTGAAG                         CTCAAAGACAGATCGGGGAAACTTCTATGAA-GAAGCGAGCTCC
genomic: AACTCTCAAGGACAAAGGCCATCTCTTGGAGCTCCTTGCAGTGTGTGAAGgtgctaaacc ... cctaggatagCTCAAAGACAGATCGGGGAAACTTCTATGAATGAAGCGAGCTCC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagcatctcgttaggttacttctagtgcactaatcctctgtgtgcctaggatagCTCAAAGACAGATCGGGGAAACTTCTATGAATGAAGCGAGCTCCAGATCTCATCAGATACTCAGATTGGTTGGCCCTTGTATAGTACTGAATGATGTGCG
                            cactaat  putative branch site (score: 2)