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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacagttcgtcttcctgttatgccttgtggtagagttttgtgtactctggatagcatgctgattgtgtttctgcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG

Basic information

species Zea mays
transcript GRMZM2G063851_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063851_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------------------gtaagacagttcgt-cttcctgttatgccttgtggtagagttttgtgtactctggatagc-atgct-gattgtgtttctg-----caaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
                                                    ||  | |  || |   ||||          |  || |     ||| ||||| | |   ||| | ||||||||||||       | ||||||||||| ||||||||| |||||||||||||||| |||||||||
gtaagtcaattagtttttgttcgttcgtgctaaatgtgtggttgaaactaccagttactatgtgccatctgtggctaggctcgaaagtggggaatgtgctctgaaaaaagatgtttgattgtgtttctaaatattatatgcagGATCTCAAGTCCCAGCTGCAGGAATTGATTCCTGAACAACAG

upper sequence: GRMZM2G063851_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------------------------------gtaagacagttcgtcttcctgttatgcct---tgtggtagagttttg--------tgtactctggatagcatgctga--ttgtgtttctgcaaatg-------cagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
                                                                       |  ||  |     ||| |||  | || ||   |  | | ||  ||          ||| ||||| | |  ||| |    ||||||| ||  | ||        |||||||||||||||||| |||||||||||||||| || ||||||
gtaagacaataatagtttgtttgtttctttgtttgtttgttcgtgctataaatatttgcatggttgaaattgatagttaccctctctaccttctgtggctggctacgattgaaattaagttggaaatgtgctctgaaaaagatgtttgatttgtgttcctaaatattatgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG

upper sequence: GRMZM2G063851_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 3
------------gtaagacagttcgtcttcctgttatgccttgtggtagagttt-tgtgtactctggatagcatgctgattgtgtttc---tgcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
             |       ||| | ||||| || ||  || | | | |  ||   | ||||   | | |  |  |  ||   |||    |    ||| |||| ||| | ||||||||| ||||||||||||| |||||||||
tgccaaccttatctttttttattctttttcctatt-tgt-ttatcgcatatcttgcttatacttctgtttgtttttttcttcctttttctttttccatgtagGACCTTCATTCCCAGTTGAAGGAATTGATTCCAGAACAACAG

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|51592469|gb|CV071615.1|CV071615
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCCTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|78109451|gb|DV527867.1|DV527867
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
EST: gi|74035022|gb|DT535512.1|DT535512
EST:     CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC                         GATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
genomic: CCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTCgtaagacagt ... gcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtagagttttgtgtactctggatagcatgctgattgtgtttctgcaaatgcagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
                             tgctgat  putative branch site (score: 3)
                                        tttctgc  putative PPT