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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgctttgtggtttcgtgcttgttttcgtttgtacaccacaagttccagattcactaatattgagatgctgtttgcacaggatcagCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTACAACCATGCCTGCGCAGACTATGCCAGGCAGAAACTTTCATCTCCAAACTTCAAGG

Basic information

species Zea mays
transcript GRMZM2G103430_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103430_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g14430.2 (Oryza sativa), 3'ss of exon 4
gtgtgctttgtggtttcgtgcttgttttcgtttgtacaccacaagttccagattcactaatattgagatgctgtttgc---acaggatcagCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTACAACCATGCCTGCGCAGACTATGCCAGGCAGAAACTTTCATCTCCAAACTTCAAGG
|||||  || || ||||    |||| ||   ||||||  || | || |||  ||  ||||||  ||  | || || |     ||||||   |||||||||| |||||||||||| |||||||||||||||||||| ||||| || || ||||||||||||||||||||| | ||| | |||||||      
gtgtgtcttttgatttcacagttgtatt---ttgtacgacaaaggtcccaagtttgctaatagagatgttctcttggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCACGCTTGTGCAGACTATGCCAGGCAGAAATTGTCAGCACCAAACT------

upper sequence: GRMZM2G103430_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g06130.2 (Oryza sativa), 3'ss of exon 4
gtgtgctttgtggtttcgtgcttgttttcgtttgtacaccacaagttccagattcactaatattgagatgctgtttg-----cacaggatcagCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTACAACCATGCCTGCGCAGACTATGCCAGGCAGAAACTTTCATCTCCAAACTTCAAGG
||||| | |||| |||| || ||||  |   ||| ||     | |  ||  |||  |||||  |||||   |||||        ||||||   ||||| |||| |||||||||||| |||||||||||||||||||| |||||||| || ||||||||||||| ||||||| | ||| | |||||||      
gtgtg-tctgtgatttcatggttgtact---ttgcactaggaaggccccgaatttgctaat--tgagaccttgttttggtcctgcagGATTTACATGATCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCATGCTTGTGCAGACTATGCCAAGCAGAAATTGTCAGCACCAAACT------
















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|40336436|gb|CK370506.1|CK370506
EST:     GGTGTTATCAACATTGAGATGTTTAAGGATCAG                    
genomic: GGTGTTATCAACATTGAGATGTTT----A--AGgtgtgctttg ... acagg
EST: gi|28910015|gb|CB331214.1|CB331214
EST:     ACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAGGATCAG                    
genomic: ACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTT----A--AGgtgtgctttg ... acagg
EST: gi|211538187|gb|FL238623.1|FL238623
EST:     ACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAG                         G
genomic: ACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAGgtgtgctttg ... acaggatcag-
EST: gi|211538187|gb|FL238623.1|FL238623
EST:     ACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAG                         G
genomic: ACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAGgtgtgctttg ... acaggatcag-
EST: gi|211538187|gb|FL238623.1|FL238623
EST:     ACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAG                         G
genomic: ACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAGgtgtgctttg ... acaggatcag-
EST: gi|211538187|gb|FL238623.1|FL238623
EST:     ACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAG                         G
genomic: ACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAGgtgtgctttg ... acaggatcag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacaccacaagttccagattcactaatattgagatgctgtttgcacaggatcagCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTACAACCATGCCTGCGCAGACTATGCCAGGCAGAAACTTTCATCTCCAAACTTCAAGG
                     cactaat  putative branch site (score: 2)
                      actaatatt  TA-rich tract