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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtactgcttgcagacatatgtctcccatgattgattcgttttgacattttccttaaattgttgcagAAGCAACTCCTAAGGGTGTCCTGAAGCTAATGAAGGCAGACAATTTGACCATTTATCATGTAAAAAGTCATCTTCAG

Basic information

species Zea mays
transcript GRMZM2G162409_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162409_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g25710.4 (Oryza sativa), 3'ss of exon 3
gtgcgtactgcttgcagacat---atgtctcccatgattga--------ttcgttttgacattttccttaaattgttgcagAAGCAACTCCTAAGGGTGTCCTGAAGCTAATGAAGGCAGACAATTTGACCATTTATCATGTAAAAAGTCATCTTCAG
||| ||| |||||  ||| ||   |  ||||| ||||||||        | | | |||||||||    | ||||||||||||||| ||||| ||||||||  | |||||||||||||||||||||||||||||||||||||| |||||||| ||||||
gtgtgtattgctttaagaaatgttacatctcctatgattgaactaattatgcatattgacatttattgtgaattgttgcagAAGCTACTCCCAAGGGTGTGTTAAAGCTAATGAAGGCAGACAATTTGACCATTTATCATGTTAAAAGTCACCTTCAG
















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|51592708|gb|CV071854.1|CV071854
EST:     GGATGCTGTCAATATACTTGGTGGCAGTGAAA                         AAGCAACTCCTAAGGGTGTCCTGAAGCTAATGAAGGCAGACAATTTGACCA
genomic: GGATGCTGTCAATATACTTGGTGGCAGTGAAAgtgcgtactg ... attgttgcagAAGCAACTCCTAAGGGTGTCCTGAAGCTAATGAAGGCAGACAATTTGACCA
EST: gi|211106908|gb|FK992455.1|FK992455
EST:     GCTTCACGAGCGCTTTGTGGATGCTGTCAATATACTTGGTGGCAGTGAAA                         AAGCAACTCCTAAGAGTGTCCTGAAGCTAATGAAGGCAGACAATTTGACCA
genomic: GCTTCACGAGCGCTTTGTGGATGCTGTCAATATACTTGGTGGCAGTGAAAgtgcgtactg ... attgttgcagAAGCAACTCCTAAGGGTGTCCTGAAGCTAATGAAGGCAGACAATTTGACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacatatgtctcccatgattgattcgttttgacattttccttaaattgttgcagAAGCAACTCCTAAGGGTGTCCTGAAGCTAATGAAGGCAGACAATTTGACCATTTATCATGTAAAAAGTCATCTTCAG
                           ttttgac  putative branch site (score: 3)
                                  attttccttaaatt  TA-rich tract