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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgtttaatatgatcttaactgtgatgctgaaagctattgtgattttcttgacatttgtaaacatacctctaacatgttgttcacctataattttccagAGAAGCAGCTTGCGAATTCCGTCAAGCAGAACAGATGCGGGTGCACCATTCTCTGATAAGACGCCTGCTTGATGTTGTACAATCTGTGTAGTCTTAGGAT

Basic information

species Zea mays
transcript GRMZM2G012269_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012269_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g51500.1 (Oryza sativa), 3'ss of exon 2
gttgtttaatatgatcttaactgtgatgctgaaagctattgt---gattttcttgaca--tttgtaaacatacctctaacatgttgttcacctataattttccagAGAAGCAGCTTGCGAATTCCGTCAAGCAGAACAGATGCGGGTGCACCATTCTCTGATAAGACGCCTGCTTGATGTTG-TACAATCTGTGTAGTCTTAGGAT-------
         | ||    ||| |   ||||| |||||| |  |   ||     ||||||  | | || ||| | || |||  |||||||    | |   |||||||||||||||||||||||||||  ||||||||||||||| ||||| ||||| || ||||| | ||||||| ||||| || |  |   ||| | |   ||||||       
---------tttggc--taatta-aatgcttaaagctttcatctagaccaatttgacacctctatatacacatctataatgtgttgttggtttctc-ctttccagagaagcagCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATACTGTGATACGCCGCCTGCCTGATGATGATGTACAATGTCTCGCTCTAGGATTTTGTAT

upper sequence: GRMZM2G012269_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g51500.2 (Oryza sativa), 3'ss of exon 2
gttgtttaatatgatcttaactgtgatgctgaaagctattgt---gattttcttgaca--tttgtaaacatacctctaacatgttgttcacctataattttccagAGAAGCAGCTTGCGAATTCCGTCAAGCAGAACAGATGCGGGTGCACCATTCTCTGATAAGACGCCTGCTTGATGTTG-TACAATCTGTGTAGTCTTAGGAT
  || | | |||     ||| |   ||||| |||||| |  |   ||     ||||||  | | || ||| | || |||  |||||||    | |   |||||||||||||||||||||||||||  ||||||||||||||| ||||| ||||| || ||||| | ||||||| ||||| || |  |   ||| | |   ||||| 
--tggt-agtatttggctaatta-aatgcttaaagctttcatctagaccaatttgacacctctatatacacatctataatgtgttgttggtttctc-ctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATACTGTGATACGCCGCCTGCCTGATGATGATGTACAATGTCTCGCTCTAGGA-
















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|148932480|gb|EC876231.2|EC876231
EST:     AATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACAGTG                         AGAAGCAGCTTGCGAATTCCGTCAAGCAGAACAGATGCGGGTGCACCATTC
genomic: AATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACAGTGgtattgccga ... aattttccagAGAAGCAGCTTGCGAATTCCGTCAAGCAGAACAGATGCGGGTGCACCATTC
EST: gi|78092668|gb|DV521042.1|DV521042
EST:     AATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACAGTG                         AGAAGCAGCTTGCGAATTCCGTCAAGCAGAACAGATGCGGGTGCACCATTC
genomic: AATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACAGTGgtattgccga ... aattttccagAGAAGCAGCTTGCGAATTCCGTCAAGCAGAACAGATGCGGGTGCACCATTC
EST: gi|71774962|gb|DR972840.1|DR972840
EST:     AATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACAGTG                         AGAAGCAGCTTGCGAATTCCGTCAAGCAGAACAGATGCGGGTGCACCATTC
genomic: AATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACAGTGgtattgccga ... aattttccagAGAAGCAGCTTGCGAATTCCGTCAAGCAGAACAGATGCGGGTGCACCATTC
EST: gi|32916985|gb|CF021797.1|CF021797
EST:     AATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCGTCAAGCAGAACAGATGCGGGTGCACCATTC
genomic: AATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACAGTGgtattgccga ... aattttccagAGAAGCAGCTTGCGAATTCCGTCAAGCAGAACAGATGCGGGTGCACCATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttgacatttgtaaacatacctctaacatgttgttcacctataattttccagAGAAGCAGCTTGCGAATTCCGTCAAGCAGAACAGATGCGGGTGCACCATTCTCTGATAAGACGCCTGCTTGATGTTGTACAATCTGTGTAGTCTTAGGAT
                       ctctaac  putative branch site (score: 2)
                                               ttttcc  putative PPT
                                          tataatttt  TA-rich tract