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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttaaaggaactttcatgtttatctttctgcggctgtgaggagttcaatttggatcctgactattctgtctgaaggaatttcgatacatttctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACTCTCCATAAATTCGTTGAACCAGTTATGATGCATTGGCCTGGCAGCAAAT

Basic information

species Zea mays
transcript GRMZM2G023798_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g04710.1 (Oryza sativa), 3'ss of exon 6
cttaaaggaactttcatgtttatctttctgcggctgtgaggagttcaatttggatcctgactattctgtctgaaggaatttcgatacat---ttctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACTCTCCATAAATTCGTTGAACCAGTTATGATGCATTGGCCTGGCAGCAAAT
  || |  |  | || | | |||||| ||           | ||| |||   ||||  || | |||| |||||| |  |||   |       || |  ||||||||||||||||||| ||||| |||||||| || ||||| || |||||||||||||| ||||| |||||||||| |||| ||| ||||||||| | |||||
--tacataatttatcctatgtatcttgcttttatcactttgtgtttaata-agatctggatttttctttctgaaagtttttttttttgggtattgtattgcagGAAGATCTGTACTATCCACATCCATTCGTGCAGGATGTATTATGGGCCACTCTCCACAAATTTGTTGAACCAGCTATGTTGCGTTGGCCTGGGAACAAAT

upper sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 7
--cttaaaggaactttcatgtttatctttctgcggctgtgaggagttcaatttggatcctgactattctgtctgaaggaatttcgatacatttctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACTCTCCATAAATTCGTTGAACCAGTTATGATGCATTGGCCTGGCAGCAAAT
     | |  || || ||| |  || ||||     |  |    | ||   ||    |     ||||  || |  | ||   |||  | ||||  |  ||||||||||||||||||||||||| ||||| || || ||| |  | ||| |  | ||| | ||| | ||||||||  || | |||||||||||||| |  || |
tctgcagaaaaatttgcatttccatttttccattaccctttttattttggttcttgtttctcctatattggc--atggggattcattgcattaattttgcagGAAGATCTGTACTACCCACATCCATTGGTGCAGGATATACTTTGGACATCCCTCGACAAAGTTGTTGAACCTATTCTAATGCATTGGCCTGGGAAAAAGT
















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|21331674|gb|BQ487055.1|BQ487055
EST:     ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAG                         GAAGATCTGTACTACCCACACCCATTTGTTCAAGATGTGTTATGGGCCACT
genomic: ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAGgtttgttaac ... tctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACT
EST: gi|211505955|gb|FL017761.1|FL017761
EST:     ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAG                         GAAGATCTGTACTACCCACACCCATTTGTTCAAGATGTGTTATGGGCCACT
genomic: ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAGgtttgttaac ... tctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACT
EST: gi|211505957|gb|FL017763.1|FL017763
EST:     ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAG                         GAAGATCTGTACTACCCACACCCATTTGTTCAAGATGTGTTATGGGCCACT
genomic: ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAGgtttgttaac ... tctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACT
EST: gi|211505958|gb|FL017764.1|FL017764
EST:     ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAG                         GAAGATCTGNACTACCCACACCCATTTGTTCAAGATGTGTTATGGGCCACT
genomic: ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAGgtttgttaac ... tctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACT
EST: gi|9733396|gb|BE512253.1|BE512253
EST:     ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAG                         GAAGATCTGTACTACCCACACCCATTTGTTCAAGATGTGTTATGGGCCACT
genomic: ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAGgtttgttaac ... tctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACT
EST: gi|211505959|gb|FL017765.1|FL017765
EST:     ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAG                         GAAGATCTGTACTACCCACACCCATTTGTTCAAGATGGGNTATGGGCCACT
genomic: ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAGgtttgttaac ... tctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACT
EST: gi|211505960|gb|FL017766.1|FL017766
EST:     ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAG                         GAAGATCTGTACTACCCACACCCATTTGTTCAAGATGTGTTATGGGCCACT
genomic: ACCCTTACAGCAAGATTGATTGGGACAAGGCCCGCAACCTATGTGCCAAGgtttgttaac ... tctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatttggatcctgactattctgtctgaaggaatttcgatacatttctgctgcagGAAGATCTGTACTACCCACACCCATTCGTTCAAGATGTGTTGTGGGCCACTCTCCATAAATTCGTTGAACCAGTTATGATGCATTGGCCTGGCAGCAAAT
         tcctgac  putative branch site (score: 2)
                                           tttctgct  putative PPT
                                      atacattt  TA-rich tract