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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattgatgattatttgataatttggccatctttggaagcaagtcaatgtgaattatatgatcttgtttaaaacttaacaattcttttcccttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAGTGAGTCTTTAGCATTAGACTTGTTTACATG

Basic information

species Zea mays
transcript GRMZM2G127453_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127453_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g56890.2 (Oryza sativa), 3'ss of exon 2
cattgatgattatttgataatttggccatctttggaagcaagtcaatgtgaattatatgatctt----gtttaaaacttaacaattcttttcccttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAGTGAGTCTTTAGCATTAGACTTGTTTACATG---
     |           |||  |||| |   |   |        | ||||||  |    |  ||    || | ||| ||| |  || || ||  || |||| |||| |||||| |||||||||| ||||||||||| |||||||||||||||||||||||||| |||||||| || |  |   ||| | || ||| |  |  ||   
---aaaccccagccaattaacatggctagtatgaaatattgtgaactgtgaaacacccaaatttttcagtcttaaatttatcc-tttttgtcatttctatgtagGTTTGGCCCCTTGATATAGAGATGAAGTTCCTGGAGCCATTTGGACGGGAACTACATTCCATGAAAAAGGTAATGCA--AGCTTGAGGCTT-TCCATCTGTTG

upper sequence: GRMZM2G127453_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g56890.1 (Oryza sativa), 3'ss of exon 2
cattgatgattatttgataatttggccatctttggaagcaagtcaatgtgaattatatgatctt----gtttaaaacttaacaattcttttcccttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAGTGAGTCTTTAGCATTAGACTTGTTTACATG
     |           |||  |||| |   |   |        | ||||||  |    |  ||    || | ||| ||| |  || || ||  || |||| |||| |||||| |||||||||| ||||||||||| |||||||||||||||||||||||||| ||||||||                                
---aaaccccagccaattaacatggctagtatgaaatattgtgaactgtgaaacacccaaatttttcagtcttaaatttatcc-tttttgtcatttctatgtagGTTTGGCCCCTTGATATAGAGATGAAGTTCCTGGAGCCATTTGGACGGGAACTACATTCCATGAAAAAG-------------------------------
















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|211045913|gb|FK963041.1|FK963041
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTC-TAGAGCCATTTGGACG
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACG
EST: gi|211042950|gb|FK963028.1|FK963028
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|211167599|gb|FL258648.1|FL258648
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGATCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|211115674|gb|FL110115.1|FL110115
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTA
EST: gi|161590278|gb|EY957950.1|EY957950
EST:     CGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: CGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgaattatatgatcttgtttaaaacttaacaattcttttcccttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAGTGAGTCTTTAGCATTAGACTTGTTTACATG
                          acttaac  putative branch site (score: 3)
                                   ttcttttcccttgtat  putative PPT
     aattatatgatcttgt  TA-rich tract