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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtggttatctggaaacgatttttttttcccaatggacacaagaaattttgccaagttctttgaagattggtgtctacttgttttctttccaagcttgatctgcagaaggcatttttattgaagcgcgtgatccatattctccctgtcataagttgtcagctaccgaagtatgtatttccattgtttcagGTCTAAATATGAGCTGCAGGAATTTCTGAAGCCAAGCTTGCGCATTGTTTCTCATCAGCCTAGTGACTCTGGAAAACATGCCGGAAATGCTTCTCATTCT

Basic information

species Zea mays
transcript GRMZM2G138349_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138349_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g10480.3 (Oryza sativa), 3'ss of exon 6
gtttgtggttatctggaaacgatttttttttcccaatggacacaagaaattttgccaagttctttgaagattggtgtctacttgttttctttccaagcttgatctgcagaaggcatttttattgaagcgcgtgatccatattctccctgtcataagttgtcagctaccgaagtatgtatttccattgtttcagGTCTAAATATGAGCTGCAGGAATTTCTGAAGCCAAGCTTGCGCATTGTTTCTCATCAGCCTAGTGACTCTGGAAAACATGCCGGAAATGCTTCTCATTCT
                                                                                     ||  | | |||  |||| ||| ||||     ||  |   ||  |  |   | ||  | |  | || |||       |   ||  |   |  || || || |  |||||||| ||||||||| | || || |||||  |||||||| | || ||||||||||||||| |||| ||||| || |||||||| || | ||| || ||||||
-------------------------------------------------------------------------------------ttgttctgcaaa-ttgaactgaagaaatagcttaaa--aaaatgt-tctcctatggtgtttcagttatat----caaatgacacatacagttaattacaattcttcagGTCAAAATATGAGTTACAAGAGTTTCTTGAGCCAAGCCTACGGATTGTTTCTCATCAGTCTAGCGACTCCGGGAAACATGCAGGCAGTGCCTCCCATTCT

upper sequence: GRMZM2G138349_T04 (Zea mays), 3'ss of exon 1
lower sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 4
gtttgtggttatctggaaacgatttttttttcccaatggacacaagaaattttgccaagttctttgaagattggtgtctacttgttttctttccaagcttgatctgcagaaggcatttttattgaagcgcgtgatccatattctccctgtcataagttgtcagctaccgaagtatgtatttcca----ttgtttcagGTCTAAATATGAGCTGCAGGAATTTCTGAAGCCAAGCTTGCGCATTGTTTCTCATCAGCCTAGTGACTCTGGAAAACATGCCGGAA-ATGCTTCTCATTCT-----
                                                                                                            | |||     |||   || | ||  |   ||| | |   |  | | | |  |    |   ||| |||  || || |    |||||||||||| ||||||||||  || || |||||||| ||||||||||| ||       |||| |   || | |||| | | | |  |   |  ||   | ||||        
------------------------------------------------------------------------------------------------------------gtagg-----ttacaaaaacccgataag-atagtgtatataccttcattaatagtttggtgaaatattcatctcaaatctttgtttcagGTCGAAATATGAGCACCAAGAGTTTCTGAAACCAAGCTTGCGGATCA-----CATCCGTG-AGGGGCTCTAGTACAAAGACTCCAGCATTTCTTTCATCGAGTCTA
















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|213172275|gb|FM186438.1|FM186438
EST:     CAGAAGCCACATTCAGATTCTACCCAGGAAGAGCGAGAAAAATTCATCAG                         GTCTAAATATGAGCTGCAGGAATTTCTGAAGCCAAGCTTGCGCATTGTTTC
genomic: CAGAAGCCACATTCAGATTCTACCCAGGAAGAGCGAGAAAAATTCATCAGgtttgtggtt ... attgtttcagGTCTAAATATGAGCTGCAGGAATTTCTGAAGCCAAGCTTGCGCATTGTTTC
EST: gi|78179014|gb|DV549387.1|DV549387
EST:     CAGAAGCCACATTCAGATTCTACCCAGGAAGAGCGAGAAAAATTCATCAG                         GTCTAAATATGAGCTGCAGGAATTTCTGAAGCCAAGCTTGCGCATTGTTTC
genomic: CAGAAGCCACATTCAGATTCTACCCAGGAAGAGCGAGAAAAATTCATCAGgtttgtggtt ... attgtttcagGTCTAAATATGAGCTGCAGGAATTTCTGAAGCCAAGCTTGCGCATTGTTTC
EST: gi|12046228|gb|BF728367.1|BF728367
EST:     CAGAAGCCACATTCAGATTCTACCCAGGAAGAGCGAGAAAAATTCATCAG                         GTCTAAATATGAGCTGCAGGAATTTCTGAAGCCAAGCTTGCGCATTGTTTC
genomic: CAGAAGCCACATTCAGATTCTACCCAGGAAGAGCGAGAAAAATTCATCAGgtttgtggtt ... attgtttcagGTCTAAATATGAGCTGCAGGAATTTCTGAAGCCAAGCTTGCGCATTGTTTC
EST: gi|211245510|gb|FK953342.1|FK953342
EST:     CAGATTCTACCCAGGAAGAGCGAGAAAAATTCATCAG                         GTCTAAATATGAGCTGCAGGAATTTCTGAAGCCAAGCTTNCKCATTGTTTC
genomic: CAGATTCTACCCAGGAAGAGCGAGAAAAATTCATCAGgtttgtggtt ... attgtttcagGTCTAAATATGAGCTGCAGGAATTTCTGAAGCCAAGCTTGCGCATTGTTTC
EST: gi|6918414|gb|AW399944.1|AW399944
EST:     CAGAAGCCACATTCAGATTCTACCCAGGAAGAGCGAGAAAAATTCATCAG                         GTCTAAATATGAGCTGCAGGAATTTCTGAAGCCAAGCTTGCGCATTGTTTC
genomic: CAGAAGCCACATTCAGATTCTACCCAGGAAGAGCGAGAAAAATTCATCAGgtttgtggtt ... attgtttcagGTCTAAATATGAGCTGCAGGAATTTCTGAAGCCAAGCTTGCGCATTGTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattctccctgtcataagttgtcagctaccgaagtatgtatttccattgtttcagGTCTAAATATGAGCTGCAGGAATTTCTGAAGCCAAGCTTGCGCATTGTTTCTCATCAGCCTAGTGACTCTGGAAAACATGCCGGAAATGCTTCTCATTCT
                                        tttccatt  CT-rich tract
                                  tatgtattt  TA-rich tract