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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatttactagcttgattcatagttttttattgtacaaggattgatatcatttggctgtccctggaaactcgctcatacttgatggttcttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCATCTGTTGTCAAGGCAAGTTTCTCAAAGATAGATTCATCTAACGATTCTG

Basic information

species Zea mays
transcript GRMZM2G002440_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002440_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g25090.2 (Oryza sativa), 3'ss of exon 3
tatatttactagcttgattcatagttttttattgtacaaggattgatatcatttggctgt-ccctggaaactcgctcatacttgatggttcttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCATCTGTTGTCAAGGCAAGTTTCTCAAAGATAGATTCATCTAACGATTCTG
                 |   || | | |   ||  || |  ||  ||  || | | | | |  ||||||   |||||    |     ||| | | |  || ||||||||||||||||||||||||||||||||||||| ||| |||||||||||||||| ||||  || ||||||||||||||| ||||||| || ||||
----------------gtctgtattctatgtctggtcatgattttttagaatcttgttttactttggaaatgagctcacgtcta----ttcatccctgtagGGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTATCTAGGGCATCATCTGTTGTAAAGGAGAGCTTCTCAAAGATAGATACATCTAATGAATCTG
















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|50332490|gb|CO527616.1|CO527616
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|37394200|gb|CF634371.1|CF634371
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|148953359|gb|EE152852.2|EE152852
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|5847121|gb|AW000200.1|AW000200
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|13237180|gb|BG355194.1|BG355194
EST:     ATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: ATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|78088183|gb|DV516576.1|DV516576
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|74234070|gb|DT641984.1|DT641984
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|74240578|gb|DT648492.1|DT648492
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|67042408|gb|CO468663.1|CO468663
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|5895637|gb|AW036883.1|AW036883
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCACGAAGTATGCCATACAG                         AGCTTCTCCAAGAGACTTGGTAGATGGTGCAGACCATTTTGTCTCGGGCAT
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAG-CTTGTTAGATGTTGCAGACAATTT-GTCTCGGGCAT
EST: gi|74234069|gb|DT641983.1|DT641983
EST:     AAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: AAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|148956597|gb|EC902445.2|EC902445
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
EST: gi|5343189|gb|AI795374.1|AI795374
EST:     TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAG                         AGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA
genomic: TTGCCAGAACAAAGCGTGAGTCAGAGAACACCAAGAAGTATGCCATACAGgttcgcgcat ... ttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatcatttggctgtccctggaaactcgctcatacttgatggttcttacatacagAGCTTCTCCAAGAGCTTGTTAGATGTTGCAGACAATTTGTCTCGGGCATCATCTGTTGTCAAGGCAAGTTTCTCAAAGATAGATTCATCTAACGATTCTG
                                          ttcttac  putative branch site (score: 2)
                                          ttcttac  CT-rich tract
                                             ttacata  TA-rich tract