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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccccaaatctaaccttctattcttctgttatgctcctagtcctagatatgttcaggttttcaataataattaggacactaaggaacctgccatctattctcacattaagctattcaaaaatgaaataattttgttctcattcactgcagTTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAGTTCATCAATACGCCACTGTATGTTGTTCATGTGATGAGCATCGACGCAATGGATGAGA

Basic information

species Zea mays
transcript GRMZM2G020002_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020002_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 8
gtaaccccaaatctaaccttctattcttctgttatgctcctagtcctagatatgtt---cag-------gttttc---aataataattaggaca--ctaaggaacctgccatct------attctcacattaagctattcaaaaatgaa---ataattttg------ttctcattcactgcagTTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAGTTCATCAATACGCCACTGTATGTTGTTCATGTGATGAGCATCGACGCAATGGATGAGA
||||   || |   |  ||||   | | |||||||||   |    || ||||||||   |||       ||||||    | |||| | | | ||   |   ||||  | ||         |||     |||        |||  | | |   |||   |||      ||||  ||| |||||||| ||||| ||||||||||| |||||||| || ||||| |||||  ||||||| ||| ||||||||||||||||||||||||| || |||||||||||||
gtaatttcacactaactcttcgcatttactgttatgcctatttatcttgatatgttggacagatcaagtgttttcttatacaatattcaagtcaatttggtgaactagacacaccatgaaatttgtgtattttctctcacaaggaaggatagataccattgagctgcttcttgttccctgcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA
















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|149082368|gb|EE171552.2|EE171552
EST:     ACCTTGGGATAACTGGTCCAGAAGGGCATGCTCTCTCAAGGCCTCCAATT                         TTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAG
genomic: ACCTTGGGATAACTGGTCCAGAAGGGCATGCTCTCTCAAGGCCTCCAATTgtaaccccaa ... ttcactgcagTTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAG
EST: gi|18659090|gb|BM500149.1|BM500149
EST:     ACCTTGGGATAACTGGTCCAGAAGGGCATGCTCTCTCAAGGCCTCCAATT                         TTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAGTTCATCAAT
genomic: ACCTTGGGATAACTGGTCCAGAAGGGCATGCTCTCTCAAGGCCTCCAATTgtaaccccaa ... ttcactgcagTTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAGTTCATCAAT
EST: gi|31355355|gb|CD439712.1|CD439712
EST:     ACCTTGGGATAACTGGTCCAGAAGGGCATGCTCTCTCAAGGCCTCCAATT                         TTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTGGCGAAGTTCATCAAT
genomic: ACCTTGGGATAACTGGTCCAGAAGGGCATGCTCTCTCAAGGCCTCCAATTgtaaccccaa ... ttcactgcagTTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAGTTCATCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattctcacattaagctattcaaaaatgaaataattttgttctcattcactgcagTTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAGTTCATCAATACGCCACTGTATGTTGTTCATGTGATGAGCATCGACGCAATGGATGAGA
  ttctcac  putative branch site (score: 2)
                                  ttttgttctcattc  putative PPT
         attaagctattcaaaa  TA-rich tract