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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtacatggttctcgtttgagttcttgacacattctattgtggttttactcttgtaagcacccttggcgatcttcatcatttctgatatgtctaatcataatctttattgtttcagACGTATGAGAAGGTGGCTTCTGTTTTCAAGTTGGATGAAGGAGTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAA

Basic information

species Zea mays
transcript GRMZM2G128171_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128171_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 6
gttagtacatggttctcgtttgagttcttgacacattctattgtggttttactcttgtaagcacccttggcgatcttcatcatttctgatatgtctaatcataatctt--tattgtttcagACGTATGAGAAGGTGGCTTCTGTTTTCAAGTTGGATGAAGGAGTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAA
||||||  ||   |||      ||||  |   ||||  |||      |||||| ||| |||            | |   |  ||   ||  || | | | ||| ||||  |||| ||| |||  ||||||||| ||||||||||||  |||||||| || |||||||| |||||||||||||| |||||||||||||  || ||||| || ||
gttagtggataactctacccaaagtttgttctacatgttatg-----tttacttttgaaag------------tttcagttgttctcgacgtgccaactaatattcttgttattattttagATATATGAGAAGCTGGCTTCTGTTTATAAGTTGGACGATGGAGTTGTAATTGCTAACCTTGATGCTGACAAACACAAAGACTTGGCCGAAAA
















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|40337309|gb|CK371379.1|CK371379
EST:     GTGTGGTCACTGCAAGAGTCTTGCACCG                         ACGTATGAGAAGGTGGCTTCTGTTTTCAAGTTGGATGAAGGAGTTGTTATT
genomic: GTGTGGTCACTGCAAGAGTCTTGCACCGgttagtacat ... attgtttcagACGTATGAGAAGGTGGCTTCTGTTTTCAAGTTGGATGAAGGAGTTGTTATT
EST: gi|60351178|gb|DN218151.1|DN218151
EST:     GTGTGGTCACTGCAAGAGTCTTGCACCG                         ACGTATGAGAAGGTGGCTTCTGTTTTCAAGTTGGATGAAGGAGTTGTTATT
genomic: GTGTGGTCACTGCAAGAGTCTTGCACCGgttagtacat ... attgtttcagACGTATGAGAAGGTGGCTTCTGTTTTCAAGTTGGATGAAGGAGTTGTTATT
EST: gi|37398024|gb|CF636321.1|CF636321
EST:     GTGTGGTCACTGCAAGAGTCTTGCACCG                         ACGTATGAGAAGGTGGCTTCTGTTTTCAAGTGGGATGAAGGAGTTGTTATT
genomic: GTGTGGTCACTGCAAGAGTCTTGCACCGgttagtacat ... attgtttcagACGTATGAGAAGGTGGCTTCTGTTTTCAAGTTGGATGAAGGAGTTGTTATT
EST: gi|71311893|gb|DR792421.1|DR792421
EST:     GTGTGGTCACTGCAAGAGTCTTGCACCG                         ACGTATGAGAAGGTGGCTTCTGTTTTCAAGTTGGATGAAGGAGTTGTTATT
genomic: GTGTGGTCACTGCAAGAGTCTTGCACCGgttagtacat ... attgtttcagACGTATGAGAAGGTGGCTTCTGTTTTCAAGTTGGATGAAGGAGTTGTTATT
EST: gi|4874414|gb|AI673934.1|AI673934
EST:     TGGTGTGGTCACTGCAAGAGTCTTGCACCG                         ACGTATGAGAAGGTGGCTTCTGTTTTCAAGTTGGATGAAGGAGTTGTTATT
genomic: TGGTGTGGTCACTGCAAGAGTCTTGCACCGgttagtacat ... attgtttcagACGTATGAGAAGGTGGCTTCTGTTTTCAAGTTGGATGAAGGAGTTGTTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttggcgatcttcatcatttctgatatgtctaatcataatctttattgtttcagACGTATGAGAAGGTGGCTTCTGTTTTCAAGTTGGATGAAGGAGTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAA
                            gtctaat  putative branch site (score: 3)
                                        tctttatt  putative PPT
                               taatcataatctttat  TA-rich tract