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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtctggaacctttctatctaattgcatttactttcttgagttcaacaattttaaaaataatattccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG

Basic information

species Zea mays
transcript GRMZM2G064023_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 16
gtccgtctggaacctttctatctaattgcatttactttcttgagttcaacaattttaaaaataa--tattccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
||  ||||  |  ||  ||   |   |   || | |  |      |||| |   || | |   |  ||| |  || ||||| |||||||| |||||||| || ||||| |||||||||||||| || |||
gttagtctaaattctagctgcatggctctcttcagtcccactgtctcaataggatttatatcgacctatcctctttcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 16
gtccgtctggaacctttctatctaattgcatttactttcttg-agttcaacaattttaaaaataatatt-----------ccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
||  ||||  ||  | ||| || || |||||   || ||||| ||| |||| || | |     | | ||            | |  ||||| |||||||| |||||||| || ||||| |||||||||||||| || |||
gttagtctaaaa--tgtctgtccaactgcatg-gctctcttgcagtccaactatctcattgggattcttatcgatctatatcctgtcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCAATCCTCACTGAGCTTGGCAAG
















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|211314254|gb|FK994154.1|FK994154
EST:     CCGAGGATCCACTTTTCCAACTG                         GTGTCCTTTTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: CCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|6020672|gb|AW065480.1|AW065480
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|5847106|gb|AW000185.1|AW000185
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|67022591|gb|CO451340.1|CO451340
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|32859372|gb|CD999053.1|CD999053
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|71450119|gb|DR831169.1|DR831169
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|4776524|gb|AI665527.1|AI665527
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|76284364|gb|DV023932.1|DV023932
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|6952534|gb|AW424602.1|AW424602
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|31361873|gb|CD446230.1|CD446230
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
EST: gi|149082724|gb|EE171942.2|EE171942
EST:     AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTG                         GTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctgg ... tccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattgcatttactttcttgagttcaacaattttaaaaataatattccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG
 atctaat  putative branch site (score: 3)
                                            ttccgtt  putative PPT
                 ttgagttcaacaattt  TA-rich tract