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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCACCACGCAGGCTTTTCTCCCCTAAGGCAGCAGCCCCTAAATCAGGGGATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccatcattctgatctcatttgtatgaggatttttgtcctcggttcttttttgtttttgctaatgtgtttgctatactgtgtttttgttaacag

Basic information

species Zea mays
transcript GRMZM2G038848_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038848_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g42110.1 (Oryza sativa), 5'ss of exon 3
TTCACCACGCAGGCTTTTCTCCCCTAAGGCAGCAGCCCCTAAATCAGGGGATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccatc---------attctg-------atctcatttgtatgaggattttt-------gtcctcggttcttttttgttt--ttgctaatgtgtttgctatactgtgtttttgttaacag
|||||| |  |  |    ||| || ||| || |||    ||||||||||||     | |||||||| || ||||| ||||||||||||||||||||||||||||   ||           |||| |       |  || ||  ||||      |||       |   ||  | || ||| |||   |||||||||||||      | |   |||   ||  |||
TTCACCGCAGAAACAGCACTCTCCCAAGACATCAGGAGTTAAATCAGGGGAGGAGGTGCGCATTGCGGTTCTAGGTGCCAGCGGTTATACTGGAGCTGAGgttgctacactctttctcctattccggctcaccacttctttgatatggtcccatttcattgaagatttctatcctctttggttcgattgctaatgtgttca----aatacatttgcattggcag

upper sequence: GRMZM2G038848_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g35170.1 (Oryza sativa), 5'ss of exon 3
TTCACCACGCAGGCTTTTCTCCCCTAAGGCAGCAGCCCCTAAATCAGGGGATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccatcattctgatctcatttgtatgaggatttttgtcctcggttcttt--------tttgtttttgctaatgtgtttgctatactgtgtttttgttaacag
||||||||  |  || | |||  ||||| || ||     ||||||||||||     | |  ||||| || ||||||||||| |||||||||||||||||||| || ||||  |   |   |  ||   ||   | || ||||  |    |  |         ||  |||   | |||||  |||  || ||||  || ||       
TTCACCACAGAAACTATACTCTTCTAAGACAACACAAGTTAAATCAGGGGAGGAGGTGCAGATTGCGGTTCTAGGGGCCAGTGGTTATACTGGAGCTGAGgtagttccattttatcgtgttatttccaattgcgtttgttgttgttatcttatacaagtgggttcctttcaacgaatgtacttgtaattctgttcttatg-------
















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|91878697|gb|EB408654.1|EB408654
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|211345290|gb|FL126063.1|FL126063
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|211345286|gb|FL126059.1|FL126059
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|211345287|gb|FL126060.1|FL126060
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCASCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|211345285|gb|FL126058.1|FL126058
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|30705270|gb|CD058727.1|CD058727
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|71448245|gb|DR829295.1|DR829295
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|211345293|gb|FL126066.1|FL126066
EST:     AT-CCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|148946555|gb|EC884293.2|EC884293
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
EST: gi|148942779|gb|EC887806.2|EC887806
EST:     ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAG                         ATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT
genomic: ATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccat ... ttgttaacagATTGTTCGGATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCACCACGCAGGCTTTTCTCCCCTAAGGCAGCAGCCCCTAAATCAGGGGATTCCATACGCATTGCAGTGCTAGGGGCCAGCGGTTATACTGGAGCTGAGgttgtcccatcattctgatctcatttgtatgaggatttttgtcctcggttcttttttgtttttgctaatgtgtttgctatactgtgtttttgttaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA