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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCGCCACCTAATCCATCGCCATCTCTTGCGTCTGCACCAGTCTTGAGCCCAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAGgtatactgttctgtttattttatttcgatgtatgatttgaatgcattgttcttttttctgattacgaggatgtgcaattattttattgttgggtttgaat...

Basic information

species Zea mays
transcript GRMZM2G144618_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144618_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g14580.1 (Oryza sativa), 5'ss of exon 7
TCCGCCACCTAATCCATCGCCATCTCTTGCGTCTGCACCAGTCTTGAGCCCAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAGgtatactgttctgtttattttatttcgatgtatgatttgaatgcattg-ttcttttttctgattacgaggatgtgcaattattttattgttgggtttgaat--
||||||||| |||||||| ||||||||||| || ||||| || |  ||||||| |||||| ||||| |||||| | ||||||||||| || ||||| ||||||| |||   |    ||||     |  |  |||||||   |   |||  |||      | | |     ||||   ||||   |||  | |    ||||    
TCCGCCACCAAATCCATCCCCATCTCTTGCATCAGCACCGGTGTACAGCCCAGTACTGTCCAGAGAAAAAGTCAGGGATGCATTACTTAGGCTTGTTGAGgtatgctgcaatagcaatttatgcacatttcatgatttatctttgttggctctcagagttaaattttgtgatg---aattgagttaaggcttcaattgaggca
















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|211239982|gb|FL466682.1|FL466682
EST:     CAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAG                         AACGATGAATTCATAGATTTAGTCTACGGCGAGATCATGAACAGACAGTAA
genomic: CAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAGgtatactgtt ... tttgtgccagAACGATGAATTCATAGATTTAGTCTACGGCGAGATCATGAACAGACAGTAA
EST: gi|78023716|gb|DV492103.1|DV492103
EST:     CAACACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAG                         AACGATGAATTCATAGATTTAGTCTACGGCGAGATCATGAACAGACAGTAA
genomic: CAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAGgtatactgtt ... tttgtgccagAACGATGAATTCATAGATTTAGTCTACGGCGAGATCATGAACAGACAGTAA
EST: gi|71443862|gb|DR824912.1|DR824912
EST:     CAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAG                         AACGATGAATTCATAGATTTAGTTTACGGCGAGATCATGAACAGACAGTAA
genomic: CAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAGgtatactgtt ... tttgtgccagAACGATGAATTCATAGATTTAGTCTACGGCGAGATCATGAACAGACAGTAA
EST: gi|50322551|gb|CO517677.1|CO517677
EST:     CAGCACTGTTTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAG                         AACGATGAATTCATAGATTTAGTTTACGGCGAGATCATGAACAGACAGTAA
genomic: CAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAGgtatactgtt ... tttgtgccagAACGATGAATTCATAGATTTAGTCTACGGCGAGATCATGAACAGACAGTAA
EST: gi|211242203|gb|FL466683.1|FL466683
EST:     CAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAG                         AACGATGAATTCATAGATTTAGTCTACGGCGAGATCATGAACAGACAGTAA
genomic: CAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAGgtatactgtt ... tttgtgccagAACGATGAATTCATAGATTTAGTCTACGGCGAGATCATGAACAGACAGTAA
EST: gi|5268916|gb|AI770880.1|AI770880
EST:     CAACACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAG                         AACGATGAATTCATAGATTTAGTCTACGGNGAGATCATGAACAGACAGTAA
genomic: CAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAGgtatactgtt ... tttgtgccagAACGATGAATTCATAGATTTAGTCTACGGCGAGATCATGAACAGACAGTAA
EST: gi|71760852|gb|DR958789.1|DR958789
EST:     CAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAG                         AACGATGAATTCATAGATTTAGTTTACGGCGAGATCATGAACAGACAGTAA
genomic: CAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAGgtatactgtt ... tttgtgccagAACGATGAATTCATAGATTTAGTCTACGGCGAGATCATGAACAGACAGTAA
EST: gi|37401707|gb|CF638221.1|CF638221
EST:     CAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAG                         AACGATGAATTCATATATTTAGTCTACCGCGAGATCATGAACAGACAGTAA
genomic: CAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAGgtatactgtt ... tttgtgccagAACGATGAATTCATAGATTTAGTCTACGGCGAGATCATGAACAGACAGTAA
EST: gi|76286409|gb|DV025977.1|DV025977
EST:     CAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAG                         AACGATGAATTCATAGATTTAGTTTACGGCGAGATCATGAACAGACAGTAA
genomic: CAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAGgtatactgtt ... tttgtgccagAACGATGAATTCATAGATTTAGTCTACGGCGAGATCATGAACAGACAGTAA
EST: gi|71762856|gb|DR960793.1|DR960793
EST:     CAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAG                         AACGATGAATTCATAGATTTAGTTTACGGCGAGATCATGAACAGACAGTAA
genomic: CAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAGgtatactgtt ... tttgtgccagAACGATGAATTCATAGATTTAGTCTACGGCGAGATCATGAACAGACAGTAA
EST: gi|94476180|gb|EB705138.1|EB705138
EST:     CAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAG                         AACGATGAATTCATAGATTTAGTTTACGGCGAGATCATGAACAGACAGTAA
genomic: CAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAGgtatactgtt ... tttgtgccagAACGATGAATTCATAGATTTAGTCTACGGCGAGATCATGAACAGACAGTAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCGCCACCTAATCCATCGCCATCTCTTGCGTCTGCACCAGTCTTGAGCCCAGCACTGTCTAGAGACAAAGTCCGAGATGCATTACTGAGACTTGTGGAGgtatactgttctgtttattttatttcgatgtatgatttgaatgcattgttcttttttctgattacgaggatgtgcaattattttattgttgggtttgaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG