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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCACTGTTGTGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctctccactaacacttgtgtttggaatctctatccaacattttctaatattgcattgtcattccag

Basic information

species Zea mays
transcript GRMZM2G107639_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107639_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g08270.4 (Oryza sativa), 5'ss of exon 7
GGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCACTGTTGTGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctctc--------------cactaacacttgtgtttggaatctctatccaacattttctaatattgcattgtcattccag
||||||||||||| |||||||  | ||||||||||||||||| | |||||| ||||| || ||||||||||||||||| ||||| | ||| ||||| || || | || ||||              |||  |||||||  || |   |  || |  |  ||||  ||||||||||   |  ||||||
GGAGAAGGTTCTGCAAGAAAACAACCCTATCCCTAAACTTGTTAGTGTTGTAAATCCTGGAAACCCCTCTGGAGCTTTCATTCCGAAGCCGATGCTCGAAgtaacctgtctctctcattcacagttcacgcacacttgcattcgaggtgact-ttaattatttcttaatattgcaccattgttccag
















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|148932368|gb|EC876010.2|EC876010
EST:     TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
genomic: TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
EST: gi|67030337|gb|CO459086.1|CO459086
EST:     TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACNAT
genomic: TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
EST: gi|149037081|gb|EE155270.2|EE155270
EST:     TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
genomic: TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
EST: gi|76286951|gb|DV026519.1|DV026519
EST:     TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTTGACA-
genomic: TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTT-GACAA
EST: gi|148963140|gb|EE014107.2|EE014107
EST:     TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
genomic: TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
EST: gi|67011573|gb|CO440322.1|CO440322
EST:     TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
genomic: TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
EST: gi|148950038|gb|EC895570.2|EC895570
EST:     TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCNAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCA
genomic: TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCA
EST: gi|149112179|gb|EE295100.2|EE295100
EST:     GAATCCGGGGAACCCCTCTGGAGCTTTTATTCTCA-GGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
genomic: GAATCCGGGGAACCCCTCTGGAGCTTTTATTC-CAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
EST: gi|149084340|gb|EE173781.2|EE173781
EST:     TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGGTGACAAT
genomic: TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
EST: gi|148947797|gb|EC893285.2|EC893285
EST:     TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
genomic: TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
EST: gi|50325408|gb|CO520534.1|CO520534
EST:     TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
genomic: TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCACTGTTGTGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctctccactaacacttgtgtttggaatctctatccaacattttctaatattgcattgtcattccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT