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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAATGTTGAAAAGCTCAAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAGgtgtttatgcttctaaatttattcaagatgacctatcaacagttctgcagagctttactttctatttagtgcgttttgctttgtgttagcacatatgttt...

Basic information

species Zea mays
transcript GRMZM2G001887_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G001887_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g34180.1 (Oryza sativa), 5'ss of exon 2
ATGAATGTTGAAAAGCTCAAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAGgtgtttat-gcttctaaatttat--tca--agatgacctatcaacagttctgcagagctttactttctatttagtgcgttttgctttgtgttagcacatatgttt
||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||   |  || ||||     ||  | | | | |||  |  |||       |||   | || | |||  | | |||| |||| |||| |   |       
ATGAATGTTGACAAGCTCAAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAGgtgtgtattattattatatttgcaaccagcatacggcatattgatggttacatgtggctgcccattgtgtttgattcatttttctttatgttgggctagt-----
















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|60394804|gb|DN227674.1|DN227674
EST:     AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|60339434|gb|DN206407.1|DN206407
EST:     GCGCACCGGGGGGAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: GCGCACCGGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|22819814|gb|BU499904.1|BU499904
EST:     AGAAGATGGCAGGTGCTGTGCGCACCNNNNNNNAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: AGAAGATGGCAGGTGCTGTGCGCACC-GGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|78087437|gb|DV515830.1|DV515830
EST:     AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|27522108|gb|CA989214.1|CA989214
EST:     AGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: AGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|161593981|gb|EY965119.1|EY965119
EST:     CGGGGGGAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: CGGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|21760021|gb|BQ635562.1|BQ635562
EST:     AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|71427873|gb|DR808923.1|DR808923
EST:     AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|211207058|gb|FL397903.1|FL397903
EST:     AGAAGATGGCAGGTGCTGTGCGCACCNNNNNNNAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: AGAAGATGGCAGGTGCTGTGCGCACC-GGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|60401056|gb|DN233863.1|DN233863
EST:     AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|211381842|gb|FL377370.1|FL377370
EST:     AGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: AGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|60342382|gb|DN209355.1|DN209355
EST:     AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|6918526|gb|AW400056.1|AW400056
EST:     ATGGCAGGTGCTGTGCGCACC-GGGGGAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: ATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|47962818|gb|CN845527.1|CN845527
EST:     GGGAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: GGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|7031231|gb|AW461119.1|AW461119
EST:     CCGGGGGGAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: CCGGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|45567234|gb|CK985471.1|CK985471
EST:     AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|149014130|gb|EE043671.2|EE043671
EST:     AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|9794276|gb|BE552584.1|BE552584
EST:     AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACATACGGCTTCA
genomic: AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|211269426|gb|FK963247.1|FK963247
EST:     AAGAAGATGGCAGGTGCTGTGCGCACCGTGGGGAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|9794715|gb|BE553023.1|BE553023
EST:     GCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: GCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|21843331|gb|BQ703912.1|BQ703912
EST:     AGAAGATGGCAGGTGCTGTGCGCACCNNNNNNNAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: AGAAGATGGCAGGTGCTGTGCGCACC-GGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
EST: gi|149017495|gb|EE045693.2|EE045693
EST:     AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA
genomic: AAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAGgtgtttatgc ... ttggtggcagGAAGAAGAAGGCAGTCCACAAGACTACAACCACAGATGACAAACGGCTTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAATGTTGAAAAGCTCAAGAAGATGGCAGGTGCTGTGCGCACCGGGGGGAAGGGTAGCGTGCGCAGgtgtttatgcttctaaatttattcaagatgacctatcaacagttctgcagagctttactttctatttagtgcgttttgctttgtgttagcacatatgttt

- - - - - - - - - AAGAAG
- - - - - - - - - -  AAGATG