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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAAATGAAATCACAAGGAACAAAGAAAGCTACAAGGATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAGgtcagctagaggtttactgccttttcttcattatctatatccctactgggcttgtttaaactggattgctttactaacag

Basic information

species Zea mays
transcript GRMZM2G030902_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030902_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g71770.1 (Oryza sativa), 5'ss of exon 6
GAAGAAATGAAATCACAAGGAACAAAGAAAGCTACAAGGATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAGgtcagctagaggtttactgccttttcttcattatctatatcccta-------------ctgggcttgtttaaa--------ctggattgctttactaacag
||||||||||||||||| ||| |||| || ||||| || |||||||||||||||||||| ||||| ||||| ||||| ||||||||||||| ||||| || || | | |||||| ||||  |   |  || ||              | | |||||  ||||           ||    |||| | | ||
GAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAGgtaagctatagcttcagt-ccttttgttcagcactcagttcacttatcagttgaatatccgagcttgcataaagactctaatcagaacattttattgatag
















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|148936779|gb|EC880917.2|EC880917
EST:     ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAG                         GCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
genomic: ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAGgtcagctaga ... ttactaacagGCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
EST: gi|22545757|gb|BU098131.1|BU098131
EST:     ATATTTGTTGCTCGAATTCCACAGTCAGGGGACGAGTCGATGTTTCGTAG                         GCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
genomic: ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAGgtcagctaga ... ttactaacagGCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
EST: gi|71769697|gb|DR967634.1|DR967634
EST:     ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAG                         GCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
genomic: ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAGgtcagctaga ... ttactaacagGCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
EST: gi|149096474|gb|EE182216.2|EE182216
EST:     ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAG                         GCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
genomic: ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAGgtcagctaga ... ttactaacagGCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
EST: gi|149000018|gb|EE037116.2|EE037116
EST:     ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAG                         GCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
genomic: ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAGgtcagctaga ... ttactaacagGCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
EST: gi|149104935|gb|EE290405.2|EE290405
EST:     ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAG                         GCATTTTTGA-GCTTTTGGAGAAATTCTTGATCTTTACATGCCCAAG
genomic: ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAGgtcagctaga ... ttactaacagGCATTTT-GAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
EST: gi|71304925|gb|DR788593.1|DR788593
EST:     ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAG                         GCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
genomic: ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAGgtcagctaga ... ttactaacagGCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
EST: gi|211138007|gb|FL213712.1|FL213712
EST:     ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAG                         GCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
genomic: ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAGgtcagctaga ... ttactaacagGCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
EST: gi|149080743|gb|EE169805.2|EE169805
EST:     ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAG                         GCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
genomic: ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAGgtcagctaga ... ttactaacagGCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
EST: gi|21432115|gb|BQ547605.1|BQ547605
EST:     ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAG                         GCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
genomic: ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAGgtcagctaga ... ttactaacagGCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
EST: gi|60350487|gb|DN217460.1|DN217460
EST:     ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAG                         GCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
genomic: ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAGgtcagctaga ... ttactaacagGCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
EST: gi|32847027|gb|CD986708.1|CD986708
EST:     ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAG                         GCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
genomic: ATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAGgtcagctaga ... ttactaacagGCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
EST: gi|26558086|gb|CA830321.1|CA830321
EST:     TTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAG                         GCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG
genomic: TTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAGgtcagctaga ... ttactaacagGCATTTTGAAGCTTTTGGAGAAATTCTTGATCTTTACATGCCAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAAATGAAATCACAAGGAACAAAGAAAGCTACAAGGATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAGgtcagctagaggtttactgccttttcttcattatctatatccctactgggcttgtttaaactggattgctttactaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA