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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACATGGATCTCCTTCGCTCTCATCTCCACAAGGTCCGGATCCCCGAGCCAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCGgtaacaaccgtgccccaccccgtcccgttcctcaactccgactcgattcgttagggctagggtctgaggcgacttggatttgtttgcttgcgtgggcgcag

Basic information

species Zea mays
transcript GRMZM2G107696_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107696_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g08200.1 (Oryza sativa), 5'ss of exon 1
GGACATGGATCTCCTTCGCTCTCATCTCCACAAGGTCCGGATCCCCGAGCCAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCGgtaa------caaccgtgc-----cccaccccgtcccgttcctcaactccgactcgattcgttagggctagggtctgaggcgacttggatttgtttgcttgcgtgggcgcag
|| |||||||||||| ||||| || |||||||||||||| ||||| |||||   || ||||||||||||||||||||||||||||||||||||||| |||||||      |||||   |     |||||||   ||   ||| |  || ||    | ||   ||||| |||||| |     |||   |||||    |               
GGCCATGGATCTCCTCCGCTCGCACCTCCACAAGGTCCGCATCCCGGAGCCCGGCAGCCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACCCCGgtaaaccaaccaaccacccacccacccacccacgccttgtcccccccttcgctctggtttcctagggttagggttt----tgacgccgatttcgccgtgcag----------

upper sequence: GRMZM2G107696_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA12G22240.1 (Glycine max), 5'ss of exon 1
GGACATGGATCTCCTTCGCTCTCATCTCCACAAGGTCCGGATCCCCGAGCCAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCGgtaacaaccgtgccccaccccgtcccgttcctcaactc-cgactcgattcgttagggctagggtctgaggcgacttggatttgtttgcttgcgtgggcgcag--
   | ||||| | || |||||  |||||  |  ||| ||||||||||| || ||||| |||||| ||||| |||| |||||||| || |||||| ||||||| |      |  |    | |||   ||||   || |   || | |  | ||| |    |   ||        ||| ||||  | |  ||   |          
ACCCTTGGATTTGCTCCGCTCCAATCTCTCCCGGGTTCGGATCCCCGAACCCACCAATCGCATCTACAAGCACGAATGCTGCGTTTCGTTCGACTCTCCGgtgatg--tttttcttctctcgtatagttctggaaatgatgaattg--ttgtttgaaacaacttcgtgttgttcttcgattgttctaatttgataattcttctt

upper sequence: GRMZM2G107696_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA06G39770.1 (Glycine max), 5'ss of exon 1
GGACATGGATCTCCTTCGCTCTCATCTCCACAAGGTCCGGATCCCCGAGCCAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCGgtaacaaccgtgccccaccccgtcccgttcctcaactccgactcgattc-gttagggctagggtctgaggcgacttggatttgtttgcttgcgtgggcgcag--
    |||||| | || |||||  |||||  |  ||| ||||||||||| || ||||| |||||| ||||| |||| |||||| | ||||||||| ||||||| |      |  |      |||   ||||   || |  || |   ||  ||| |  | ||  ||        |||  |||  | |  ||  ||          
----ATGGATTTGCTCCGCTCCTATCTCTCCCGGGTTCGGATCCCCGAACCCACCAATCGCATCTACAAGCACGAATGCTGCATTTCCTTCGACTCTCCGgtgatg--tttttcttctttcgtatagttctagaaat--gattaatttttgtttgaaccagcttcgtgtcgttcttccattgttctaatttggtttttcttctt

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|22489369|gb|BU049292.1|BU049292
EST:     CAACCANCCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCG                         AGGTCAGAGGGAGGTCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
genomic: CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCGgtaacaaccg ... gtgggcgcagAGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
EST: gi|211002367|gb|FL015700.1|FL015700
EST:     CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCG                         AGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
genomic: CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCGgtaacaaccg ... gtgggcgcagAGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
EST: gi|149014868|gb|EE044579.2|EE044579
EST:     CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCG                         AGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
genomic: CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCGgtaacaaccg ... gtgggcgcagAGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
EST: gi|17970241|gb|BM277005.1|BM277005
EST:     CGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCG                         AGGTCAGAGGGAGGTCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
genomic: CGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCGgtaacaaccg ... gtgggcgcagAGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
EST: gi|76924845|gb|DV170158.1|DV170158
EST:     CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCG                         AGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
genomic: CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCGgtaacaaccg ... gtgggcgcagAGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
EST: gi|87298812|gb|DY470815.1|DY470815
EST:     CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGCCACTCCG                         AGGTCAGAGGGAGGTCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
genomic: CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCGgtaacaaccg ... gtgggcgcagAGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
EST: gi|148962640|gb|EE013533.2|EE013533
EST:     CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCG                         AGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
genomic: CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCGgtaacaaccg ... gtgggcgcagAGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
EST: gi|18385124|gb|BM418323.1|BM418323
EST:     AACCAACCGCATCCACAAGGACGAGTGCTGCTGTCTCCTTCGACACTCCG                         AGGTCAGAGGGAGGTCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
genomic: AACCAACCGCATCCACAAGGACGAGTGCTGC-GTCTCCTTCGACACTCCGgtaacaaccg ... gtgggcgcagAGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
EST: gi|31363710|gb|CD448067.1|CD448067
EST:     CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCG                         AGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
genomic: CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCGgtaacaaccg ... gtgggcgcagAGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
EST: gi|32804639|gb|CD956875.1|CD956875
EST:     CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCG                         AGGTCAGAGGGAGGTCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
genomic: CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCGgtaacaaccg ... gtgggcgcagAGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
EST: gi|50331231|gb|CO526357.1|CO526357
EST:     CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCG                         AGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
genomic: CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCGgtaacaaccg ... gtgggcgcagAGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
EST: gi|148944899|gb|EC890058.2|EC890058
EST:     CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCG                         AGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
genomic: CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCGgtaacaaccg ... gtgggcgcagAGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
EST: gi|149109487|gb|EE190226.2|EE190226
EST:     CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCG                         AGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG
genomic: CAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCGgtaacaaccg ... gtgggcgcagAGGTCAGAGGGAGGCCTGTACGTGGACATGGTCTCGTTCCTGGGGTTCGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACATGGATCTCCTTCGCTCTCATCTCCACAAGGTCCGGATCCCCGAGCCAACCAACCGCATCCACAAGGACGAGTGCTGCGTCTCCTTCGACACTCCGgtaacaaccgtgccccaccccgtcccgttcctcaactccgactcgattcgttagggctagggtctgaggcgacttggatttgtttgcttgcgtgggcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC