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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTATTCTTATGGAGTATATTGGCAAGGATGACTCAAACATTCGTATTGGAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaactagtgcttataattgtgtcttactgcctcataatttggtgttgttttgttaatcagtactgtttctaattttcag

Basic information

species Zea mays
transcript GRMZM2G155384_T03
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155384_T03 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 5'ss of exon 16
TGCTATTCTTATGGAGTATATTGGCAAGGATGACTCAAACATTCGTATTGGAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaactagtgcttataattgtgtcttactgcctcataatttggtgttgttttgttaatcagtac-tgtt-tct-aattttcag
||||||||| |||||||| |||  |||||||||| |||||||||| ||||| ||||| ||||||||||| ||||||||||| ||||| |||||||| |||||||||  ||    || | ||| |||  |  | |   | ||     | |   | ||||   ||  || || | ||| || ||||||
TGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGGATTGGGGCAATCTTGGGTCTTGGTATTGCATATGCGGGTTCTCAGAAAGAGGAGgtgggatttaagaattgttattctgtgcttttacaaaaaaaaacattttctatatgttccacataacctgctatctgaaatttcag

upper sequence: GRMZM2G155384_T03 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 16
TGCTATTCTTATGGAGTATATTGGCAAGGATGACTCAAACATTCGTATTGGAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaactagtgcttataattgtgtcttactgcctcataatttggtgttgttttgttaatca-gtactgtttctaattttcag-----------------------------------
 ||  ||||    || ||||| |  || || ||| |    ||  | ||||| |||||  ||||| | |||||||||||||||||||||||||| ||  |||||     |  | ||   ||||   | ||     ||  | | |   | || |||  | |   |  || |  ||   |||| ||                                    
GGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAATCAGGATTGGTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAGgtgttctgtttttctctaaatt---ttttgaaatcttgttagt-aatattatttgttgagatacatattacttactatttgcaaatgcattttttaaaatatattcttgcttctttcag

upper sequence: GRMZM2G155384_T03 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA12G13410.1 (Glycine max), 5'ss of exon 16
TGCTATTCTTATGGAGTATATTGGCAAGGATGACTCAAACATTCGTATTGGAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaactagtgcttataattgt-----gtcttact-gcctcataatttggtgttgtt--ttgttaatcagtactgtttctaattttcag--------------------
 ||  ||||    || ||||| |  || || ||| |    |   | ||||| |||||  ||||| | |||||||||||||||||||||||||| ||  |||||     |  | ||   | || |      ||||  | |    ||||| ||   |   |  ||  || |    | |||    | |||| |                     
GGCACTTCTAGGTGACTATATAGATAAAGAAGACACTTCAACAAGGATTGGTGCAATTATGGGTTTGGGAATTGCATATGCTGGTTCCCAGAATGAGCAGgtgttctgtttttctctaatttctttgaaatcttgttagtaatataatatgagatacatacttactatttgcaaatgtaaaaagtttttaatttattctcgtttctttcag

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|32940220|gb|CF045039.1|CF045039
EST:     GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAG                         CTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG
genomic: GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaacta ... taattttcagCTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG
EST: gi|32943723|gb|CF048542.1|CF048542
EST:     GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAG                         CTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG
genomic: GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaacta ... taattttcagCTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG
EST: gi|32929231|gb|CF034043.1|CF034043
EST:     GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAG                         CTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG
genomic: GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaacta ... taattttcagCTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG
EST: gi|32848175|gb|CD987856.1|CD987856
EST:     GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAG                         CTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG
genomic: GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaacta ... taattttcagCTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG
EST: gi|32928692|gb|CF033504.1|CF033504
EST:     GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAG                         CTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG
genomic: GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaacta ... taattttcagCTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTATTCTTATGGAGTATATTGGCAAGGATGACTCAAACATTCGTATTGGAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaactagtgcttataattgtgtcttactgcctcataatttggtgttgttttgttaatcagtactgtttctaattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG