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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAACCTCCTCCTCCGACCCTGCCGCCAAGAAGAAAGCCATCCCCCGCCGCGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACAgtatgtcatgctcctaactttctaatttatttatgctattgatttttcttttggatctatctcatcgtgtaaatatttacag

Basic information

species Oryza sativa
transcript LOC_Os08g45240.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g45240.4 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G016106_T01 (Zea mays), 5'ss of exon 1
GCAACCTCCTCCTCCGACCCTGCCGCCAAGAAGAAAGCCATCCCCCGCCGCGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACAgtatgtcatgctcctaact--ttctaatttatttatgct--attgatttttctt-------ttggatctatctcatcgtgtaaatatttacag
    ||    ||||||| ||  |  |||  |||||  |||||||||||||||| ||||| ||||||||||||||||| |||||||| |||||||| || ||||  | |     || | |  |||   ||  ||| || |  || |||    |||       |||  | | ||||| |   |||  |||| |||
AACGCCAGGCCCTCCGATCCCTCTACCAGCAAGAAGCCCATCCCCCGCCGCGCTGCCGGACAATCCTGGGAGGATCCTACCCTCACTGACTGGCCTGAAAgtagctaacataacttattaattcagtttcctttgtgtttaatggatcacccttatttggtttgcttgtgtctcaactcctaacaatttgcag

upper sequence: LOC_Os08g45240.4 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G068255_T01 (Zea mays), 5'ss of exon 1
GCAACCTCCTCCTCCGACCCTGCCGCCAAGAAGAAAGCCATCCCCCGCCGCGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACAgtatgtcatgctcctaactttctaattta-----------tttatgctattgattt--ttcttttggatctatctcatcgtgtaaatatttacag
    ||     |||||| ||  |  |||  |||||  |||||||||| ||||| ||||| ||||||||||||||||| |||||||| || |||||||| |||| |       | |||| |  ||||  |           ||||||||  |   ||  ||| |||   | | | ||| |   |||  |||| |||
AACGCCAGGCTCTCCGATCCCTCTACCAGCAAGAAGCCCATCCCCCGTCGCGCTGCCGGACAATCCTGGGAGGATCCTACCCTCACTGAATGGCCCGAAAgta-gcagccaacataacctattaatccagtttcctttgttttatgcttctcccttatttcatttccttgtgtttcaactcttaacaatttgcag
















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|33684393|gb|CF312632.1|CF312632
EST:     CGCCGCCGGCCAATTCTGGGAGGATCCCACCCTCACCGACTGGCCCGACA                         ATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG
genomic: CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACAgtatgtcatg ... atatttacagATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG
EST: gi|58599191|gb|CK009719.1|CK009719
EST:     CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACA                         ATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG
genomic: CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACAgtatgtcatg ... atatttacagATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG
EST: gi|88368173|gb|CI575055.1|CI575055
EST:     CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGAGTGGCCCGACA                         ATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG
genomic: CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACAgtatgtcatg ... atatttacagATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG
EST: gi|88742490|gb|CI765998.1|CI765998
EST:     CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCAACGACTGGCCCGACA                         ATGACTATCGCTTATTTGGTGGAGAT
genomic: CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACAgtatgtcatg ... atatttacagATGACTATCGCTTATTTTGTGGAGAT
EST: gi|38475426|gb|CF959559.1|CF959559
EST:     CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACA                         ATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG
genomic: CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACAgtatgtcatg ... atatttacagATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG
EST: gi|86829522|gb|CI286725.1|CI286725
EST:     CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACA                         ATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG
genomic: CGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACAgtatgtcatg ... atatttacagATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAACCTCCTCCTCCGACCCTGCCGCCAAGAAGAAAGCCATCCCCCGCCGCGCCGCCGGCCAATCCTGGGAGGATCCCACCCTCACCGACTGGCCCGACAgtatgtcatgctcctaactttctaatttatttatgctattgatttttcttttggatctatctcatcgtgtaaatatttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT