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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGACATCCCGCCGGAGCAGCATGCGCTTGTGCCATCTTTTATGGGCGGCGGGGGAAAGAGGATCCACCCGCTTCCTTATGCGGATCCCAATCTACCTGgtgcgcacttgagttatgatcagctatttttttacttgtgatgttttatgaatagaatcagctaaaggtagttgtgctacag

Basic information

species Oryza sativa
transcript LOC_Os07g24190.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g24190.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G028353_T02 (Zea mays), 5'ss of exon 4
GATGACATCCCGCCGGAGCAGCATGCGCTTGTGCCATCTTTTATGGGCGGCGGGGGAAAGAGGATCCACCCGCTTCCTTATGCGGATCCCAATCTACCTGgtgcgcacttgagtt--atgatcagctatttt--tttacttgtgat----gttttatgaatagaatcagctaaaggtagttgtgctacag
||||||||||| ||||||||||| ||||| ||||| ||||| |||||||| ||||||||||| ||||| || || ||||||||||||||||   ||||||||  |   |||  ||  ||||||| |         ||| ||||| |    || |  |||||  | |  | ||| | | || ||| | |||
GATGACATCCCACCGGAGCAGCACGCGCTGGTGCCTTCTTTCATGGGCGGTGGGGGAAAGAGAATCCATCCCCTCCCTTATGCGGATCCCAGCTTACCTGgtatgtgtttggtttggatgatcatcagccaaaacttagttgtggtcatggtgtcctgaatgtacttggttaatgtttgtggtgttccag

upper sequence: LOC_Os07g24190.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G025231_T03 (Zea mays), 5'ss of exon 4
GATGACATCCCGCCGGAGCAGCATGCGCTTGTGCCATCTTTTATGGGCGGCGGGGGAAAGAGGATCCACCCGCTTCCTTATGCGGATCCCAATCTACCTGgtgcgcacttgagttatgatcagctatttttttacttgtgat----gttttatgaatagaatcagctaaaggtagttgtgctacag
||||||||||| ||||||||||| ||||| ||||| ||||| ||||| || |||||||||||||| || || |||||||||||||||||||   ||||||||  | |  ||  | || |||||| |     | | ||||| |    ||    |||||  ||     ||| ||| |||||| | |||
GATGACATCCCACCGGAGCAGCACGCGCTGGTGCCTTCTTTCATGGGTGGTGGGGGAAAGAGGATACATCCCCTTCCTTATGCGGATCCCAGCTTACCTGgtatgtatctggatgatcatcagccaaaacat-agttgtggtcatggtgccctgaatgtaactgattaacggttgttgtgttccag
















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|29680102|gb|CB676377.1|CB676377
EST:     CGGGGGAAAGAGGATCCACCCGCTTCCTTATGCGGATCCCAATCTACCTG                         TTCAACCAAGATCTATGGACCCATCCAAGGATCTTGCTGCATACGGTTATG
genomic: CGGGGGAAAGAGGATCCACCCGCTTCCTTATGCGGATCCCAATCTACCTGgtgcgcactt ... tgtgctacagTTCAACCAAGATCTATGGACCCATCCAAGGATCTTGCTGCATACGGTTATG
EST: gi|29681223|gb|CB677498.1|CB677498
EST:     CGGGGGAAAGAGGATCCACCCGCTTCCTTATGCGGATCCCAATCTACCTG                         TTCAACCAAGATCTATGGACCCATCCAAGGATCTTGCTGCATACGGTTATG
genomic: CGGGGGAAAGAGGATCCACCCGCTTCCTTATGCGGATCCCAATCTACCTGgtgcgcactt ... tgtgctacagTTCAACCAAGATCTATGGACCCATCCAAGGATCTTGCTGCATACGGTTATG
EST: gi|29676590|gb|CB672865.1|CB672865
EST:     CGGGGGAAAGAGGATCCACCCGCTTCCTTATGCGGATCCCAATCTACCTG                         TTCAACCAAGATCTATGGACCCATCCAAGGATCTTGCTGCATACGGTTATG
genomic: CGGGGGAAAGAGGATCCACCCGCTTCCTTATGCGGATCCCAATCTACCTGgtgcgcactt ... tgtgctacagTTCAACCAAGATCTATGGACCCATCCAAGGATCTTGCTGCATACGGTTATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGACATCCCGCCGGAGCAGCATGCGCTTGTGCCATCTTTTATGGGCGGCGGGGGAAAGAGGATCCACCCGCTTCCTTATGCGGATCCCAATCTACCTGgtgcgcacttgagttatgatcagctatttttttacttgtgatgttttatgaatagaatcagctaaaggtagttgtgctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT