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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaccctttgatctgctagagtaagtttcatgatgcaacacatcagtagttaagaattatcctaattatccagttattgatagaattcattttatgaagGTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACAAAAGATGCAACAGATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTT

Basic information

species Oryza sativa
transcript LOC_Os01g64650.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G178244_T01 (Zea mays), 3'ss of exon 2
atgaccctttgatctgctagagtaagtttcatgatgcaacacatcagtagttaagaattatccta-attatccagttattgatagaattcattttatgaagGTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACAAAAGATGCAACAGATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTT---------
 ||      | |      ||  |   |    |     ||  | ||| |  ||   | |     ||    || ||| | ||||||  ||  |||| |||||||| ||||| || |||||||||||||| |||||||| |||||| |||||||   ||||| |||          ||||||||| ||||| ||||||| || |         
-tgggtaactaactgagcagtctttatccactatcaaaatgcttcacttctttgtagtccctttatgagattcagatgttgatatgatggatttcatgaagGTTCTTGATGAGTACCAGAAGGCTTTTGGGGACTCCTGGAAATCTGCTACTGCAGATGGAAC---------TCAACAGTGGGCTTTCCTGACAGACGCCTTGGCAAGAT
















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|218482998|gb|FG956126.1|FG956126
EST:     TTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG                         GTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACA
genomic: TTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAGgtatgagcct ... ttttatgaagGTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACA
EST: gi|4879970|gb|AU064269.1|AU064269
EST:     TATGGATGATCACTATCCTGTACGA-GTGCAATTTTCTCTTCTGAATAAG                         GTACTTGACGAATACCAGAAGGTTTTCGGGGACT
genomic: TATGGATGATCACTATCCTGTACGAAGTGCA-TTTTCTCTTCTGAATAAGgtatgagcct ... ttttatgaagGTACTTGACGAATACCAGAAGGCTTTCGGGGACT
EST: gi|27578119|gb|CB000814.1|CB000814
EST:     TTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG                         GTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACA
genomic: TTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAGgtatgagcct ... ttttatgaagGTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtagttaagaattatcctaattatccagttattgatagaattcattttatgaagGTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACAAAAGATGCAACAGATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTT
                                         ttcatttt  CT-rich tract
                             ttattgatagaattca  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgaccctttgatctgctagagtaagtttcatgatgcaacacatcagtagttaagaattatcctaattatccagttattgatagaattcattttatgaagGTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACAAAAGATGCAACAGATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG