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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATTATCAGATTGATGATTTACTCACCACTGAAGAGCAGTCTATCAGGAAGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACGgtatgtcaattccgaaacaagtatgtttctggcattattgcatccttgaagtttttgcctatcatgtaaaccacagtaaacttgacctcctttatggaat...

Basic information

species Oryza sativa
transcript LOC_Os01g06600.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g06600.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G862219_T02 (Zea mays), 5'ss of exon 3
CTATTATCAGATTGATGATTTACTCACCACTGAAGAGCAGTCTATCAGGAAGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACGgtatgtcaattccgaaacaagtatgtttctggcattattgcatccttg---aagtttttgcctatcatgtaaaccacagtaaacttgacctcctttatggaat
 ||||| |||  ||||||||| || |||| ||||||||  |||||||||| ||| ||||||| ||| ||||| ||||||||||| ||||||||| || |||||||| || |  ||    | ||  | ||||  | | ||   |  |     ||||  ||||| |  |||     ||   | |   |  | |  |   | | ||
TTATTACCAGTCTGATGATTTGCTGACCAGTGAAGAGCGCTCTATCAGGATGAAGGTCAGGGGTATTATGGAAAAAGAAATTGCTCCCATTATGTCAGCGgtatgttaaattggag--tattaactatctgaaactgtttgcttatgacataagtcattgccaaatatgctt-tcatttttataataccttgttagtttgcat
















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|2312322|gb|C28477.1|C28477
EST:     AGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACG                         TACTGGGAGAAAGCAGAGTTCCCATTTCATGCCATTCCTAAACTTTCAAGC
genomic: AGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACGgtatgtcaat ... gctactgcagTACTGGGAGAAAGCAGAGTTCCCATTTCATGCCATTCCTAAACTTTCAAGC
EST: gi|29666427|gb|CB662702.1|CB662702
EST:     AGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACG                         TACTGGGAGAAAGCAGAGTTCCCATTTCATGCCATTCCTAAACTTTCAAGC
genomic: AGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACGgtatgtcaat ... gctactgcagTACTGGGAGAAAGCAGAGTTCCCATTTCATGCCATTCCTAAACTTTCAAGC
EST: gi|29666426|gb|CB662701.1|CB662701
EST:     AGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACG                         TACTGGGAGAAAGCAGAGTTCCCATTTCATGCCATTCCTAAACTTTCAAGC
genomic: AGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACGgtatgtcaat ... gctactgcagTACTGGGAGAAAGCAGAGTTCCCATTTCATGCCATTCCTAAACTTTCAAGC
EST: gi|29676104|gb|CB672379.1|CB672379
EST:     AGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACG                         TACTGGGAGAAAGCAGAGTTCCCATTTCATGCCATTCCTAAACTTTCAAGC
genomic: AGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACGgtatgtcaat ... gctactgcagTACTGGGAGAAAGCAGAGTTCCCATTTCATGCCATTCCTAAACTTTCAAGC
EST: gi|58666043|gb|CK054729.1|CK054729
EST:     AGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACG                         TACTGGGAGAAAGCAGAGTTCCCATTTCATGCCATTCCTAAACTTTCAAGC
genomic: AGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACGgtatgtcaat ... gctactgcagTACTGGGAGAAAGCAGAGTTCCCATTTCATGCCATTCCTAAACTTTCAAGC
EST: gi|11863268|gb|AU063379.2|AU063379
EST:     AGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACG                         TACTGGGAGAAAGCAGAGTTCCCATTTCATGCCATTCCTAAACTTTCAAGC
genomic: AGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACGgtatgtcaat ... gctactgcagTACTGGGAGAAAGCAGAGTTCCCATTTCATGCCATTCCTAAACTTTCAAGC
EST: gi|29666428|gb|CB662703.1|CB662703
EST:     AGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACG                         TACTGGGAGAAAGCAGAGTTCCCATTTCATGCCATTCCTAAACTTTCAAGC
genomic: AGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACGgtatgtcaat ... gctactgcagTACTGGGAGAAAGCAGAGTTCCCATTTCATGCCATTCCTAAACTTTCAAGC
EST: gi|29678764|gb|CB675039.1|CB675039
EST:     AGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACG                         TACTGGGAGAAAGCAGAGTTCCCATTTCATGCCATTCCTAAACTTTCAAGC
genomic: AGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACGgtatgtcaat ... gctactgcagTACTGGGAGAAAGCAGAGTTCCCATTTCATGCCATTCCTAAACTTTCAAGC
EST: gi|33675069|gb|CF303308.1|CF303308
EST:     AGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACG                         TACTGGGAGAAAGCAGAGTTCCCATTTCATGCCATTCCTAAACTTTCAAGC
genomic: AGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACGgtatgtcaat ... gctactgcagTACTGGGAGAAAGCAGAGTTCCCATTTCATGCCATTCCTAAACTTTCAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATTATCAGATTGATGATTTACTCACCACTGAAGAGCAGTCTATCAGGAAGAATGTCAGGGCTATAATGGAGAAAGAAATTGCACCCATTATGGCAACGgtatgtcaattccgaaacaagtatgtttctggcattattgcatccttgaagtttttgcctatcatgtaaaccacagtaaacttgacctcctttatggaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA