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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGGGCCGGAGACCGACCAGGGCACGGTGGACAAGATCAGGGAGGCCATCAGGGAGCAGAAGGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCGgtaatgctccaaactctggacacgaatccctctcttgaactggatagatattgagattttagatgatatacagtagtactgttggatgatgtagaagctctgatgattttgtctgattttggattgttgtgtgatcag

Basic information

species Oryza sativa
transcript LOC_Os04g23890.3
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23890.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G032351_T01 (Zea mays), 5'ss of exon 6
CAAGGGCCGGAGACCGACCAGGGCACGGTGGACAAGATCAGGGAGGCCATCAGGGAGCAGAAGGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCGgtaatgctccaaactctggacacgaatccctct---cttgaactggatagatattgagattttagatgatatacagtagtactgttggatgatgtagaagctctgatgattttgtctgattttggattgttgtg---tgatcag
|||||||| |||||||||  |  ||| || || |||||| |||| || ||| |||| ||||| || ||||| ||||||||||||||||||||||||||||||||   |    | | |   |   ||  |       | ||| |     |  | ||   |   ||||   ||  || || ||    ||  |||||| |  ||| |    | |     |  | |  |||||||||    ||| |||
CAAGGGCCAGAGACCGACATGTCCACAGTTGATAAGATCCGGGAAGCTATCCGGGAACAGAAAGAAATCACTGTCCAGCTAATCAACTACACCAAGAGCGgtaa-attttgcattttaaccggaaaaactagaaagcatgagcaattgaccttttcctaccatagagtttagtcaata-tatgtatgattgatgtgggtgctatatatactgatatttttctacgattgttgttcattgaccag
















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|29612810|gb|CB617823.1|CB617823
EST:     CAGGGAGCAGAAGGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCG                         GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG
genomic: CAGGGAGCAGAAGGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCGgtaatgctcc ... gtgtgatcagGGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG
EST: gi|14571435|gb|BI118803.1|BI118803
EST:     CAGGGAGCGGAAGGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCG                         GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG
genomic: CAGGGAGCAGAAGGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCGgtaatgctcc ... gtgtgatcagGGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG
EST: gi|29666947|gb|CB663222.1|CB663222
EST:     CAGGGAGCAGAAGGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCG                         GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG
genomic: CAGGGAGCAGAAGGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCGgtaatgctcc ... gtgtgatcagGGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG
EST: gi|58587914|gb|CF986222.1|CF986222
EST:     GGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCG                         GGAAGAAGTTCTGGAACTGGTGCCACCTTCAACCCATGCGCGACCAGAAG
genomic: GGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCGgtaatgctcc ... gtgtgatcagGGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG
EST: gi|29615865|gb|CB620877.1|CB620877
EST:     CAGGGAGCAGAAGGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCG                         GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG
genomic: CAGGGAGCAGAAGGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCGgtaatgctcc ... gtgtgatcagGGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG
EST: gi|29686409|gb|CB682684.1|CB682684
EST:     CAGGGAGCAGAAGGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCG                         GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG
genomic: CAGGGAGCAGAAGGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCGgtaatgctcc ... gtgtgatcagGGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG
EST: gi|29680789|gb|CB677064.1|CB677064
EST:     CAGGGAGCAGAAGGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCG                         GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG
genomic: CAGGGAGCAGAAGGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCGgtaatgctcc ... gtgtgatcagGGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG
EST: gi|29613843|gb|CB618856.1|CB618856
EST:     CAGGGAGCAGAAGGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCG                         GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG
genomic: CAGGGAGCAGAAGGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCGgtaatgctcc ... gtgtgatcagGGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG
EST: gi|29646469|gb|CB651476.1|CB651476
EST:     CAGGGAGCAGAAGGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCG                         GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG
genomic: CAGGGAGCAGAAGGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCGgtaatgctcc ... gtgtgatcagGGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGGGCCGGAGACCGACCAGGGCACGGTGGACAAGATCAGGGAGGCCATCAGGGAGCAGAAGGAGATCACGGTCCAGCTAATCAACTACACCAAGAGCGgtaatgctccaaactctggacacgaatccctctcttgaactggatagatattgagattttagatgatatacagtagtactgttggatgatgtagaagctctgatgattttgtctgattttggattgttgtgtgatcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA