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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGATGAAACTCTTCTTCCCGAGCTTGAGGCAGATGTTAGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAGgtaatcattaacttcgcctttctttgtttgtcttgccatcatacaagagctggagtgtaaaatggaactgcttgtgtgtagcatgttttggatccattat...

Basic information

species Oryza sativa
transcript LOC_Os04g41910.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41910.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G353114_T01 (Zea mays), 5'ss of exon 13
GCCGATGAAACTCTTCTTCCCGAGCTTGAGGCAGATGTTAGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAGgtaatcattaacttcgcctttctttgtttgtcttgccatcatacaagagctggagtgtaaaatggaactgcttgtgtgtagcatgttttggatccattat-
|| ||||||   |||||| | ||||||||||| ||||||||||| |||||||| ||| ||||||  || |||||||||||||||  | | | |  |   | | |   ||| |  ||   |  |     |    || | | |       ||        | | | | |    | | || ||  
GCTGATGAAGAGCTTCTTTCTGAGCTTGAGGCTGATGTTAGAGAGGAATGCATCAAGTTTGGTCTGGTGGATAATGTCAAGgtacacctaacccccagatatatagtttttttgtgaacttgtctggaaaacaga-tctgaccaaccgctttccaaaggaaacttctcaccgtttcagtaac

upper sequence: LOC_Os04g41910.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G074351_T01 (Zea mays), 5'ss of exon 11
GCCGATGAAACTCTTCTTCCCGAGCTTGAGGCAGATGTTAGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAGgtaatcattaacttcgcctttctttgtttgtcttgccatcatacaagagctggagtgtaaaatggaactgcttgtgtgtagcatgttttggatccattat------
|| ||||||   |||||| | ||||||||| | ||||||||||| |||||||| ||| ||||||| || |||||||||||||||  | |||||  |   | | |   ||| |  ||   |  |     |    || |         |||||| | ||   | ||   ||   |||  ||        
GCTGATGAAGAGCTTCTTTCTGAGCTTGAGACTGATGTTAGAGAGGAATGCATCAAGTTTGGTCCTGTGGATAATGTCAAGgtacac-ttaaccccagatatatagcttttttgtgaacttgtctggaaaacagatttggcc----aactgcatttg-aaaacagacttctcatcagttcaagaaat

upper sequence: LOC_Os04g41910.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G084716_T01 (Zea mays), 5'ss of exon 11
GCCGATGAAACTCTTCTTCCCGAGCTTGAGGCAGATGTTAGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAGgtaatcattaacttcgcctttctttgtttgtcttgccatcatacaagagctggagtgtaaaatggaactgcttgtgtgtagcatgttttggatccattat-
|| ||||||   ||||||   ||||||||||| ||||||||||| |||||||| ||| ||||||  || |||||||||||||||  | | | |  ||  | | |   ||| |  ||   |  |     |    || | | |        |        | | | | |    | | || ||  
GCTGATGAAGAGCTTCTTTTTGAGCTTGAGGCTGATGTTAGAGAGGAATGCATCAAGTTTGGTCTGGTGGATAATGTCAAGgtacacctaacccccggatatatagtttttttgtgaacttgtctggaaaacaga-tctgaccaaccgttttccaaaggaaacttctcaccgtttcagtaac

upper sequence: LOC_Os04g41910.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G074351_T02 (Zea mays), 5'ss of exon 10
-------------------GCCGATGAAACTCTTCTTCCCGAGCTTGAGGCAGATGTTAGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAGgtaatcattaacttcgcctttctttgtttgtcttgccatcatacaagagctggagtgtaaaatggaactgcttgtgtgtagcatgttttggatccattat------
                   || ||||||   |||||| | ||||||||| | ||||||||||| |||||||| ||| ||||||| || |||||||||||||||  | |||||  |   | | |   ||| |  ||   |  |     |    || |         |||||| | ||   | ||   ||   |||  ||        
AACCAATAATATCCTTCAGGCTGATGAAGAGCTTCTTTCTGAGCTTGAGACTGATGTTAGAGAGGAATGCATCAAGTTTGGTCCTGTGGATAATGTCAAGgtacac-ttaaccccagatatatagcttttttgtgaacttgtctggaaaacagatttggcc----aactgcatttg-aaaacagacttctcatcagttcaagaaat

upper sequence: LOC_Os04g41910.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G411893_T01 (Zea mays), 5'ss of exon 10
------------------GCCGATGAAACTCTTCTTCCCGAGCTTGAGGCAGATGTT-AGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAGgtaatcattaacttcgcctttctttgtttgtcttgccatcatacaagagctggagtgtaaaatggaactgcttgtgtgtagcatgttttggatccattat-
                  || ||||||   |||||| | ||||||||||| ||| || ||||| |||||||| ||| ||||||  || |||||||||||||||  | | | |  ||  | | |   ||| |  ||   |  |     |    || | | |       ||        | | | | |      |  | ||  
ACCGATAATATCCCGCAGGCTGATGAAGAGCTTCTTTCTGAGCTTGAGGCTGATTTTTAGAGAGGAATGCATCAAGTTTGGTCTGGTGGATAATGTCAAGgtacacctaacccccggatatatagtttttttgtgaacttgtctggaaaacaga-tctgaccaaccgctttccaaaggaaacttctcaccattttagtaac

upper sequence: LOC_Os04g41910.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G171660_T02 (Zea mays), 5'ss of exon 11
GCCGATGAAACTCTTCTTCCCGAGCTTGAGGCAGATGTTAGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAGgtaatcattaacttcgcctttctttgtttgtcttgccatcatacaagagctggagtgtaaaatggaactgcttgtgtgtagcatgttttggatccattat-
|| ||||||   |||||||| ||||||||||| ||||||||||| |||||||| ||| ||||||| || |||||||||||||||  | | | |  ||  | | |   ||| |  ||   |  |     |    || | | |       ||        | | | | |    | | || ||  
GCTGATGAAGAGCTTCTTCCTGAGCTTGAGGCTGATGTTAGAGAGGAATGCATCAAGTTTGGTCCGGTGGATAATGTCAAGgtacacctaacccccggatatatagtttttttgtgaacttgtctggaaaacaga-tctgaccaaccgctttccaaaggaaacttctcaccgtttcagtaac

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|88225768|gb|CI225684.1|CI225684
EST:     TTGATAATGTCAAG                         GTCTGTG-AAATCATCCAGAGGGTGTTATTTTGGTGAAATTCAAAGACCGG
genomic: TTGATAATGTCAAGgtaatcatta ... ctgcttgcagGTCTGTGAAAATCATCCAGAGGGTGTTATTTTGGTGAAATTCAAAGACCGG
EST: gi|89176352|gb|CI043373.1|CI043373
EST:     CAGATGTTAGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAG                         GTCTGTGAAAATCATCCAGAGGGTGTTATTTTGGTGAAATTCAAAGACCGG
genomic: CAGATGTTAGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAGgtaatcatta ... ctgcttgcagGTCTGTGAAAATCATCCAGAGGGTGTTATTTTGGTGAAATTCAAAGACCGG
EST: gi|29616209|gb|CB621221.1|CB621221
EST:     CAGATGTCAGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAG                         GTCTGTGAAAATCATCCAGAGGGTGTTATTTTGGTGAAATTCAAAGACCGG
genomic: CAGATGTTAGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAGgtaatcatta ... ctgcttgcagGTCTGTGAAAATCATCCAGAGGGTGTTATTTTGGTGAAATTCAAAGACCGG
EST: gi|86887329|gb|CI313232.1|CI313232
EST:     ATGTTAGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAG                         GTCTGTGAAAATCATCCAGAGGGTGTTATTTTGGTGAAATTCAAAGACCGG
genomic: ATGTTAGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAGgtaatcatta ... ctgcttgcagGTCTGTGAAAATCATCCAGAGGGTGTTATTTTGGTGAAATTCAAAGACCGG
EST: gi|29636734|gb|CB641743.1|CB641743
EST:     CAGATGTTAGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAG                         GTCTGTGAAAATCATCCAGAGGGTGTTATTTTGGTGAAATTCAAAGACCGG
genomic: CAGATGTTAGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAGgtaatcatta ... ctgcttgcagGTCTGTGAAAATCATCCAGAGGGTGTTATTTTGGTGAAATTCAAAGACCGG
EST: gi|27549049|gb|CA766863.2|CA766863
EST:     CAGATGTCAGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAG                         GTCTGTGAAAATCATCCAGAGGGTGTTATTTTGGTGAAATTCAAAGACCGG
genomic: CAGATGTTAGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAGgtaatcatta ... ctgcttgcagGTCTGTGAAAATCATCCAGAGGGTGTTATTTTGGTGAAATTCAAAGACCGG
EST: gi|88961566|gb|CI096841.1|CI096841
EST:     GCTTGGTCCAGTTGATAATGTCAAG                         GTCTGTGAAAATTATCCAGAGGGTGTTATTTTGGTGAAATTCAAAGACCGG
genomic: GCTTGGTCCAGTTGATAATGTCAAGgtaatcatta ... ctgcttgcagGTCTGTGAAAATCATCCAGAGGGTGTTATTTTGGTGAAATTCAAAGACCGG
EST: gi|29676261|gb|CB672536.1|CB672536
EST:     CAGATGTTAGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAG                         GTCTGTGAAAATCATCCAGAGGGTGTTATTTTGGTGAAATTCAAAGACCGG
genomic: CAGATGTTAGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAGgtaatcatta ... ctgcttgcagGTCTGTGAAAATCATCCAGAGGGTGTTATTTTGGTGAAATTCAAAGACCGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGATGAAACTCTTCTTCCCGAGCTTGAGGCAGATGTTAGAGAAGAATGCATGAAGCTTGGTCCAGTTGATAATGTCAAGgtaatcattaacttcgcctttctttgtttgtcttgccatcatacaagagctggagtgtaaaatggaactgcttgtgtgtagcatgttttggatccattat

- - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC