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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtacagttccacgagaaatattattaattgtttgggttttggtatgtcaggacatccttgatcaacttacttggttgtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG

Basic information

species Oryza sativa
transcript LOC_Os02g05630.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 2
----gtactgtacagttccacgagaaatattattaatt-gtttgggttttggtatgtcag--------gacatccttgatcaacttactt----ggt--------------tgtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG
    ||| ||   |||  ||   |||||  ||| ||||   |||| | ||   ||| |||        ||   | |||||    | ||||    |||              |||   | |||| || || ||||   |||| ||||| || || |||||||| ||||||||||||||||| || || ||||||||||||| ||||| |||| ||||||| |
gtatgtattgcctagtgacatctgaaatcatatcaattcagttggttcttctaatgccagcgctccacgatggcattgatattttcacttataaggtgagcatgttttttctgtttctgtagGTCACGGAGGAGTCAGAGCAGCTGAGTACGTTAAGCAGCATCTTTTCAGCAATTTAATCAAACACCCAAAGTTCATCACTGATACCAAGGCCGCTATTG

upper sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G829894_T02 (Zea mays), 3'ss of exon 1
----gtactgtacagttccacgagaaatattattaattgtttgggttttggta-tgtcaggacatccttgatcaacttacttg-----gttgtaca------------------------tatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG
    ||| |    ||   ||   ||| |  ||| ||||     ||||||  || || ||  || ||  |||| || ||  | |     ||||||                          | |||| ||||| ||||  ||||| ||||| ||||| |||||||||||||||||||||||||| || || ||||||||||||| ||||| |||| | |||||||
gtatgtattcgctagcgacatctgaagtgatatcaattcccgcggttttcctaatgccaccac-tctctgatgaagttggtagtttgagttgtaaggttgagggcatggttttctgtttctgtagGTCATGGAGGAGTCCGAGCAGCTGAGTATGTTAAGCAGCACCTTTTCAGCAATTTAATCAAACACCCAAAGTTCATCACTGATACCAAGGCTGCTATCG

upper sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 3
----gtactgtacagttccacgagaaatattattaattgtttgggttttggt-----atgtcaggacatccttgatcaacttacttggttgtacatat-agGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG
    || | |  |      | | |   ||   || || | | | | ||         || | ||   || ||||   |   | || |  ||    | | ||| ||||| || |||||||| ||||||||||| || ||  ||||||| || ||||| || | |||||||||||||||   |||||  || || ||||| |
ccatgtgccgctcgcaaatatgggtt-tagctttgatagatcgagcttccaatgtcaatattagataatgcttgcgtattcttctggtatggttgtctcagGTCATGGAGGTGCTCGAGCAGCTGAATATGTTAAACAAAACCTTTTTAGTAATTTGATCAGGCATCCAAAGTTCATTTCTGATACAAAATCAGCTATAG

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|29688008|gb|CB684283.1|CB684283
EST:     AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACG                         GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
genomic: AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtaca ... gtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
EST: gi|5803440|gb|AI978410.1|AI978410
EST:     AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACG                         GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
genomic: AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtaca ... gtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
EST: gi|29668036|gb|CB664311.1|CB664311
EST:     AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACG                         GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
genomic: AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtaca ... gtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
EST: gi|58670044|gb|CK058730.1|CK058730
EST:     AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACG                         GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
genomic: AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtaca ... gtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
EST: gi|33680351|gb|CF308590.1|CF308590
EST:     AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACG                         GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
genomic: AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtaca ... gtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
EST: gi|88445125|gb|CI589603.1|CI589603
EST:     AATCGATGGTGTTGATGGAGAGAC-ATTGGATTATTTGGCGTATTCGACG                         GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
genomic: AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtaca ... gtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
EST: gi|33675133|gb|CF303372.1|CF303372
EST:     AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGTCGTATTCGACG                         GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
genomic: AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtaca ... gtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
EST: gi|29686520|gb|CB682795.1|CB682795
EST:     AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACG                         GCCATGGCGGATCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
genomic: AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtaca ... gtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
EST: gi|5003494|gb|AU068643.1|AU068643
EST:     AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACG                         GCCATGGCGGA-CTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
genomic: AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtaca ... gtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
EST: gi|218495837|gb|FG960245.1|FG960245
EST:     GGCGTA-TCGACG                         GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAATGCAGCACCTTATTCAG
genomic: GGCGTATTCGACGgtactgtaca ... gtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAA-GCAGCACCTT-TTCAG
EST: gi|44671917|gb|CR285351.1|CR285351
EST:     AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACG                         GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
genomic: AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtaca ... gtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
EST: gi|29662047|gb|CB658322.1|CB658322
EST:     AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACG                         GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
genomic: AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtaca ... gtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgggttttggtatgtcaggacatccttgatcaacttacttggttgtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG
                                aacttac  putative branch site (score: 2)
                                              tacatata  TA-rich tract