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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAGTGCTCCTGGGAAAAGGGCTTCAATGGAGGATTTCTACGAGACGAGAATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtacagttccacgagaaatattattaattgtttgggttttggtatgtcaggacatccttgatcaacttacttggttgtacatatag

Basic information

species Oryza sativa
transcript LOC_Os02g05630.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g05630.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA06G06310.1 (Glycine max), 5'ss of exon 2
GCAAGTGCTCCTGGGAAAAGGGCTTCAATGGAGGATTTCTACGAGACGAGAATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtacagttccacgagaaatattattaattgtttgggttttggt--------atgtcaggacatccttgatc-aacttacttggt-tgtacatatag
|| ||  ||||||| || ||  |||||||||| ||||| || ||||| ||||| |||||||||||||| ||   | ||||  | || || || || || ||||   |    |    |        | ||    || |||     || |        ||| ||  | ||  |   |  |||| |     | ||| | | |  
GCTAGCTCTCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGATGGTGAAGTCGTTGGCCTTTTCGGAGTTTTTGATGgtatatttttatcttcctctcttcttcatctcctggttgtacactgattggaaaatatgccaaaatattgtacgtagaactcatgctatgtgttcttctg-

upper sequence: LOC_Os02g05630.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 5'ss of exon 3
GCAAGTGCTCCTGGGAAAAGGGCTTCAATGGAGGATTTCTACGAGACGAGAATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtacagttccacgagaaatattattaattgttt-------gggttttggtat--gtcaggacatccttgatcaacttacttggttgtacatatag-
|| ||| |||| ||||||||| |||||||||| ||||| || ||||| ||||| ||||||||||| |||||||   ||||  | ||||| || || || |||||| |    |||            |  ||    |             |   | ||  ||  | | || ||  ||  | |   |||||    | | ||  
GCTAGTTCTCCCGGGAAAAGGTCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGAAGGAGAGATAGTTGGCCTTTTTGGAGTCTTTGATGgtactctttctttctctttctctctcttctacccatcccccaacaacactcaagcataggtaggtagattctgcatgcagtc-tttggtgtagcttgtatc
















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|5003494|gb|AU068643.1|AU068643
EST:     AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACG                         GCCATGGCGGA-CTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
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|29639786|gb|CB644795.1|CB644795
EST:     AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACG                         GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
genomic: AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtaca ... gtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
EST: gi|58670044|gb|CK058730.1|CK058730
EST:     AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACG                         GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
genomic: AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtaca ... gtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
EST: gi|29666851|gb|CB663126.1|CB663126
EST:     AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACG                         GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
genomic: AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtaca ... gtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
EST: gi|29688008|gb|CB684283.1|CB684283
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|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|29640127|gb|CB645136.1|CB645136
EST:     AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACG                         GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
genomic: AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtaca ... gtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
EST: gi|29662047|gb|CB658322.1|CB658322
EST:     AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACG                         GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA
genomic: AATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtaca ... gtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAGTGCTCCTGGGAAAAGGGCTTCAATGGAGGATTTCTACGAGACGAGAATCGATGGTGTTGATGGAGAGACCATTGGATTATTTGGCGTATTCGACGgtactgtacagttccacgagaaatattattaattgtttgggttttggtatgtcaggacatccttgatcaacttacttggttgtacatatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA