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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTGgtaaatcccctcacagaatcacaaccaaaccttcgaaaatcttctaatctgtttcttccatctgatagtcaaaatagctaattgttcaccactgaaattt...

Basic information

species Oryza sativa
transcript LOC_Os02g10480.3
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10480.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G138349_T03 (Zea mays), 5'ss of exon 8
AAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTGgtaa---atcccctcacagaatcacaac-caaaccttcgaaaatcttctaatctgtttcttccatctgatagtcaaaatagctaattgttcac-cactgaaattt------------------------------
||||| ||||| || || ||||| | ||||||||| ||||||||||| |||||||| |||||||||||||| |||||||| || ||||| || |||||||   |   |  ||       | | | || ||  |   | ||  |   ||||   | ||     |   | | |  ||  | | |||  ||  | ||   ||                                
AAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAAGAACTGAAGCTCTCTGTTCCCCAGCAATATGGACCTCTGAAGCTGgtaatgaactacaccattactatatatcacatacagtaacagataatgccatctaaattttgagggtcccaataattatgccaacttgaacaaaccctttgatccgttctttcactcacgcaacaatgaaagcag

upper sequence: LOC_Os02g10480.3 (Oryza sativa), 5'ss of exon 9
lower sequence: AT4G21160.4 (Arabidopsis thaliana), 5'ss of exon 7
AAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTGgtaaatcccctcacagaatcacaaccaaaccttcgaaaatcttctaatctgtttcttccatctgatagtcaaaatagctaattgttcaccactgaaattt------
|| || ||| |  | ||  | ||   |||| | |||||||||||||| || ||||||| |||||||||||||||  | || ||| |  | ||| |||||||           |       | ||   ||| ||||||     |  |  | ||        ||  | | |  || |  |   | ||   | |  |||      
AAGGCTCAATCTACTGTAGTGAAGAGCAACTTAAACCCTGTCTGGAATGAGGAACTCATGCTCTCTGTTCCTCATAACTATGGCTCAGTGAAATTGgtaaa-----------agcttggtctaatatttccaaaatc-----actttctactcttgatgaatcattacagaagtttttcccttacattttatgtttttgcag
















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|29645547|gb|CB650554.1|CB650554
EST:     ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG                         CAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
genomic: ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTGgtaaatcccc ... ttggatgcagCAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
EST: gi|86862468|gb|CI345545.1|CI345545
EST:     ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG                         CAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
genomic: ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTGgtaaatcccc ... ttggatgcagCAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
EST: gi|9866250|gb|AU102000.1|AU102000
EST:     ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG                         CAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
genomic: ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTGgtaaatcccc ... ttggatgcagCAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
EST: gi|88904257|gb|CI001990.1|CI001990
EST:     ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG                         CAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
genomic: ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTGgtaaatcccc ... ttggatgcagCAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
EST: gi|88246217|gb|CI246066.1|CI246066
EST:     CTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG                         CAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
genomic: CTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTGgtaaatcccc ... ttggatgcagCAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
EST: gi|88729941|gb|CI753162.1|CI753162
EST:     ACGAAGAACTCAAGCTCTCTGGTCCTCAGCAATACGGCCCTCTCAAACTG                         CAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
genomic: ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTGgtaaatcccc ... ttggatgcagCAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
EST: gi|86531246|gb|CI171452.1|CI171452
EST:     ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG                         CAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
genomic: ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTGgtaaatcccc ... ttggatgcagCAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
EST: gi|88218270|gb|CI218119.1|CI218119
EST:     CAGCAATACGGCCCTCTCAAACTG                         CAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
genomic: CAGCAATACGGCCCTCTCAAACTGgtaaatcccc ... ttggatgcagCAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
EST: gi|13806102|gb|AU181353.1|AU181353
EST:     ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG                         CAAGTGTTNGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
genomic: ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTGgtaaatcccc ... ttggatgcagCAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
EST: gi|88828823|gb|CI073693.1|CI073693
EST:     GCCCTCTCAAACTG                         CAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
genomic: GCCCTCTCAAACTGgtaaatcccc ... ttggatgcagCAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
EST: gi|86862016|gb|CI330640.1|CI330640
EST:     ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG                         CAAGTGTTCGACCACAACATGCTTTCCAA-GACGACCTGATGGGGGAGGCC
genomic: ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTGgtaaatcccc ... ttggatgcagCAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
EST: gi|29657516|gb|CB653791.1|CB653791
EST:     ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG                         CAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
genomic: ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTGgtaaatcccc ... ttggatgcagCAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
EST: gi|86507268|gb|CI149901.1|CI149901
EST:     ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG                         CAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGNCC
genomic: ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTGgtaaatcccc ... ttggatgcagCAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
EST: gi|86502666|gb|CI145299.1|CI145299
EST:     ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG                         CAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
genomic: ACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTGgtaaatcccc ... ttggatgcagCAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
EST: gi|88989405|gb|CI043884.1|CI043884
EST:     CGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG                         CAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC
genomic: CGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTGgtaaatcccc ... ttggatgcagCAAGTGTTCGACCACGACATGCTGTCCAAGGACGACCTGATGGGGGAGGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTGgtaaatcccctcacagaatcacaaccaaaccttcgaaaatcttctaatctgtttcttccatctgatagtcaaaatagctaattgttcaccactgaaattt

- - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT