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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACCAGGAACCCCGTGGATGGCTTCTCGGCTGGTCTAGTCGATGATAGCAACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttggaagccatgacgcggcggctcgctgccgtgggcctttactttgtgctacccgggacgagttttcattttgctttgtttgggctagggagag...

Basic information

species Chlamydomonas reinhardtii
transcript EDP03036
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP03036 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: LOC_Os05g38550.2 (Oryza sativa), 5'ss of exon 2
TCACCAGGAACCCCGTGGATGGCTTCTCGGCTGGTCTAGTCGATGATAGCAACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttggaagccatgacgcggcggctcgctgccgtgggcct-ttactttgtg--ctacccgggacgagttttcattttgctttgtttgggctagggagag
|| | | ||||||||||||||| |||||||| || || || || ||||||||||||||||||||||||||||||||||| || || || || || || |||||||||      |||  || |  |  ||    || | | |  |  |  |||||         ||     |  |     | ||  ||||| |  || |     
TCGCGAAGAACCCCGTGGATGGGTTCTCGGCGGGGCTTGTGGACGATAGCAACGTGTTCGAGTGGCAGGTCACCATCATCGGCCCGCCCGATACCCTGTAgtaagttcaattcccac-accccccctctaatcgctgcgcgattgctggtttgtagatcgattggtttacgcctattcgtcgccgtgttttgattatgttt--

upper sequence: EDP03036 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: LOC_Os01g62244.1 (Oryza sativa), 5'ss of exon 2
TCACCAGGAACCCCGTGGATGGCTTCTCGGCTGGTCTAGTCGATGATAGCAACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttggaagccatgacgcggcg--gctcgctgccgtgggcc-tttactttgtgc-tacccgggacgagttt-tcattttgctttgtttgggctagggagag
|| | | | ||||||||||||| |||||||||||  ||||||| || |||||||| ||||||||||||||||| ||||| || || || || || || |||| |||| |     |    |    ||  ||  ||| || ||   | | | | |  | | |   |  | |  |    |    ||  || || |   |  |      
TCGCGAAGCACCCCGTGGATGGGTTCTCGGCTGGGTTAGTCGACGACAGCAACGTCTTCGAGTGGCAGGTCACAATCATCGGCCCGCCTGACACCCTATAgtgagttggattctctctccaattcgatgcatgcttccatgaatcatctgcctcatccgtgttcatgccatgcgagtggagttttttcgtgtatacccgc-----

upper sequence: EDP03036 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: GRMZM2G007300_T02 (Zea mays), 5'ss of exon 2
TCACCAGGAACCCCGTGGATGGCTTCTCGGCTGGTCTAGTCGATGATAGCAACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttggaagccatgacgcggcggctcgctgccgtgggcctttactttgtgctacccgggacgagttttcattttgctttgtttgggctagggagag--
|| ||| | |||| |||||||| ||||||||||| || ||||| ||||| ||||| ||||||||||||||||||||||| || || || || || || |||| |||| |||  |||  ||    ||  |  || |||||     |     ||   | |  |      || |   |      |  | ||| ||| |  |    
TCGCCAAGCACCCGGTGGATGGGTTCTCGGCTGGGCTGGTCGACGATAGTAACGTATTCGAGTGGCAGGTCACCATCATCGGCCCGCCCGATACCCTATAgtgagtt-ggatcccaccacttcacgcgtt-cttccgtgccttgtcgaaatgaattgcttgtttgttgtgtctgtgccatgtcctatggactatgatggtgt

upper sequence: EDP03036 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: GRMZM2G007276_T03 (Zea mays), 5'ss of exon 2
TCACCAGGAACCCCGTGGATGGCTTCTCGGCTGGTCTAGTCGATGATAGCAACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttggaagccatgacgcggcggctcgctgccgtgggcctttactttgtgctacccgggacgagttttcattttgctttgtttgggctagggagag-
|  | | ||||||||||||||| ||||| || || || || || ||||||||||| ||||||||||||||||||||||| || || || || || || |||| |||| | |    | ||  |             |  ||                                                             
TTGCGAAGAACCCCGTGGATGGGTTCTCCGCAGGGCTTGTAGACGATAGCAACGTCTTCGAGTGGCAGGTCACCATCATCGGCCCGCCCGACACCCTATAgtgagttcg-agtttacgaatcaagcttgaatcatcccggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn

upper sequence: EDP03036 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: GRMZM2G085600_T03 (Zea mays), 5'ss of exon 2
TCACCAGGAACCCCGTGGATGGCTTCTCGGCTGGTCTAGTCGATGATAGCAACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttggaagccatgacgcggcggctcgctgccgtgggcctttactttgtgctacccgggacgagttttcattttgctttgtttgggctagggagag-
|| | | | |||| |||||||| ||||| ||||| || ||||| || ||||| || ||||||||||||||||||||||| || || || || || || |||| |||  |     |   |       ||  ||| || ||     | |   ||   | |  |      || |   |    |      ||| ||| |  |   
TCGCGAAGCACCCGGTGGATGGGTTCTCTGCTGGGCTGGTCGACGACAGCAATGTCTTCGAGTGGCAGGTCACCATCATCGGACCGCCTGACACCCTATAgtgagtcagatcctctccatttca-agcgtgcttccatgccttgtcaagatgaattgcttgtttgttgtgtcggtgccacgagcaatggactacgatggtg

upper sequence: EDP03036 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: GRMZM2G012052_T01 (Zea mays), 5'ss of exon 2
TCACCAGGAACCCCGTGGATGGCTTCTCGGCTGGTCTAGTCGATGATAGCAACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttggaa-------gccatgacgcggcggctcg-ctgccgtgggcctttactttgtgctacccgggacgagttttcattttgcttt---gtttgggctagggagag
|  | | ||||||||||||||| ||||| || || || || || || |||||| | ||||||||||||||||||||||| || || || || || || |||| |||| | |        ||  |     | | || |   |||  | ||  | ||  ||||   |  |  || | ||   ||   |  |||   |||  || |        
TTGCGAAGAACCCCGTGGATGGGTTCTCCGCCGGGCTTGTAGACGACAGCAACATCTTCGAGTGGCAGGTCACCATCATCGGACCGCCTGACACCCTATAgtgagttcgaattttgcctgctctatactgactgcacaattgctcttgggatatagattgt---atgcttgatgggtgcgcaaagtcgtttcaggttcaggtt--------

upper sequence: EDP03036 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: GRMZM2G434519_T01 (Zea mays), 5'ss of exon 2
TCACCAGGAACCCCGTGGATGGCTTCTCGGCTGGTCTAGTCGATGATAGCAACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttggaagccatgacgcggcggctcgctgccgtgggcctttactttgtgctacccgggacgagttttcattttgctttgtttgggctagggagag-
|| | | | |||| |||||||| |||||  |||| || ||||| || ||||| || ||||||||||||||||||||||| || || || || || || |||| |||  |     |   |       ||  ||| || ||     | |   ||   | |  |      || |   |           ||| ||| |  |   
TCTCGAAGCACCCGGTGGATGGGTTCTCTACTGGGCTGGTCGACGACAGCAATGTCTTCGAGTGGCAGGTCACCATCATCGGACCGCCTGACACCCTATAgtgagtcagatcctctccatttca-agcgtgcttccatgccttgtcaagatgaattgcttgtttgttgtgtcggtgcaatgagcaatggactacgatggtg

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|22072232|gb|BQ821570.1|BQ821570
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|10786718|gb|AV643390.1|AV643390
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|9458744|gb|BE452391.1|BE452391
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|10780562|gb|AV637242.1|AV637242
EST:     ACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: ACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCC-GGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|10790337|gb|AV627703.1|AV627703
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|15370119|gb|BI529545.1|BI529545
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|15369580|gb|BI529006.1|BI529006
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|22076740|gb|BQ825516.1|BQ825516
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|23365625|gb|BU653445.1|BU653445
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|14239428|gb|BG858244.1|BG858244
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|49463699|gb|BP091612.1|BP091612
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|6545148|gb|AV390932.1|AV390932
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|22054891|gb|BQ811579.1|BQ811579
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|10776972|gb|AV633652.1|AV633652
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|8576455|gb|BE128996.1|BE128996
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|22076252|gb|BQ825028.1|BQ825028
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|49469196|gb|BP097057.1|BP097057
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|49462955|gb|BP090868.1|BP090868
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|10770484|gb|AV621309.1|AV621309
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|22049970|gb|BQ809002.1|BQ809002
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|22068226|gb|BQ818165.1|BQ818165
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|10772869|gb|AV623692.1|AV623692
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|10126146|gb|BE724850.1|BE724850
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
EST: gi|10784030|gb|AV640702.1|AV640702
EST:     AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTA                         CGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA
genomic: AACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttgg ... gcccttgcagCGAGGGGGGATTCTTTAATGCGCGGCTGACGTTCCCTAAGGACTACCCCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACCAGGAACCCCGTGGATGGCTTCTCGGCTGGTCTAGTCGATGATAGCAACGTGTTCGAGTGGCAGGTCACCATCATTGGGCCCCCGGAGACACTCTAgtaagtttggaagccatgacgcggcggctcgctgccgtgggcctttactttgtgctacccgggacgagttttcattttgctttgtttgggctagggagag

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