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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGATGCGCGTGGTGATGCTGGGCCTGGACGCGGCAGGAAAGACCACCATCCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCGgtgagtcagagtatgatctaaagtctagaaacaaggttgggagtctgtctgcatgggcctctgtcacctggaacgggcccggtcccgaggcggaacgtgc...

Basic information

species Chlamydomonas reinhardtii
transcript EDP05355
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP05355 (Chlamydomonas reinhardtii), 5'ss of exon 1
lower sequence: LOC_Os10g42940.1 (Oryza sativa), 5'ss of exon 2
GAGATGCGCGTGGTGATGCTGGGCCTGGACGCGGCAGGAAAGACCACCATCCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCGgtgagtcagagtatgatctaaagtctagaaacaaggttgggagtctg--tctgcatgggcctctgtc--acctggaacgggcccggtcccgaggcggaacgtgc--
         ||||||||||| || || || || || || ||||||||||| ||||| ||||| ||||||||||| || ||| |||| || || ||||| |||  ||           |     ||      |    | |    | |   | ||  | |  |    ||  | |   | |   |    ||   |     | | |||  
---------GTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAGCTGCACATCGGCGAAGTTCTCTCCACCGTCCCCACTATAGgtaggttcactctcatccctccctccctccgcctcatcgaatcttttattttgttttgagccaaatccaaacccaacctaacatcatcatcatcatcatcatgcag

upper sequence: EDP05355 (Chlamydomonas reinhardtii), 5'ss of exon 1
lower sequence: LOC_Os02g47110.1 (Oryza sativa), 5'ss of exon 2
GAGATGCGCGTGGTGATGCTGGGCCTGGACGCGGCAGGAAAGACCACCATCCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCGgtgagtcagagtatgatctaaagtctagaaacaaggttgggagtctgtc-tgcatgggcctctgtcacctggaacg-ggcccggtcccgaggcggaacgtgc
         || |||||||| || ||||| || || || || ||||||||||| |||||||| |||||||| ||||| ||  | ||||| || || || |||  ||    |  |  | |   | | | |       ||  |    |||| |   || |    |   |  |  | |  |||         |  |    |  | 
---------GTCGTGATGCTTGGGCTGGATGCCGCGGGCAAAACCACCATCCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTGgtatgttgctgattactttgtcg-caatattttttttttcgctcatgtcctctgtgcgaaattcgaagttaaatcaaggctttacggttaaactagtcaag-

upper sequence: EDP05355 (Chlamydomonas reinhardtii), 5'ss of exon 1
lower sequence: PP1S37_304V6.1 (Physcomitrella patens), 5'ss of exon 2
GAGATGCGCGTGGTGATGCTGGGCCTGGACGCGGCAGGAAAGACCACCATCCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCGgtgagtcagagtatgatctaaagtctagaaacaaggtt---gggagtctgtctgcatgggcctctgt-cacctggaacgg--gcccggtcccgaggcggaac-gtgc--------------------------------------------------------------------------
         ||||||||||| ||  ||||||||||||| || |||||||| ||||| ||||| || || || ||| |  |  |||| || || || |||||| | |     ||| |  |  |||| |      |  ||   || |||  | ||    |   ||  ||  |  ||| || |  |     | |   |  | ||| ||                                                                            
---------GTGGTGATGCTTGGATTGGACGCGGCAGGCAAAACCACCATTCTCTATAAGCTGCATATTGGAGAGATTTTGTCCACAGTCCCCACCATCGgtaatttgacttatcacttgtagtcaatccttcatttttttggtagtgcgcctcttcgtttctgagtatagatggcactgttgttttatacaatgttgcaaccgtatttcctgccaagtgcatgtgagtgtttttgagggtaacatctgttgctaaattacattttccattcaattttcag

upper sequence: EDP05355 (Chlamydomonas reinhardtii), 5'ss of exon 1
lower sequence: PP1S47_298V6.1 (Physcomitrella patens), 5'ss of exon 2
GAGATGCGCGTGGTGATGCTGGGCCTGGACGCGGCAGGAAAGACCACCATCCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCGgtgagtcagagtatgatctaaagtctagaaacaaggttgggagtctgtctgcatgggcctctgtcacctggaacgggcccggtcccgaggcggaacgtgc--------------------------------------------------------------------------------------
         ||||||||||| ||  ||||||||||||| || || ||||| ||||| |||||||| ||||| ||| | ||  |||| || || || || |||   |     ||  |  |  |||  |       |  |  ||    | |    |  |  ||||     | ||  |     | |     | |||    |                                                                                        
---------GTGGTGATGCTTGGATTGGACGCGGCAGGCAAAACTACCATTCTCTATAAGCTTCATATCGGGGAGATTCTATCCACCGTTCCTACCATTGgtagcttgacttaacacttccagttgatccttttgtatttgaaagagcccctcttcgtttctgcttatttga-tgtatttgcttatttgacggtgttttgtttgatgtattattctgtgtcgagtgctggtgaatttgctttcgaggatgtcatttgttaagttgttgtggttatgcaatattcag

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|15369495|gb|BI528921.1|BI528921
EST:     CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCG                         GCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
genomic: CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCGgtgagtcaga ... aaaccgacagGCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
EST: gi|10128241|gb|BE726945.1|BE726945
EST:     CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCG                         GCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
genomic: CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCGgtgagtcaga ... aaaccgacagGCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
EST: gi|10773660|gb|AV624483.1|AV624483
EST:     CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCG                         GCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
genomic: CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCGgtgagtcaga ... aaaccgacagGCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
EST: gi|14232246|gb|BG851062.1|BG851062
EST:     CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCG                         GCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
genomic: CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCGgtgagtcaga ... aaaccgacagGCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
EST: gi|10771075|gb|AV621898.1|AV621898
EST:     CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCG                         GCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
genomic: CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCGgtgagtcaga ... aaaccgacagGCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
EST: gi|161818070|gb|FC102257.1|FC102257
EST:     CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCG                         GCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
genomic: CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCGgtgagtcaga ... aaaccgacagGCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
EST: gi|23362323|gb|BU650143.1|BU650143
EST:     CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCG                         GCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
genomic: CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCGgtgagtcaga ... aaaccgacagGCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
EST: gi|6547469|gb|AV393253.1|AV393253
EST:     CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCG                         GCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
genomic: CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCGgtgagtcaga ... aaaccgacagGCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
EST: gi|15694043|gb|BI718348.1|BI718348
EST:     CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCG                         GCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
genomic: CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCGgtgagtcaga ... aaaccgacagGCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
EST: gi|15370728|gb|BI530154.1|BI530154
EST:     CTCTACAAGCTTCACANTCGGCGAGGTGCTCACCACTGTGCCGACTATCG                         GCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
genomic: CTCTACAAGCTTCACA-TCGGCGAGGTGCTCACCACTGTGCCGACTATCGgtgagtcaga ... aaaccgacagGCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
EST: gi|7616308|gb|AW721748.1|AW721748
EST:     CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCG                         GCTTCAACGTTGAGAAGGTGCAATACAAGAACG
genomic: CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCGgtgagtcaga ... aaaccgacagGCTTCAACGTTGAGAAGGTGCAATACAAGAACG
EST: gi|15372769|gb|BI532195.1|BI532195
EST:     CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCG                         GCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
genomic: CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCGgtgagtcaga ... aaaccgacagGCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
EST: gi|16072772|gb|BI874768.1|BI874768
EST:     CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCG                         GCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG
genomic: CCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCGgtgagtcaga ... aaaccgacagGCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGATGCGCGTGGTGATGCTGGGCCTGGACGCGGCAGGAAAGACCACCATCCTCTACAAGCTTCACATCGGCGAGGTGCTCACCACTGTGCCGACTATCGgtgagtcagagtatgatctaaagtctagaaacaaggttgggagtctgtctgcatgggcctctgtcacctggaacgggcccggtcccgaggcggaacgtgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agagtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgtct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgtca