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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcgaggcgtatggcacatgcaaccttgagccagccagtttctgtagagcttttgcgctacccgccgccggcacccctgacctgaccggctctgctccagGTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCGGTCAACTGGCTCATCTCCTACTCCAAGTACACCAAGTCCCTGGAGCCCT

Basic information

species Chlamydomonas reinhardtii
transcript EDP07903
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP07903 (Chlamydomonas reinhardtii), 3'ss of exon 8
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 13
ctcgaggcgtatggcacatgcaaccttgagccagcc----agtt---tctgtagagcttttgcgctacccgccgccggcacccctgacctgac-cggctctgctccagGTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCGGTCAACTGGCTCATCTCCTACTCCAAGTACACCAAGTCCCTGGAGCCCT
        ||| || |  ||| |  || | ||| ||    | ||   | |  | | ||||    || |  |      |         | | || |  |||   | ||||| || |||||  |||| ||||||||||| ||  | ||||||||||| || ||||| ||||||||||| ||||| || ||| | |||             
--------gtaaggaaactgctagattaatccaacctttgaattaaattttcaaacctttctaactgcatgttcattgtttgataatcttaactcctctcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG-------------

upper sequence: EDP07903 (Chlamydomonas reinhardtii), 3'ss of exon 8
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 14
-------------------ctcgaggcgtatggcacatgcaacc-----ttgagccagccagtttctgtaga------gcttttgcgctacccgccgcc--------ggcacc----cctgacctgaccggctctgctccagGTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCGGTCAACTGGCTCATCTCCTACTCCAAGTACACCAAGTCCCTGGAGCCCT
                   |||     ||    ||||| | |||     ||     |||||    |  |         ||| |   | | |  | |  |        || ||     | |    | |  |  | |     ||||||| ||||| || |||||||| || || ||||| || ||||| ||  | || ||||||||||| |||||||||||||||||  ||             
gttggtatttgtacctcctctcatccagtgcaccacattctaccagatattctctaagccaaagcccatgagaagttggctatgatgttgcatgtcttccaagcgaaggaactaaagcatattgtaaatgcatgttgattagGTGTTTTGGGGGCTCGACAAGAAACTTGCTCAGCGGAAACATTTTCCAGCAGTGAACTGGCTCATTTCCTACTCCAAGTACACGCAG-------------

upper sequence: EDP07903 (Chlamydomonas reinhardtii), 3'ss of exon 8
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 14
-------------------------------------------------------------ctcgaggcgtatggcacatgcaaccttgagccagccagtttctgtagagcttttgcgctacccgccgccggcacccctgacctgaccggctctgctccagGTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCGGTCAACTGGCTCATCTCCTACTCCAAGTACACCAAGTCCCTGGAGCCCT
                                                             | |    ||||       ||  |     |  ||   |   |   |  |  ||||  | |     |       |    ||     |        |   |||||||| ||||| || ||||||||||| || || ||||| ||||| ||  | || || |||||||| |||||||||||||||||  ||             
gttagtcatttgtgtacttgcactgattgtgctacatcctatcgtcaatttcagaattactcgctcaccgtagatttattgagatagcaaagcattgatcctgaatgcattttttatg-tggttacttgaaaaatggatg-ttaaatgcatgtggagtcagGTGTTTTGGGGACTTGACAAGAAGCTTGCTCAACGTAAACATTTTCCAGCTGTGAATTGGCTCATTTCCTACTCCAAGTACACTCAG-------------

upper sequence: EDP07903 (Chlamydomonas reinhardtii), 3'ss of exon 8
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 14
ctcgaggcgtatggcacatgcaaccttgagccagccagtttctgtagagcttttgcgctacccgccgccggcacccctgacctgaccggctctgctccagGTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCGGTCAACTGGCTCATCTCCTACTCCAAGTACACCAAGTCCCTGGAGCCCT
                                     || | |||     ||||     |       | || || |           |  | || | |||||||| ||||| || ||||||||||| |||||  | |||||||||||| | ||||||||||| || || || || ||||| ||| ||             
-------------------------------------gtctttgtgccagttttttttcagtgttgactgggacact-------gttg--tttgttgcagGTGTTTTGGGGACTTGACAAGAAGCTTGCGCAAAGAAAGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAG-------------

upper sequence: EDP07903 (Chlamydomonas reinhardtii), 3'ss of exon 8
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 13
ctcgaggcgtatggcacatgcaaccttgagccagccagtttctgtagagcttttgcgctacccgccgccggcacccctgacctgaccggc----tctgctccagGTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCGGTCAACTGGCTCATCTCCTACTCCAAGTACACCAAGTCCCTGGAGCCCT
                                                |  |||| || |   |       ||    ||||  |  |       | || | |||||||| ||||| || ||||||||||| |||||  | |||||||||||| | ||||||||||| || || || || ||||| ||| ||             
------------------------------------------------gtctttgtgccagttgttttt--cagtgttgactgggacactgttgtttgttgcagGTGTTTTGGGGACTTGACAAGAAGCTTGCGCAAAGAAAGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAG-------------

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|14240718|gb|BG859534.1|BG859534
EST:     GTGGTGATTTCTCGGACCCCGACACGGGTGCCACCCTGGCCATCGTGCAG                         GTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGGGTAAGCATTTCCCTTCG
genomic: GTGGTGATTTCTCGGACCCCGTCACGGCTGCCACCCTGGCCATCGTGCAGgtgagcgcgg ... tctgctccagGTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCG
EST: gi|34981587|gb|CF555504.1|CF555504
EST:     GTGGTGATTTCTCGGACCCCGTCACGGCTGCCACCCTGGCCATCGTGCAG                         GTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCG
genomic: GTGGTGATTTCTCGGACCCCGTCACGGCTGCCACCCTGGCCATCGTGCAGgtgagcgcgg ... tctgctccagGTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCG
EST: gi|15693797|gb|BI718102.1|BI718102
EST:     GTGGTGATTTCTCGGACCCCGTCACGGCTGCCACCCTGGCCATCGTGCAG                         GTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCG
genomic: GTGGTGATTTCTCGGACCCCGTCACGGCTGCCACCCTGGCCATCGTGCAGgtgagcgcgg ... tctgctccagGTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCG
EST: gi|161802427|gb|FC092966.1|FC092966
EST:     GTGGTGATTTCTCGGACCCCGTCACGGCTGCCACCCTGGCCATCGTGCAG                         GTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCG
genomic: GTGGTGATTTCTCGGACCCCGTCACGGCTGCCACCCTGGCCATCGTGCAGgtgagcgcgg ... tctgctccagGTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCG
EST: gi|15696329|gb|BI720634.1|BI720634
EST:     GTGGTGATTTCTCGGACCCCGTCACGGCTGCCACCCTGGCCATCGTGCAG                         GTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCG
genomic: GTGGTGATTTCTCGGACCCCGTCACGGCTGCCACCCTGGCCATCGTGCAGgtgagcgcgg ... tctgctccagGTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCG
EST: gi|15704784|gb|BI729089.1|BI729089
EST:     GTGGTGATTTCTCGGACCCCGTCACGGCTGCCACCCTGGCCATCGTGCAG                         GTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCG
genomic: GTGGTGATTTCTCGGACCCCGTCACGGCTGCCACCCTGGCCATCGTGCAGgtgagcgcgg ... tctgctccagGTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCG
EST: gi|15704783|gb|BI729088.1|BI729088
EST:     GTGGTGATTTCTCGGACCCCGTCACGGCTGCCACCCTGGCCATCGTGCAG                         GTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCG
genomic: GTGGTGATTTCTCGGACCCCGTCACGGCTGCCACCCTGGCCATCGTGCAGgtgagcgcgg ... tctgctccagGTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCG
EST: gi|16432426|gb|BI997652.1|BI997652
EST:     GTGGTGATTTCTCGGACCCCGTCACGGCTGCCACCCTGGCCATCGTGCAG                         GTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCG
genomic: GTGGTGATTTCTCGGACCCCGTCACGGCTGCCACCCTGGCCATCGTGCAGgtgagcgcgg ... tctgctccagGTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagcttttgcgctacccgccgccggcacccctgacctgaccggctctgctccagGTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCGGTCAACTGGCTCATCTCCTACTCCAAGTACACCAAGTCCCTGGAGCCCT
                                  acctgac  putative branch site (score: 3)
                                            ctctgctcc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcgaggcgtatggcacatgcaaccttgagccagccagtttctgtagagcttttgcgctacccgccgccggcacccctgacctgaccggctctgctccagGTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCGGTCAACTGGCTCATCTCCTACTCCAAGTACACCAAGTCCCTGGAGCCCT

- - - - - - - -acatgca
- - - - - - - - - - - - - - - - - - - tttctgt