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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGACGCTCAAGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgggcgaacgattcagccggggcgggcgggcggggcggttggtgtgcgggttcgatcgctcggccagcggtgggacagcagcggggcacggtg...

Basic information

species Chlamydomonas reinhardtii
transcript EDP06728
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP06728 (Chlamydomonas reinhardtii), 5'ss of exon 4
lower sequence: PP1S41_59V6.1 (Physcomitrella patens), 5'ss of exon 3
----------------------------------------GAGACGCTCAAGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgggcgaacgattcagccggggcgggc---gggcggggcggttggtgtgcgggtt--cgatcgctcggccagcggtgggacagcagcggggcacggtg
                                        || ||  | ||| | ||  |||| ||||||||||||||||||||||| ||   ||| |||||  |    || | ||  || | |      |      | |  | || ||||    | | | |   ||    |  ||    |   | | |  | |    ||     
ACAAGACTATGCGGAACGAGTTCTGCCTTCTGTTGTTCAGGAAACTTTAAAGGCCGTTGTTGCTCAGTACAACGCCAGCCAGCTCATTACGCAGCGTGAGgtaggttgtggtggactgttgatcttttttgaattttgtgtagagctgttgccaagagtgatgatgacgaatatgcacttgcgtgaaaatgaacaaaaca-----

upper sequence: EDP06728 (Chlamydomonas reinhardtii), 5'ss of exon 4
lower sequence: EFJ20024 (Selaginella moellendorffii), 5'ss of exon 3
----------------------------------------GAGACGCTCAAGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgggcgaacgattcagccggggcgggcgggcggggcggttggtgtgcgggttcgatcgctcggccagcggtgggacagcagcggggcacggtg
                                        |||||||| ||||||||  |||||||||||||||| || |||||||||||   ||| ||||||||       || || ||| ||  |   |  |   | |||   || ||                                                  
ACAGGACTACGCGGAGAGGGTCTTGCCTTCGATCATTCACGAGACGCTTAAGTCGGTGGTTGCGCAGTACAACGCAAGTCAGCTCATCACTCAGCGAGAGgtgagc----aagagcgtttctgcgagtttgtactcacagggt--tttgtag------------------------------------------------
















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|7615357|gb|AW720803.1|AW720803
EST:     AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAG                         GTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
genomic: AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgg ... cacgcaccagGTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
EST: gi|161814815|gb|FC100657.1|FC100657
EST:     AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAG                         GTGGTGTCCCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
genomic: AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgg ... cacgcaccagGTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
EST: gi|22072634|gb|BQ821972.1|BQ821972
EST:     AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAG                         GTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTT
genomic: AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgg ... cacgcaccagGTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTT
EST: gi|22050250|gb|BQ809141.1|BQ809141
EST:     AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAG                         GTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTT
genomic: AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgg ... cacgcaccagGTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
EST: gi|22068051|gb|BQ818019.1|BQ818019
EST:     AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAG                         GTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
genomic: AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgg ... cacgcaccagGTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
EST: gi|22055652|gb|BQ811951.1|BQ811951
EST:     AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAG                         GGTTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACT
genomic: AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgg ... cacgcaccagG-T-GGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACT
EST: gi|15369591|gb|BI529017.1|BI529017
EST:     AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAG                         GNNTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACT
genomic: AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgg ... cacgcaccagG--TGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACT
EST: gi|161821633|gb|FC108134.1|FC108134
EST:     AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAG                         GTGGTGTCCCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
genomic: AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgg ... cacgcaccagGTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
EST: gi|22067190|gb|BQ817392.1|BQ817392
EST:     AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAG                         GTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
genomic: AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgg ... cacgcaccagGTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
EST: gi|22064606|gb|BQ815890.1|BQ815890
EST:     AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAG                         GTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
genomic: AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgg ... cacgcaccagGTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
EST: gi|22070334|gb|BQ819715.1|BQ819715
EST:     AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAG                         GTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
genomic: AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgg ... cacgcaccagGTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
EST: gi|22073537|gb|BQ822875.1|BQ822875
EST:     AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAG                         GTGGTGTCGCGCGACAT
genomic: AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgg ... cacgcaccagGTGGTGTCGCGCGACAT
EST: gi|22074365|gb|BQ823420.1|BQ823420
EST:     AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAG                         GTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
genomic: AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgg ... cacgcaccagGTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
EST: gi|23364284|gb|BU652104.1|BU652104
EST:     AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAG                         GTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
genomic: AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgg ... cacgcaccagGTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
EST: gi|161801894|gb|FC090730.1|FC090730
EST:     AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAG                         GTGGTGTCCCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
genomic: AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgg ... cacgcaccagGTGGTGTCGCGCGACATCCGCCGCATCCTGACGGAGCGCGCCCGCTACTTC
EST: gi|22071207|gb|BQ820545.1|BQ820545
EST:     AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCACGAG                         GTGGTGTCGCGCGACA
genomic: AGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgg ... cacgcaccagGTGGTGTCGCGCGACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGACGCTCAAGTCGGTCATTGCGCAGTACAACGCCAGCCAGCTCATCACCATGCGCGAGgtgagaccgggcgaacgattcagccggggcgggcgggcggggcggttggtgtgcgggttcgatcgctcggccagcggtgggacagcagcggggcacggtg

- - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttggtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagcagc