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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggactcgcttctacgctgccgcgacgcctgcagcagcgaccttaccagattttgttccgcgtggctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGGCGAGGGTGTTCAATGACCCGCAAATTGACCCTCGCAGATGCCAGCAG

Basic information

species Chlamydomonas reinhardtii
transcript EDP04926
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP04926 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: PP1S41_154V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------------------------------------gtaaggactcgcttctacgctgccgcgacgcctgcagcagcgaccttaccagattt----tgttccgcgtggctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGGCGAGGGTGTTCAATGACCCGCAAATTGACCCTCGCAGATGCCAGCAG
                                                                                       || |||      || |  | | | | |        |    |    | |    ||||    |  |||| |  | | || |||| || |||||||| ||||||||||| || ||| |||| ||||||||||| ||| | |||||||||||||   |  | ||  ||||  | ||    |||
gtgagtttcaattgcttctaaaatgagatagatctgtccagaagtgattaagatctggcgggggcagagtggaggggaattattttggtgagg--cgaattgtgtgtttcggagggtgtcttactgacattttaattttatttctgtttctccgtgctgattttacagCTGAATTCTCGCCGTTCTATGGCATTGAGAAGAGCGCCGTGCTGCAGGAAGCGCGCGTGTTCAATGACCGAGAGCTCGATGCTCGTCGGTGTGCACAG
















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|49466252|gb|BP094165.1|BP094165
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|10794354|gb|AV631720.1|AV631720
EST:     GAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|49465037|gb|BP092950.1|BP092950
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|49469013|gb|BP096874.1|BP096874
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|49467949|gb|BP095810.1|BP095810
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|49468728|gb|BP096589.1|BP096589
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|49469720|gb|BP097581.1|BP097581
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|10791117|gb|AV628483.1|AV628483
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|10793000|gb|AV630366.1|AV630366
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|49468010|gb|BP095871.1|BP095871
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|49467077|gb|BP094990.1|BP094990
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|10794486|gb|AV631852.1|AV631852
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|49467098|gb|BP095011.1|BP095011
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|10786480|gb|AV643152.1|AV643152
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|49465976|gb|BP093889.1|BP093889
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|49470909|gb|BP098770.1|BP098770
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|10786326|gb|AV642998.1|AV642998
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|49469972|gb|BP097833.1|BP097833
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|49469982|gb|BP097843.1|BP097843
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|10791497|gb|AV628863.1|AV628863
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
EST: gi|49465126|gb|BP093039.1|BP093039
EST:     GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGA                         CGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG
genomic: GGCTCCCCTGCGGGGGCCTGAGAAGAAGGACGAGGACCGCGAGGACGAGAgtaaggactc ... gctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgcgacgcctgcagcagcgaccttaccagattttgttccgcgtggctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGGCGAGGGTGTTCAATGACCCGCAAATTGACCCTCGCAGATGCCAGCAG
                    accttac  putative branch site (score: 3)
                              attttgtt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggactcgcttctacgctgccgcgacgcctgcagcagcgaccttaccagattttgttccgcgtggctattgcagCGGAGTTCTCGCCCTTCTATGGCATCGACAAGGGCGCGGTGCTGCAGGAGGCGAGGGTGTTCAATGACCCGCAAATTGACCCTCGCAGATGCCAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG