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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctcggaggcgctcacgctcatggactggcgaccaggccagctgcagctgtgtaatgactattttaccgagttgttgatcgttggatgcttcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGCCCGTCTTCCACAAGAAG

Basic information

species Chlamydomonas reinhardtii
transcript EDP05070
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP05070 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 2
gctcggaggcgctcacgctcatggactggcgaccaggccagctgcagctgtgtaatgac--tattttaccgagttgttgat---cgttggatgcttcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGCCCGTCTTCCACAAGAAG
    ||      |   |    || |   |  | |   ||      ||   || ||||||   | |||  | | || | ||    |  |  ||| || |   ||||| ||| |  | || ||| | || || || || ||||| |||||||||||||| |||||||||||||||
----ggtcaaattttaggatctgcatgtgaaatcttacctatcctagacctg-aatgacgtcagtttttcaatttttagaagtacaatatatgattgtatggcagGTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG

upper sequence: EDP05070 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: PP1S74_73V6.1 (Physcomitrella patens), 3'ss of exon 2
---gctcggaggcgctcacgctcatggactggcgaccaggccagctgcagctgtgtaatgactattttaccgagttgttgatcgttggatgcttcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGCCCGTCTTCCACAAGAAG
   ||  ||||  | |||   | | |   | | |      |  |  |     |      |||| |  |     ||   |   |||    |   |      |||| ||| | || || ||| | ||||| || |||||||| |||||||||||||| ||||| |||||||||
tctgcgtggagttggtcat-tttaggctttagtgtttgttcgggtcgatatcgaagtgggactgtcattatacgtaact--ccgtcttctctattcgtgacagGGAAGAGGCGTTATGACAGGAAGCAATCCGGTTACGGAGGTCAGACCAAGCCTGTCTTTCACAAGAAG

upper sequence: EDP05070 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: PP1S6_198V6.1 (Physcomitrella patens), 3'ss of exon 2
gctcgga-ggcgctcacgctcatgg--actggcgaccaggccagctgcagctgtgtaatgactattttaccgagttgttgatcgttggatgcttcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGCCCGTCTTCCACAAGAAG
  | |    ||  |  || |  | |  |||  |    |    |  |||  ||   | || |||   ||   |  |||   ||| || |       |   ||||| ||| | || || ||  | ||||||||||||||||| |||||||||||||||||||| |||||||||
atttgactagcattttcgtttttagtgactcacattgatagtaa-tgctactccttcataactgcgtt--tgtattgaacatcctttgtctgcattccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGCCCGTCTTTCACAAGAAG

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|7709538|gb|AW772956.1|AW772956
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|34987515|gb|CF561432.1|CF561432
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|22066976|gb|BQ817267.1|BQ817267
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|34987514|gb|CF561431.1|CF561431
EST:     GATGAAGGTCCCCCAGTACAAGACTGGCAAGGCCTCCCTTTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|10786240|gb|AV642912.1|AV642912
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|34984015|gb|CF557932.1|CF557932
EST:     AGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: AGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|7546035|gb|AW676523.1|AW676523
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|22055211|gb|BQ811714.1|BQ811714
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTTTTCGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTGGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|34983766|gb|CF557683.1|CF557683
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|161805193|gb|FC091718.1|FC091718
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|34990343|gb|CF564260.1|CF564260
EST:     GATGAAGGTCACCCAGTACAAGACAGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|10788173|gb|AV644845.1|AV644845
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|6550594|gb|AV396378.1|AV396378
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|10784804|gb|AV641476.1|AV641476
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|34994842|gb|CF568759.1|CF568759
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|34988338|gb|CF562255.1|CF562255
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|22074012|gb|BQ823256.1|BQ823256
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|34981145|gb|CF555062.1|CF555062
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTTTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|34989175|gb|CF563092.1|CF563092
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|34988337|gb|CF562254.1|CF562254
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTTTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|34984261|gb|CF558178.1|CF558178
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|34982457|gb|CF556374.1|CF556374
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTTTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|10789531|gb|AV645260.1|AV645260
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGCGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|7545738|gb|AW676226.1|AW676226
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|7546172|gb|AW676660.1|AW676660
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|7545739|gb|AW676227.1|AW676227
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|34984533|gb|CF558450.1|CF558450
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTTTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTTCGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|34981094|gb|CF555011.1|CF555011
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|10789373|gb|AV645102.1|AV645102
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|22075594|gb|BQ824370.1|BQ824370
EST:     TATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|34987789|gb|CF561706.1|CF561706
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|7546171|gb|AW676659.1|AW676659
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
EST: gi|22055213|gb|BQ811715.1|BQ811715
EST:     GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGG                         GCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC
genomic: GATGAAGGTCACCCAGTACAAGACTGGCAAGGCCTCCCTCTACGCGCAGGgtgagttgtt ... tcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctgtgtaatgactattttaccgagttgttgatcgttggatgcttcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGCCCGTCTTCCACAAGAAG
                           tgttgat  putative branch site (score: 4)
                                         tgcttctt  putative PPT
       taatgactatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctcggaggcgctcacgctcatggactggcgaccaggccagctgcagctgtgtaatgactattttaccgagttgttgatcgttggatgcttcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGCCCGTCTTCCACAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - acgctca
- - - - - - - - - - - - - - - - - - - - - - - -ctgtgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttggatg