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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgcccaccattctgccttccccgccttctgcaccgcgcactgcgcggcactggccctgcaactcccccgcgctccgcctccgcctcctcctccgccacagGACCCGGTGCAGGCCATGATGAAGGACCAGTTTGGCAACTACGTGGTGCAGAAGGTGCTGGAGGTGTGCAGCGACGAGCAGCGCGAGGTGATGCTGGCGC

Basic information

species Chlamydomonas reinhardtii
transcript EDO96479
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO96479 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: LOC_Os02g57390.1 (Oryza sativa), 3'ss of exon 9
cgcccaccattctgccttccccgccttctgcaccgcgcactgcgcggcactggccctgcaactcccccgcgctccgcctccgcctcctcctccgccacagGACCCGGTGCAGGCCATGATGAAGGACCAGTTTGGCAACTACGTGGTGCAGAAGGTGCTGGAGGTGTGCAGCGACGAGCAGCGCGAGGTGATGCTGGCGC------------
            |    |       ||||  |  |    |   || |   |||   | ||  |  | | |  |||   ||             || |  |   |   | ||||| |||||||| ||||||||||  ||||||||||||||||||||  |||||   ||    ||| || | || ||  |||| ||  | |            
------ttggaataagatattgcttttctaaaatgataccgttgctgtggtggatat-ca--tggctcacattcc---tctaaaatgattaaagcaaatgtttcttctccagGCAATGATGAAAGACCAGTTTGCTAACTACGTGGTGCAGAAGGTTTTGGAGACTTGTGATGACCAGAACCGTGAATTGATCCTTTCACGTATCAAAGTAC

upper sequence: EDO96479 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: LOC_Os01g62650.1 (Oryza sativa), 3'ss of exon 8
cgcccaccattctgccttccccgccttctgcaccgcgcactgcg-cggcactggccctgcaactcc-cccgcgctccgcctccgcctcctcctccgccacagGACCCGGTGCAGGCCATGATGAAGGACCAGTTTGGCAACTACGTGGTGCAGAAGGTGCTGGAGGTGTGCAGCGACGAGCAGCGCGAGGTGATGCTGGCGC------------
              ||  ||        ||||     || |  |    | |||    |     |        | |  |  |  |  |  |  |     | |  | |   ||||||||||||||||||| |||||||| ||||| || || ||||| || ||||||   ||    ||  ||||||| ||| |||| ||| | |            
--------------ccccccggaaaagttgcattcaacattctgatctctctgtttttttgtttttgtttttgttttgtttttgtgttttttttttgaaaaataacacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAGACTTGTGATGATCAGCAGCGTGAGTTGATCCTGTCACGAGTAAAGGTTC

upper sequence: EDO96479 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM2G042623_T02 (Zea mays), 3'ss of exon 8
---------cgcccaccattctgccttccccgccttct-gcaccgcgcact-gcgcggcactggccctgcaactcccccgc-gctccgcctccgcctcctcctccgccacagGACCCGGTGCAGGCCATGATGAAGGACCAGTTTGGCAACTACGTGGTGCAGAAGGTGCTGGAGGTGTGCAGCGACGAGCAGCGCGAGGTGATGCTGGCGC------------
          |      | | | | ||  |  | ||   | |      | |   ||   | || ||       |    | |  ||  |      | |     | |       |   || |  |||  |||||||| ||||||||||| ||||| ||||||||||||||| | ||    ||   |||  ||||| | ||| |||| ||  |              
gtatggtgatgtttgaaacttttctttatcttctttgaagtagtttttatttaagcacaagtgaccgaatgctttgttcaccacttagtactgacatgggtttgcattgtctgttgcgat--agGTAATGATGAAAGACCAGTTTGGAAACTATGTGGTGCAGAAGGTGTTAGAAACTTGTGACGATCAGCAGAGAGAGATGATCCTAACAAGGATAAAGACAC

upper sequence: EDO96479 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM2G038818_T02 (Zea mays), 3'ss of exon 1
---------cgcccaccattctgccttccccgccttctgcaccgcgcactgcgcggcactggccctgca------actcccccgcgctccgcctccgcctcctcctccgccacagGACCCGGTG-----CAGGCCATGATGAAGGACCAGTTTGGCAACTACGTGGTGCAGAAGGTGCTGGAGGTGTGCAGCGACGAGCAGCGCGAGGTGATGCTGGCGC------------
         |  | |     |||      |  | ||    |     || | |  ||   ||   |||||      | |  |   |  ||    |      |  |    |  |   || |   ||     ||||| |||||||| |||||||| |  ||||| |||||||||||||| |||||| | ||    ||| || | || ||  |||| ||  | |            
gttcgttttcaacaattggactgagcatgctccttttaaaaaaaaacagtaccaggatttgctgctgcagggttgaatttcatacattctaagtttctaacaacacttgtaatgtgaacttatgttccccagGCAATGATGAAAGACCAGTTCGCAAACTATGTGGTGCAGAAGGTTCTGGAGATATGTGATGACCAGAACCGTGAATTGATTCTTTCCCGTATCAAGGTCC

upper sequence: EDO96479 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: AT3G10360.1 (Arabidopsis thaliana), 3'ss of exon 9
cgcccaccattctgccttccccgccttctgcaccgcgcactgcgcggcactggccctgcaactcccccgcgctccgcctccgcctcctcctccgccacagGACCCGGTGCAGGCCATGATGAAGGACCAGTTTGGCAACTACGTGGTGCAGAAGGTGCTGGAGGTGTGCAGCGACGAGCAGCGCGAGGTGATGCTGGCGC------------
                                  |    |       | |    | ||    ||  |   |   ||         || |    |    |  |     ||||||| |||||||||||||  ||||| ||||| || ||||||||||| || ||    ||    ||  |    |  |   | || ||  | |            
----------------------------------gtctgcaatctaactccc-tcatgtctttctgcaatgtctcgaaaaaagtcccactaaagttggaacaatt--tgcagGCGATGATGAAGGACCCATTTGGGAACTATGTAGTGCAGAAGGTTCTTGAAACATGTGATGATCAAAGTCTTGCACTCATTCTTTCTCGCATCAAAGTAC

upper sequence: EDO96479 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: PP1S96_93V6.1 (Physcomitrella patens), 3'ss of exon 9
------------------------------------------------------cgcccaccattctgccttccccgccttct-gcaccgcgcactgcgcggcactggccctgcaactcccccgcgctccgcctc---------cgcctcctcctccg-ccacagGACCCG--GTGCAGGCCATGATGAAGGACCAGTTTGGCAACTACGTGGTGCAGAAGGTGCTGGAGGTGTGCAGCGACGAGCAGCGCGAGGTGATGCTGGCGC------------
                                                       |        ||| |  |  |    |    | |  |  |    | |||    || | || || | |   |      | ||           |  | |   || |  || |||  | |   ||||||| |||||||||||||||||||  || ||||| || ||||||||  ||||    ||    ||    || || ||| || |||| |  |            
gtaaggcatggggttgataaataagatttcggacctcgcttcagttgatagtcatggagcttgatctactattacgttgtgggagtaatgttcttcactcggtttcggtcttgtaagtgcgtaggaaggggtcttgtgtgatggtgaatgcatgtctgatcataggttctgttatgcagGCAATGATGAAGGACCAGTTTGCAAATTACGTTGTTCAGAAGGTCTTGGAAACCTGTGATGAATCTCAACGGGAGCTGCTGCTTGGCCGAATTCGTGTGC

upper sequence: EDO96479 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: PP1S35_216V6.1 (Physcomitrella patens), 3'ss of exon 9
cgcccaccattctgccttccccgccttctgcaccgcgcactgcgcggcactggccctgcaactcccccgcgctccgcctccgcctcctcctccgccacagGACCCGGTGCAGGCCATGATGAAGGACCAGTTTGGCAACTACGTGGTGCAGAAGGTGCTGGAGGTGTGCAGCGACGAGCAGCGCGAGGTGATGCTGGCGC------------
             |  ||   |   |   | |    |   || |      ||        | |      || |  || |  |  |   |    |      ||   | ||||||| |||||||| ||||||||||  ||||||||||| ||||||||| ||||    ||    ||    || |||||| || ||||||  |            
------------ggatttgtacctgtggaggaagctgatttgtgttatggtgaatgcctcaattgtttccggtatgcgtatgagtagcctgatgttcggtgatgtgatgcagGCAATGATGAAAGACCAGTTTGCAAACTACGTGGTCCAGAAGGTGTTGGAAACCTGTGATGAATCTCAACGCGAGCTGTTGCTGGGTCGTATTCGGGTTC

upper sequence: EDO96479 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: PP1S96_110V6.1 (Physcomitrella patens), 3'ss of exon 9
cgcccaccattctgccttccccgccttctgcaccgcgcactgcgcggc--actggccctgcaactcccccgcgctccgcctccgcctcctcctccgccacagGACCCGGTGCAGGCCATGATGAAGGACCAGTTTGGCAACTACGTGGTGCAGAAGGTGCTGGAGGTGTGCAGCGACGAGCAGCGCGAGGTGATGCTGGCGC------------
            || | |    |   |    |  | ||  ||   ||   | |||   |  |  |   | |   | |      ||   |      |      ||  | |||||||| |||||||| |||||||| |  ||||||||||| ||||||||| ||||   ||||   ||   |||||||||  || ||||||  |            
------------tgtcgtgtg-gtggtgcatatggtgcggtggagggttgagtgggtgtagaggtaggctgatttacaggga-gctgacgttgatgttgggtgatgctgtgcagGCAATGATGAAAGACCAGTTCGCAAACTACGTGGTCCAGAAGGTGTTGGAAACGTGCGATGAGTCGCAGCGCGAACTGTTGCTGGGTCGTATTCGGGTGC

upper sequence: EDO96479 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: EFJ35801 (Selaginella moellendorffii), 3'ss of exon 5
cgcccaccattctgccttccccgccttctgcaccgcgcactgcgcggcactggccctgcaactcccccgcgctccgcctccgcctcctcctccgccacagGACCCGGTGCAGGCCATGATGAAGGACCAGTTTGGCAACTACGTGGTGCAGAAGGTGCTGGAGGTGTGCAGCGACGAGCAGCGCGAGGTGATGCTGGCGC------------
                                             |  |   |     || |      | | |   | |    |||   ||| ||  ||   | |   |||||| |||||||||||||||||||  |||||||||||||| |||||  |||||   ||||| ||| |||| || ||| || | ||||  |            
---------------------------------------------gtaaagagatgaacagcaagagagagtttttcgttttgctcacgctcggctcca---ctccacgcagGCGATGATGAAGGACCAGTTTGCAAACTACGTGGTGCAAAAGGTTTTGGAGACTTGCAGTGACCAGCAACGAGAGATGCTCCTGGGTCGTATCAAAGTCC

upper sequence: EDO96479 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: EFJ36402 (Selaginella moellendorffii), 3'ss of exon 6
cgcccaccattctgccttccccgccttctgcaccgcgcactgcgcggcactggccctgcaactcccccgcgctccgcctccgcctcctcctccgccacagGACCCGGTGCAGGCCATGATGAAGGACCAGTTTGGCAACTACGTGGTGCAGAAGGTGCTGGAGGTGTGCAGCGACGAGCAGCGCGAGGTGATGCTGGCGC------------
                                    | |  | |  | || |     |  | |      || |  ||   |||      |  | ||||          |||||| |||||||||||||||||||  |||||||||||||| |||||  |||||   ||||| ||| |||| || ||| || | ||||  |            
------------------------------------gtaaagagatgaacagcaaaagagagtttttttcgttttgctcacgctcggctccactccac----------gcagGCGATGATGAAGGACCAGTTTGCAAACTACGTGGTGCAAAAGGTTTTGGAGACTTGCAGTGACCAGCAACGAGAGATGCTCCTGGGTCGTATCAAAGTCC

upper sequence: EDO96479 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: EFJ32290 (Selaginella moellendorffii), 3'ss of exon 5
cgcccaccattctgccttccccgccttctgcaccgcgcactgcgcggcactggccctgcaactcccccgcgctccgcctccgcctcctcctccgccacagGACCCGGTGCAGGCCATGATGAAGGACCAGTTTGGCAACTACGTGGTGCAGAAGGTGCTGGAGGTGTGCAGCGACGAGCAGCGCGAGGTGATGCTGGCGC------------
                                                                    |         |  |   |  | | |         |    | ||||| |||||||||||||| |||| |||||||||||||||||| || |||||| | ||   ||||   ||| | ||  |  |  || | |            
----------------------------------------------------------------gtaggaaagaaagatttgtgactccattcatatacatccttttttcagGCTATGATGAAGGACCAATTTGCCAACTACGTGGTGCAGAAAGTACTGGAGATTTGTGACGACCGCCAGAGGGAAATTCTTTTGACTCGTATCAAAGTTC

upper sequence: EDO96479 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: EFJ20967 (Selaginella moellendorffii), 3'ss of exon 5
cgcccaccattctgccttccccgccttctgcaccgcgcactgcgcggcactggccctgcaactcccccgcgctccgcctccgcctcctcctccgccacagGACCCGGTGCAGGCCATGATGAAGGACCAGTTTGGCAACTACGTGGTGCAGAAGGTGCTGGAGGTGTGCAGCGACGAGCAGCGCGAGGTGATGCTGGCGC------------
                                                         | |          | |  |   || |||||   ||    |||   |    | ||||| |||||||||||||| |||| |||||||||||||||||| || |||||| | ||   ||||   ||| | ||  |  |  || | |            
---------------------------------------------------------gtaggaaaga-aagatttgtgaccccctccat-tcatatacatc-cttttttcagGCTATGATGAAGGACCAATTTGCCAACTACGTGGTGCAGAAAGTACTGGAGATTTGTGACGACCGCCAGAGGGAAATTCTTTTGACTCGTATCAAAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcactggccctgcaactcccccgcgctccgcctccgcctcctcctccgccacagGACCCGGTGCAGGCCATGATGAAGGACCAGTTTGGCAACTACGTGGTGCAGAAGGTGCTGGAGGTGTGCAGCGACGAGCAGCGCGAGGTGATGCTGGCGC
                ctcccccgcgctccgc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgcccaccattctgccttccccgccttctgcaccgcgcactgcgcggcactggccctgcaactcccccgcgctccgcctccgcctcctcctccgccacagGACCCGGTGCAGGCCATGATGAAGGACCAGTTTGGCAACTACGTGGTGCAGAAGGTGCTGGAGGTGTGCAGCGACGAGCAGCGCGAGGTGATGCTGGCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
cgcccac
- - - - - - - - - - - - - - - - -cgcgcac