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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccgtgcctctaggactgccagcctgcgtgtggtaacgtgccctgtgtgtcgtcagcctaaccccgtaaacctcttggcgtggcctcccggccgctgcagGTACCTGGTGCCTTCAGACCTGACCGTCGGGCAATTTGTGTACGTCATCCGCAAGCGGATAAAGCTGAGCCCCGAGAAGGCCATCTTCATTTTCGTGAAG

Basic information

species Chlamydomonas reinhardtii
transcript EDO98830
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO98830 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: GRMZM2G014975_T01 (Zea mays), 3'ss of exon 2
-----gccgtgcctctaggactgccagcctgcgtgtggtaac-gtgccctgtgtgtcgtcagcctaaccccgtaaacctcttggcgtggcctcccggccgctgcagGTACCTGGTGCCTTCAGACCTGACCGTCGGGCAATTTGTGTACGTCATCCGCAAGCGGATAAAGCTGAGCCCCGAGAAGGCCATCTTCATTTTCGTGAAG
      ||    |   ||||   |  || |    ||   | |   | || |  ||  |      |   ||   ||    | ||   | || | |       ||||||||||| || ||  | ||||| || || || || |||||||||||  | || ||||| || ||||| ||| |||||||||| |||||||| |||||||||
cattaaccaattcagaaggaactcttgcttatcggtacaagccaagaccagcttgcagcatctgtgtgcctccaagtaacatgcgattgcttgca------tgcagGTACCTTGTCCCCGCCGACCTCACAGTGGGACAGTTTGTGTACGTGGTGCGGAAGCGCATCAAGCTCAGCGCCGAGAAGGCGATCTTCATCTTCGTGAAG

upper sequence: EDO98830 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: GRMZM2G134613_T01 (Zea mays), 3'ss of exon 3
--gccgtgcctctaggactgccagcctgcgtgtggtaacgtgccctgtgtgtcgtcagcctaaccccgtaaacctcttggcgtggcctcccggccgctgcagGTACCTGGTGCCTTCAGACCTGACCGTCGGGCAATTTGTGTACGTCATCCGCAAGCGGATAAAGCTGAGCCCCGAGAAGGCCATCTTCATTTTCGTGAAG
            |  || ||    | ||  | | |  ||  | |  |     |  || | |      ||   ||       |||   |         ||||||||||| || ||| | ||||| || ||||| || |||||||| ||  | || |||||||| ||||| ||| | |||||||| |||||||| ||||| |||
ttaattaattcatcagaatgaggtcttgtttatcggtacaaggcaagaccagctgcaacat--ttgtgtggcccctgatatgtgaattgtgattgcttgcagGTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACGGAAGCGGATCAAGCTCAGCGCTGAGAAGGCAATCTTCATCTTCGTAAAG

upper sequence: EDO98830 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: GLYMA06G46270.2 (Glycine max), 3'ss of exon 4
gccgtgcctctaggactgccagcctgcgtgtggtaacgtgcc--ctgtgtgtcgtcagcctaaccccgtaaacctcttggcgtggcctcccggccgc-tgcagGTACCTGGTGCCTTCAGACCTGACCGTCGGGCAATTTGTGTACGTCATCCGCAAGCGGATAAAGCTGAGCCCCGAGAAGGCCATCTTCATTTTCGTGAAG
        |  | |   |   |  | | ||   |   ||  |  || | |    ||  | | |           | ||   ||    |   ||  |  || ||||| ||||| ||| | ||  |||| || || || |||||||| ||  | || ||| | || |||||||| ||||||||||||||||||||||| || |||
---tcatttgaatgttcgagtgaatacatgccatcttgtttcatctcttttctttcctctttatttatggtgtgtattattgttcttttttggatgaatgtagGTATCTGGTCCCTGCTGATTTGACTGTTGGCCAGTTTGTGTATGTGGTGCGGAAGAGAATCAAGCTGAGTCCCGAGAAGGCCATCTTCATTTTTGTTAAG

upper sequence: EDO98830 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: PP1S249_49V6.2 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------------gccgtgcctctaggactgccagcctgcgtgtggt---aacgtgccctgtgtgtcgtcagcctaaccccgtaaacctcttggcgtggcctcccggccgc---tgcagGTACCTGGTGCCTTCAGACCTGACCGTCGGGCAATTTGTGTACGTCATCCGCAAGCGGATAAAGCTGAGCCCCGAGAAGGCCATCTTCATTTTCGTGAAG
                                                            |  | | ||    |  |  |    ||  || ||    ||        ||  ||   ||    |     | |      |||   ||   |   |  |||   || |||||||| |||||  | ||| |||| || ||||| ||||| ||||||||  | ||||| || ||| | ||  | |||||||||||||||||||||||||||
gtatgtagtttgtgttctttttgtaacgagcttgacattattttcctttcatattttggggttgagtctgattggtt-tcgttttgtttggggcctaaataattttagttcgtgcgcactgaattgtggcacgttctttgaattgatatgaggaacgcctgtgtagGTACCTTGTGCCAGCCGACTTGACGGTTGGGCAGTTTGTCTACGTCATAAGAAAGCGCATCAAGTTAAGTTCTGAGAAGGCCATCTTCATTTTCGTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtcgtcagcctaaccccgtaaacctcttggcgtggcctcccggccgctgcagGTACCTGGTGCCTTCAGACCTGACCGTCGGGCAATTTGTGTACGTCATCCGCAAGCGGATAAAGCTGAGCCCCGAGAAGGCCATCTTCATTTTCGTGAAG
          gcctaac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccgtgcctctaggactgccagcctgcgtgtggtaacgtgccctgtgtgtcgtcagcctaaccccgtaaacctcttggcgtggcctcccggccgctgcagGTACCTGGTGCCTTCAGACCTGACCGTCGGGCAATTTGTGTACGTCATCCGCAAGCGGATAAAGCTGAGCCCCGAGAAGGCCATCTTCATTTTCGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - tgcgtgt
- - - - - - - - - - - - - - - - - - - - - -tgtgtgt