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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttgcacgggccgccaagttgtggtgcccctcaaagccactgctaaggtggctggccccctcaccgtgtcccctcacccttgggactccgccgcacagCCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAG

Basic information

species Chlamydomonas reinhardtii
transcript EDP09161
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP09161 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: LOC_Os01g16190.1 (Oryza sativa), 3'ss of exon 2
---tttttgcacgggccgccaagttgtggtgcccctcaaagccactgctaaggtggctggccccctcaccgtgtcccctcacccttgggactccgccgcacagCCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAG
    | |    | |     | ||   |  |  |  | |    ||| | |   ||   | | |   | | ||||         ||    |  |   |   |||| || || ||||||||||||||||| ||||| || || || || || || ||||| ||||| || ||||||||||| ||||||
acactctcagtctgatgatctagaattatttacttttatttacaccgtt---gtttttaggctgtttaacgtgattttgtggccacttgtgttatctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG

upper sequence: EDP09161 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 2
-------tttttgcacgggccgccaagttgtggtgcccctcaaagccactgctaaggtggctggccccctcaccgtgtcccctcacccttgggactccgccgcacagCCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAG
       | ||||       ||  || |    |||      |     |   ||||  |    |    |  |    ||  ||       || |   || ||     || || ||||||||||||||||||||||| || || || || || || |||||| |||| |||||||||||||| || ||||||
ctacttatatttgattcatgcgtaaactgaacgtgatgtgtacgaatatgtctaaaatactagaaatcaccttgatg--cctgtgttgtttgtgttctgc-----agACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG

upper sequence: EDP09161 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: PP1S146_35V6.1 (Physcomitrella patens), 3'ss of exon 2
tttttgcacgggccgccaagttgtgg-tgcccctcaaagccactgctaaggtggctggccccctcaccgtgtcccctcacc----cttgggactccgccgcacagCCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAG
         | ||   | |  ||||  |  | || | | | | |   |  ||        |  |  || | |    | |      |||     ||        || || |||||||| || || ||||| || ||||| || || || ||||||||| |||| |||||||||||||| ||||| |||
----aaattgagctttccatgtgtgaatatcactaacaactaat-taacagttttcatttcgatttccatattgatttataatgacttttctttctattttgtagGCCTGAGATGGTCGTTGGGTGGTATCATTCACATCCAGGGTTTGGCTGCTGGTTGTCTGGCGTGGATATCAATACGCAACAG

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|15695776|gb|BI720081.1|BI720081
EST:     GACCCCGTGTTCCAGACAAAGATGCTTGACATGCTTAAACAAGTGGGCCG                         CCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTG
genomic: GACCCCGTGTTCCAGACAAAGATGCTTGACATGCTTAAACAAGTGGGCCGgtgagtggtt ... cgccgcacagCCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTG
EST: gi|16431951|gb|BI997177.1|BI997177
EST:     GACCCCGTGTTCCAGACAAAGATGCTTGACATGCTTAAACAAGTGGGCCG                         CCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTG
genomic: GACCCCGTGTTCCAGACAAAGATGCTTGACATGCTTAAACAAGTGGGCCGgtgagtggtt ... cgccgcacagCCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTG
EST: gi|15369702|gb|BI529128.1|BI529128
EST:     GACCCCGTGTTCCAGACAAAGATGCTTGACATGCTTAAACAAGTGGGCCG                         CCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTG
genomic: GACCCCGTGTTCCAGACAAAGATGCTTGACATGCTTAAACAAGTGGGCCGgtgagtggtt ... cgccgcacagCCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaggtggctggccccctcaccgtgtcccctcacccttgggactccgccgcacagCCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAG
                           ccctcac  putative branch site (score: 3)
                                          ctccgcc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttgcacgggccgccaagttgtggtgcccctcaaagccactgctaaggtggctggccccctcaccgtgtcccctcacccttgggactccgccgcacagCCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
tttttgc
- - - - - - - - - - ttgtggt
- - - - - - - - - - - - - - - - - aaagcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctcac