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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatcaggcgatgcgcgaggcgacgcctggagtgcgcaacaatgccaatcaacctcctgacataatctgcccttgttcatcattcccgccatgcttacagAGACGTGAAGCCGCACAACGTGATGATTGACCACTCCAAGCGGCAGCTGCGGCTCATAGACTGGGGCCTGGCGGAGTTCTACTTCCCGGAGCGCGAGTTC

Basic information

species Chlamydomonas reinhardtii
transcript EDO97438
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO97438 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------agatcaggcgatgc--gcgaggcgacgcctggagtgcgcaacaatgccaat-caacctcctgacataatc-----tgc---ccttgt----tcatcattcccgccatgct---tacagAGACGTGAAGCCGCACAACGTGATGATTGACCACTCCAAGCGGCAGCTGCGGCTCATAGACTGGGGCCTGGCGGAGTTCTACTTCCCGGAGCGCGAGTTC
                     | |  | |  | |   | |        |        |||   ||   |||      | |||||  | ||     |||   | |||     |   ||||| |       |    |||| || |||||||| ||||||||||||||||||||     ||||| ||||  |||| || ||||                                      
ttttaaaattcttcctatcttggtttgccattcctaacaacttattatcatactcatgcagagatataaatgtgggttactgacggagtcattgttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCACACAACGTGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACT--------------------------------------

upper sequence: EDO97438 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: EFJ28543 (Selaginella moellendorffii), 3'ss of exon 3
---agatcaggcgatgc-gcgaggcgacgcctggagtgcgcaacaatgccaatcaacctcctgacataatctgcccttgttcatcattcccgccatgcttacagAGACGTGAAGCCGCACAACGTGATGATTGACCACTCCAAGCGGCAGCTGCGGCTCATAGACTGGGGCCTGGCGGAGTTCTACTTCCCGGAGCGCGAGTTC
   || |      |  |   | ||    | || | | |       |||    |     |    |   | ||   |  ||  ||        |   |    |||| ||||||||||||||||| ||||||||||| |||    ||||  ||||||| ||||| ||||                                      
gtgaggttttttaaccccatgtggattggacttgggaggattttgatgttgcttg-tttttgcagGCACTCGATCACTGC-CACTCGCAAGGAATTATGCACAGGGACGTGAAGCCGCACAATGTGATGATTGATCACGAGCAGCGCAAGCTGCGCCTCATCGACT--------------------------------------

upper sequence: EDO97438 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 3
agatcaggcgatgcg-cgaggcgacgcctggagtgcgcaacaatgccaatcaacctcctgacataatctgcccttgttcatcatt-cccgcca-----tgcttacagAGACGTGAAGCCGCACAACGTGATGATTGACCACTCCAAGCGGCAGCTGCGGCTCATAGACTGGGGCCTGGCGGAGTTCTACTTCCCGGAGCGCGAGTTC
   | |||   |    |     |  |  |||| |  |  |  ||    |||     | ||   |     || || | |||      | ||| |     |    |||| ||||||||||||||||| ||||||||||| |||    ||||  ||||||||||||| ||||                                      
--gtgaggttttttaaccccatgtggattggact-tgggaggattttgatc--ttgcttgtttttgcagGCACTCGATCACTGCCACTCGCAAGGAATTATGCACAGGGACGTGAAGCCGCACAATGTGATGATTGATCACGAGCAGCGCAAGCTGCGGCTCATCGACT--------------------------------------

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|161804206|gb|FC088079.1|FC088079
EST:     GAGCTGCTCAAGGCGCTGCAGTACTGCCACTCCATGGGCATCATGCACAG                         AGACGTGAAGCCGCACAACGTGATGATTGACCACTCCAAGCGGCAGCTGCG
genomic: GAGCTGCTCAAGGCGCTGCAGTACTGCCACTCCATGGGCATCATGCACAGgcgagtgcgg ... atgcttacagAGACGTGAAGCCGCACAACGTGATGATTGACCACTCCAAGCGGCAGCTGCG
EST: gi|161800270|gb|FC084426.1|FC084426
EST:     GAGCTGCTCAAGGCGCTGCAGTACTGCCACTCCATGGGCATCATGCACAG                         AGACGTGAAGCCGCACAACGTGATGATTGACCACTCCAAGCGGCAGCTGCG
genomic: GAGCTGCTCAAGGCGCTGCAGTACTGCCACTCCATGGGCATCATGCACAGgcgagtgcgg ... atgcttacagAGACGTGAAGCCGCACAACGTGATGATTGACCACTCCAAGCGGCAGCTGCG
EST: gi|161803595|gb|FC089415.1|FC089415
EST:     GAGCTGCTCAAGGCGCTGCAGTACTGCCACTCCATGGGCATCATGCACAG                         AGACGTGAAGCCGCACAACGTGATGATTGACCACTCCAAGCGGCAGCTGCG
genomic: GAGCTGCTCAAGGCGCTGCAGTACTGCCACTCCATGGGCATCATGCACAGgcgagtgcgg ... atgcttacagAGACGTGAAGCCGCACAACGTGATGATTGACCACTCCAAGCGGCAGCTGCG
EST: gi|161797321|gb|FC084873.1|FC084873
EST:     GAGCTGCTCAAGGCGCTGCAGTACTGCCACTCCATGGGCATCATGCACAG                         AGACGTGAAGCCGCACAACGTGATGATTGACCACTCCAAGCGGCAGCTGCG
genomic: GAGCTGCTCAAGGCGCTGCAGTACTGCCACTCCATGGGCATCATGCACAGgcgagtgcgg ... atgcttacagAGACGTGAAGCCGCACAACGTGATGATTGACCACTCCAAGCGGCAGCTGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatcaacctcctgacataatctgcccttgttcatcattcccgccatgcttacagAGACGTGAAGCCGCACAACGTGATGATTGACCACTCCAAGCGGCAGCTGCGGCTCATAGACTGGGGCCTGGCGGAGTTCTACTTCCCGGAGCGCGAGTTC
         tcctgac  putative branch site (score: 2)
              acataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatcaggcgatgcgcgaggcgacgcctggagtgcgcaacaatgccaatcaacctcctgacataatctgcccttgttcatcattcccgccatgcttacagAGACGTGAAGCCGCACAACGTGATGATTGACCACTCCAAGCGGCAGCTGCGGCTCATAGACTGGGGCCTGGCGGAGTTCTACTTCCCGGAGCGCGAGTTC

- - - - - - - - - - - - - - - - - cgcaaca
- - - - - - - - - - - - - - - - - - - - - - -caatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacata