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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggcgggggcatgatgggctaccaaacgcacttcgttggaagccgctgaatgtgggttgcatgtggcgcatccttgcatgcatgttgcttggtcgtgcagTACGCCAAGATTGTACAGAAGCTGGGCTTCCCTGCCACGTTCAAGGAGTTTAAGATCCAAAACATCGTGGGCTCCTGTGACGTCAAGTTCCCCATCCGCT

Basic information

species Chlamydomonas reinhardtii
transcript EDP05450
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP05450 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: EFJ36040 (Selaginella moellendorffii), 3'ss of exon 5
aggcgggggcatgatgggctaccaaacgcacttcgttggaagccgctgaatgtgggttgcatgtggcgcatccttgcatgcatgttgcttggtcgtgcagTACGCCAAGATTGTACAGAAGCTGGGCTTCCCTGCCACGTTCAAGGAGTTTAAGATCCAAAACATCGTGGGCTCCTGTGACGTCAAGTTCCCCATCCGCT
                                  ||  |||| ||   ||       ||      || ||  |||    | |   | | || ||  |||| |    |||||     | |   | ||||  ||||  ||||| |||      |  |      |   | |||  | |  | |||   | ||| | | |    
----------------------------------gtatgaagacga-aaacacattgtggtctgagctcaaactta---gtaacgtccgtgatc--gcagGATTTTAAGATCCAGAACATTGTTGGCT--CCTGTGACGTT-AAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC----

upper sequence: EDP05450 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: EFJ04980 (Selaginella moellendorffii), 3'ss of exon 5
aggcgggggcatgatgggctaccaaacgcacttcgttggaagccgctgaatgtgggttgcatgtggcgcatccttgcatgcatgttgcttggtcgtgcagTACGCCAAGATTGTACAGAAGCTGGGCTTCCCTGCCACGTTCAAGGAGTTTAAGATCCAAAACATCGTGGGCTCCTGTGACGTCAAGTTCCCCATCCGCT
                               |  |  | |     |  | |||||  ||      || ||  |||    | |   | | || ||  |||| |    |||||     | |   | ||||  ||||| ||||| |||      |  |      |   | |||  | |  | |||   | ||| | | |    
------------------------------gtatgaagaagaaaacacattgtggtctg-----agctcaaactta---gtaacgtccatgatc--gcagGATTTTAAGATCCAGAACATTGTTGGCT--CCTGCGACGTT-AAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC----
















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|15702725|gb|BI727030.1|BI727030
EST:     CCAAGAGCGAGGATGACTCCCGCACGGCCGCGCGTCGT                         TACGCCAAGATTGTACAGAAGCTGGGCTTCCCTGCCACGTTCAAGGAGTTT
genomic: CCAAGAGCGAGGATGACTCCCGCACGGCCGCGCGTCGTgtaagtacct ... ggtcgtgcagTACGCCAAGATTGTACAGAAGCTGGGCTTCCCTGCCACGTTCAAGGAGTTT
EST: gi|15695028|gb|BI719349.1|BI719349
EST:     TGTGCACGGGCGCCAAGAGCGAGGATGACTCCCGCACGGCCGCGCGTCGT                         TACGCCAAGATTGTACAGAAGCTGGGC
genomic: TGTGCACGGGCGCCAAGAGCGAGGATGACTCCCGCACGGCCGCGCGTCGTgtaagtacct ... ggtcgtgcagTACGCCAAGATTGTACAGAAGCTGGGC
EST: gi|14226210|gb|BG845026.1|BG845026
EST:     TGTGCACNGGCGCCAAGAGCGAGGATGACTCCCGCACGGCCGCGCGTCGT                         TACGCCAAGATTGTACAGAAGCTGGGCTTCCCTGCCACGTTCAAGGAGTT-
genomic: TGTGCACGGGCGCCAAGAGCGAGGATGACTCCCGCACGGCCGCGCGTCGTgtaagtacct ... ggtcgtgcagTACGCCAAGATTGTACAGAAGCTGGGCTTCCCTGCCACGTTCAAGGAGTTT
EST: gi|14226211|gb|BG845027.1|BG845027
EST:     TGTGCACGGGCGCCAAGAGCGAGGATGACTCCCGCACGGCCGCGCGTCGT                         TACGCCAAGATTGTACAGAAGCTGGGCTTCCCTGCCACGTTCAAGGAGT
genomic: TGTGCACGGGCGCCAAGAGCGAGGATGACTCCCGCACGGCCGCGCGTCGTgtaagtacct ... ggtcgtgcagTACGCCAAGATTGTACAGAAGCTGGGCTTCCCTGCCACGTTCAAGGAGT
EST: gi|15368028|gb|BI527454.1|BI527454
EST:     TGTGCACGGGCGCCAAGAGCGAGGATGACTCCCGCACGGCCGCGCGTCGT                         TACGCCAAGATTGTACAGAAGCTGGGCTTCCCTGCCACGTTC
genomic: TGTGCACGGGCGCCAAGAGCGAGGATGACTCCCGCACGGCCGCGCGTCGTgtaagtacct ... ggtcgtgcagTACGCCAAGATTGTACAGAAGCTGGGCTTCCCTGCCACGTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggcgggggcatgatgggctaccaaacgcacttcgttggaagccgctgaatgtgggttgcatgtggcgcatccttgcatgcatgttgcttggtcgtgcagTACGCCAAGATTGTACAGAAGCTGGGCTTCCCTGCCACGTTCAAGGAGTTTAAGATCCAAAACATCGTGGGCTCCTGTGACGTCAAGTTCCCCATCCGCT

- - - - - - - - - - - -aaacgca
- - - - - - - - - - - - - - - - - - - - - - - - - tgtgggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgct