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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttttccttgtgctctttaacacacacacacacacacacacacacacacacacacgcacgcacgcacgcacgcacacaaacaaacacgtacacacacagACGCGGACGGCTTCTTCCACACGGGCGACGTGGGCGAGCTGGTGACGGACGGAACCCTCAAGATCATCGACCGCAAGAAGAACATCTTCAAGCTCAGCCA

Basic information

species Chlamydomonas reinhardtii
transcript EDO96800
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO96800 (Chlamydomonas reinhardtii), 3'ss of exon 12
lower sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
tgttttccttgtgctctttaacacacacacacacacacacacacacacacacacacgcacgcacgcacgcacgcacacaaacaaacacgtacacacacagACGCGGACGGCTTCTTCCACACGGGCGACGTGGGCGAGCTGGTGACGGACGGAACCCTCAAGATCATCGACCGCAAGAAGAACATCTTCAAGCTCAGCCA------------------------
                           || |   | | | ||  ||      ||| | | ||    ||     | |   |   ||  | |      || | | |     | |   |       || ||| | || |||  |  | | || |||| | | |||||||| || ||||||||||||||||||||||||  |||                        
-----------------------ttttcatatcaaaagagactgacctgttaaca-gaatgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA

upper sequence: EDO96800 (Chlamydomonas reinhardtii), 3'ss of exon 12
lower sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 15
tgttttccttgtgctctttaacacacacacacacacacacacacacacacacacacgcacgcacgcacgcacgcacacaaacaaacacgtacacacacagACGCGGACGGCTTCTTCCACACGGGCGACGTGGGCGAGCTGGTGACGGACGGAACCCTCAAGATCATCGACCGCAAGAAGAACATCTTCAAGCTCAGCCA------------------------
                 || | | | |  |  |   | ||   |   || | |  |    | |       |    | |||    | ||||     ||| | |    |    |  || |   | || ||| | || |||  |  | | ||||||| | | |||||||| |||||||||||||||||||||||||||   ||                        
--------------gtcttgaaagagatcctgattta-acttgccatcagaaatgcctttgaa-------attttcccaagtcta-acgtttgttcactgccaaatattaatatttac-tgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA

upper sequence: EDO96800 (Chlamydomonas reinhardtii), 3'ss of exon 12
lower sequence: GRMZM2G104847_T01 (Zea mays), 3'ss of exon 15
tgttttccttgtgctctttaacacacacacacaca-cacacacacacacacacacacgcacgcacgcacgcacgcacacaaacaaacacgtacacacacagACGCGGACGGCTTCTTCCAC--ACGGGCGACGTGGGCGAGCTGGTGACGGACGGAACCCTCAAGATCATCGACCGCAAGAAGAACATCTTCAAGCTCAGCCA------------------------
            |      || | | | |  ||   | |||        |    |||  |          ||  ||   || ||     ||  |  |   ||    | |  |  | |       | || ||  | || |||  |    |  | || ||  | |||||||||||| | ||||||||||||||||||||   |||                        
------------gtgaaagaataaaaaaaatcatttctcacttcttttaatttgcacctaactgaaggatcagtcagtgaagcagctg-gtcgattcgtggaacttgtcatcaccctatgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAAAGAAGAACATCTTCAAGCTGTCCCAGGGGGAGTATGTGGCAGTTGAGGT

upper sequence: EDO96800 (Chlamydomonas reinhardtii), 3'ss of exon 12
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 15
tgttttccttgtgctctttaacacacacacacacacacacacacacacacacacacgcacgcacgcacgcacgcacacaaacaaacacgtacacacacagACGCGGACGGCTT-CTTCCACACGGGCGACGTGGGCGAGCTGGTGACGGACGGAACCCTCAAGATCATCGACCGCAAGAAGAACATCTTCAAGCTCAGCCA------------------------
                           | || |    ||      |    |   | |     | |  | |          |        |  | |||     || || | |||   |   ||| || || || || |||  |    | || || | | | || || |||||||||||||||||||| ||||||||    ||                        
----------------------gtttgctcatattggcatttcttcttgaat-taagttttgaggtcctctattttgtggattcgtttcttta-acaaccttgctgatgacttatcttttcacagGGGATGTTGGTGAGTGGCAACCTGATGGGAGCATGAAAATTATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAA

upper sequence: EDO96800 (Chlamydomonas reinhardtii), 3'ss of exon 12
lower sequence: PP1S218_19V6.1 (Physcomitrella patens), 3'ss of exon 16
----------------------tgttttcctt----gtgctctttaacacacacacacacacacacacacacacacacacacgcacgcac-gcacgcacgcacacaaacaaacacgtacacaca---cagACGCGGACGGCTTCTTCCACAC---GGGCGACGTGGGCGAGCTGGTGACGGACGGAACCCTCAAGATCATCGACCGCAAGAAGAACATCTTCAAGCTCAGCCA------------------------
                       |||||| ||     |  | |  | |   |     | | || | |    |         ||   | |  |     |   ||||     |||   | || |      | |  | ||     |     | ||    || ||  | || |||  |  ||  || ||| || | |||||||||||| | |||||||||||||||||| |    ||                        
gtaatgtcttctctttaattgacgttttctttttaaataatttggatcttgctttttccctcagagagtgtctttttgtttcgttggaattgtttatattaacactgtggaactgctgcatatggtctacattctgattctcttcgtaaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGAAGAAGAACATCTTCAAGTTGTCACAGGGTGAATACGTTGCTGTCGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacacacacacgcacgcacgcacgcacgcacacaaacaaacacgtacacacacagACGCGGACGGCTTCTTCCACACGGGCGACGTGGGCGAGCTGGTGACGGACGGAACCCTCAAGATCATCGACCGCAAGAAGAACATCTTCAAGCTCAGCCA
                                 aaacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttttccttgtgctctttaacacacacacacacacacacacacacacacacacacgcacgcacgcacgcacgcacacaaacaaacacgtacacacacagACGCGGACGGCTTCTTCCACACGGGCGACGTGGGCGAGCTGGTGACGGACGGAACCCTCAAGATCATCGACCGCAAGAAGAACATCTTCAAGCTCAGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
tgttttc
- - - - ttgtgct
- - - - - - - - -ttaacac
- - - - - - - - - - acacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - -cacgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaaca