Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgggaacgcggcagtgggtgcagggggaatcgtggatattgcggatgtgtacaccgcaccgcataccggcctcgcccggacgggatgcggcgtccgcat...

Basic information

species Chlamydomonas reinhardtii
transcript EDO97314
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO97314 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: GRMZM2G007260_T02 (Zea mays), 5'ss of exon 4
TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgg-gaacgcggcagtgggtgcagggggaatcgtgga-tattgcggatgtgtacaccgcaccgcataccggcc---tcgcccggacgggatgcggcgtccgcat------------------------------------------------------------------------------
| |||||||| || ||||| ||  |||||||||| ||||||||||||||||| || ||||| |||||||| ||  |||| || || |||||   |  |      ||   |  |      ||  || | ||   |   | ||| |    ||| || |  |       | ||    | ||  |   |  |  | ||                                                                              
TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctcatatttgtcactcaacctatcatgttgaaataaccccattttgttcgat-cactgcctgtctattgtattgctgtaatggattattgtatttgtatccagtagaaagctgaaagctcatgcatttggtcccacctaactgaattggcattgttataatttcaattgccatatag

upper sequence: EDO97314 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: GRMZM2G007260_T01 (Zea mays), 5'ss of exon 5
TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgg-gaacgcggcagtgggtgcagggggaatcgtgga-tattgcggatgtgtacaccgcaccgcataccggcc---tcgcccggacgggatgcggcgtccgcat
| |||||||| || ||||| ||  |||||||||| ||||||||||||||||| || ||||| |||||||| ||  |||| || || |||||   |  |      ||   |  |      ||  || | ||   |   | ||| |    ||| || |  |       | ||    | ||  |   |  |      
TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAGgtattgctcatatttgtcactcaacctatcatgttgaaataaccccattttgttcgat-cactgcctgtctattgtattgctgtaatggattattgtattt----

upper sequence: EDO97314 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: AT5G62540.1 (Arabidopsis thaliana), 5'ss of exon 5
TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgggaacgcggcagtgggtgcagggggaatcgtggatattgcggatgt-gtacaccgcaccgcataccggcctcgc-ccggacgggatgcggcgtccgcat
| ||||| || || ||||||||| |||| ||| | |||||||||||||| ||||||||||||||||| ||  | || || ||||| |||||    ||     | |   |       | ||| |    |||| ||| ||  | ||  | ||   |    | |||        || |                
TTTATGCTGATGGAAGCATTTGCTTGGATATCTTGCAAAACCAGTGGAGCCCCATCTACGACGTTGCTGCAGTTCTCACATCAATTCAGgttttgacttctgaattcttc--atttgtatcttttgcattgtggaggttatgcat-gaactaaaccaagaccttttgttttacag----------------

upper sequence: EDO97314 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: AT1G14400.2 (Arabidopsis thaliana), 5'ss of exon 5
TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgggaacgcggcagtgggtgcaggg-----ggaatcgtggatattgcggatgtgtacaccgcaccgcataccggcctcgcccggacgggatgcggcgtccgcat
| ||||| || ||||| || ||| ||||||| || ||||||||||||||||| ||||| || ||||| || || || || || |||||||||    |           || |        |    | |  | |    | || ||    |  |  | |  | | |  |  |||        ||| |         
TTTATGCAGATGGGAGTATCTGCTTGGACATTCTACAAAACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAGgtgaattcaaaatgccatatgaacatctcttgatgcccttaaaagcttgaat-tgctttcttcttctctaatccgtttttccctttgttattgcag---------

upper sequence: EDO97314 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 5'ss of exon 4
TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgggaacgcggcagtgggtgcagggggaatcgtggatattgcggatgtgtacaccgcaccg---cataccggcctcgcccgga-cgggat-gcggcgtccgcat
| ||||||||||| ||||| ||| | || ||||| ||||| |||||||| || ||||||||||| || || ||  |||| || || |||||| |     |   |||    |||  ||  ||   || ||||    |  ||  |       |   | ||  ||     || ||| || ||  | || ||  | | 
TATATGCGGACGGTAGCATCTGCTTAGATATCCTGCAAAATCAGTGGAGCCCGATCTACGACGTGGCAGCGATTTTGACTTCGATTCAGgtgag----tgatcgtgatgccagcaggtgtccgtgacattgtaagtcggttgattcggttgagacgtagtggtgcgaccaggaacgtgagaggggtgttggaa-

upper sequence: EDO97314 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 5'ss of exon 4
TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgggaac-----gcggcagtgggtgcagggggaatcgtggat-attgcggatgtgtacaccgcaccgcataccggcctcgcccg-gacgggatgcggcgtccgcat
| || |||||||| ||||| ||| |||| ||  | ||||| ||||||||||||||||||||||| || || |||||||| || || |||||| | |      ||  |||  ||||   |    |  ||  ||   |   ||  | |   ||    |  |    ||    |   | |  ||||||  | |       
TATACGCGGACGGCAGCATCTGCTTGGATATTTTGCAAAATCAGTGGAGTCCCATCTACGACGTGGCAGCGATCCTGACTTCGATTCAGgtgagtatttgtggccccagcaggtgtccgtaacactgtaaatcggtcaagacatttctgccagcactaaggttggaggggtgtgtggagggatgttgtg-------

upper sequence: EDO97314 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: PP1S91_88V6.1 (Physcomitrella patens), 5'ss of exon 4
TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgggaacgcggcagtgggtgcagggggaatcgtggatattgcggatgtgtacaccgcaccg---cataccggcctcgcccggacgggatgcggcgtccgcat--
| ||||||||||| ||||| ||| | || ||||| ||||| |||||||| || ||||||||||| || || ||  |||| || || |||||| |     |   |||    |||  ||  ||   || ||||    |  ||  |       |   | ||  ||     || |||  |   |  |  | || |   
TATATGCGGACGGTAGCATCTGCTTAGATATCCTGCAAAATCAGTGGAGCCCGATCTACGACGTGGCAGCGATTTTGACTTCGATTCAGgtgag----tgatcgtgatgccagcaggtgtccgtgacattgtaagtcggttgattcggttgagacgtagtggtgcgaccaggaacgtgag-agtattcgaagta

upper sequence: EDO97314 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: EFJ23951 (Selaginella moellendorffii), 5'ss of exon 4
TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgggaacgcggcagtgggtgcagggggaatcgtggatattgcggatgtgtacaccgcaccgcataccggcctcgcccggacgggatgcggcgtccgcat
| ||||| || || |||||||| || |||||||||||||| |||||||| || || || || ||||| || || ||||| || ||||||||  |  |  || ||||          ||   ||| | | |  |  |          |      | |  |     || |                     
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATTTATGATGTTGCCGCAATACTGACATCGATCCAGgtttg--cttggaagtgtt--------gagctgtgaacact--gactccaagtttttctttttgttcttgttcttccag---------------------

upper sequence: EDO97314 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 4
TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgggaacgcggcagtgggtgcagggggaatcgtggatattgcggatgtgtacaccgcaccgcataccggcctcgcccggacgggatgcggcgtccgcat
| ||||| || || |||||||| || |||||||||||||| |||||||| || ||||| || ||||| || || ||||| || ||||||||  |   ||    || |          |   | | | | ||       ||    |    ||     |    ||  || |                    
TTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAGgtttgcttgcaagtgttg----------agctgcgaacactgactccaagtttttcttttcgttcttcttgttcttccag--------------------

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|16072081|gb|BI874077.1|BI874077
EST:     ACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG                         AGTCTGCTGTCCGACCCCAACCCCAACTCGCCG
genomic: ACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgggaacgc ... tgtcgcgcagAGTCTGCTGTCCGACCCCAACCCCAACTCGCCG
EST: gi|10779605|gb|AV636285.1|AV636285
EST:     ACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG                         AGTCTGCTGTCCGACCCCAACCCCAACTCGCCGGCCAACGGAGAGTGCGGC
genomic: ACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgggaacgc ... tgtcgcgcagAGTCTGCTGTCCGACCCCAACCCCAACTCGCCGGCCAACGGAGAG-GCGGC
EST: gi|15693474|gb|BI717779.1|BI717779
EST:     ACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG                         AGTCTGCTGTCCGACCCCAACCCCAAC
genomic: ACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgggaacgc ... tgtcgcgcagAGTCTGCTGTCCGACCCCAACCCCAAC
EST: gi|161807152|gb|FC089347.1|FC089347
EST:     ACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG                         AGTCTGCTGTCCGACCCGAACCCCAACTCGCCAGCCAACGGAGAGGCGGCC
genomic: ACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgggaacgc ... tgtcgcgcagAGTCTGCTGTCCGACCCCAACCCCAACTCGCCGGCCAACGGAGAGGCGGCC
EST: gi|6544973|gb|AV390757.1|AV390757
EST:     ACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG                         AGTCTGCTGTCCGACCCCAACCCCAACTCGCCGGCCAACGGAGAGGCGGCC
genomic: ACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgggaacgc ... tgtcgcgcagAGTCTGCTGTCCGACCCCAACCCCAACTCGCCGGCCAACGGAGAGGCGGCC
EST: gi|23362539|gb|BU650359.1|BU650359
EST:     ACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG                         AGTCTGCTGTCCGACCCCAACCCCAACTCGCCGGCCAACGGAGAG
genomic: ACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgggaacgc ... tgtcgcgcagAGTCTGCTGTCCGACCCCAACCCCAACTCGCCGGCCAACGGAGAG
EST: gi|161817678|gb|FC104413.1|FC104413
EST:     ACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG                         AGTCTGCTGTCCGACCCGAACCCCAACTCGCCAGCCAACGGAGAGGCGGCC
genomic: ACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgggaacgc ... tgtcgcgcagAGTCTGCTGTCCGACCCCAACCCCAACTCGCCGGCCAACGGAGAGGCGGCC
EST: gi|10773934|gb|AV624757.1|AV624757
EST:     ACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG                         AGTCTGCTGTCCGACCCCAACCCCAACTCGCCGGCCAACGGAGAGGCGGCC
genomic: ACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgggaacgc ... tgtcgcgcagAGTCTGCTGTCCGACCCCAACCCCAACTCGCCGGCCAACGGAGAGGCGGCC
EST: gi|15693601|gb|BI717906.1|BI717906
EST:     ACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG                         AGTCTGCTGTCCGACCCCAACCCCAACTCGCCGGCCAACGGAGAGGCGGCC
genomic: ACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgggaacgc ... tgtcgcgcagAGTCTGCTGTCCGACCCCAACCCCAACTCGCCGGCCAACGGAGAGGCGGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAGgtgggaacgcggcagtgggtgcagggggaatcgtggatattgcggatgtgtacaccgcaccgcataccggcctcgcccggacgggatgcggcgtccgcat

- - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgcatac