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

GCGCGCAAGACTGCGCAGGCGTACTTCCAGACCTACAAGGAGCACATCCCGGTGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACACgtgagtggggcaccttgaatgtgcagggcccaatgatggacacggacgatgcctgaacccgattagtgccaagagcgttgcttatcaaacacagcttaac...

Basic information

species Chlamydomonas reinhardtii
transcript EDO97600
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO97600 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: GRMZM5G850355_T02 (Zea mays), 5'ss of exon 7
GCGCGCAAGACTGCGCAGGCGTACTTCCAGACCTACAAGGAGCACATCCCGGTGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACAC-
                                       ||||| || || ||  ||||||| ||||| ||||| || |||||||||||||||||||||| || || |     | || || |  |       || |     |   | ||      | |   |    | |||| |     ||  |  ||| | | |   | |      
---------------------------------------GAGCATATACCTGTAACACAGCTTGTGCGGGAGACTGCTGCTGTGATGCAGGAGTTCACACAGTCAGGgtatttaactagacttagttacttacattttcccatcggtacatacaataatggcatgcactgcctaatttattattgttcataaaaaagctgatgccat

upper sequence: EDO97600 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: GRMZM5G850355_T08 (Zea mays), 5'ss of exon 6
GCGCGCAAGACTGCGCAGGCGTACTTCCAGACCTACAAGGAGCACATCCCGGTGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACAC-
                                       ||||| || || ||  ||||||| ||||| ||||| || |||||||||||||||||||||| || || |     | || || |  |       || |     |   | ||      | |   |    | |||| |     ||  |  ||| | | |   | |      
---------------------------------------GAGCATATACCTGTAACACAGCTTGTGCGAGAGACTGCTGCTGTGATGCAGGAGTTCACACAGTCAGGgtatttaactagacttagttacttacattttcccatcggtacatacaataatggcatgcactgcctaatttattattgttcataaaaaagctgatgccat
















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|161791694|gb|FC078615.1|FC078615
EST:     GGTGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACAC                         AGACGGGTGGCGTGCGCCCCTTCGGTGTGTCGCTGCTGATGGCGGGCTACG
genomic: GGTGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACACgtgagtgggg ... ctcgctgcagAGACGGGTGGCGTGCGCCCCTTCGGTGTGTCGCTGCTGATGGCGGGCTACG
EST: gi|22061674|gb|BQ814385.1|BQ814385
EST:     GGTGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACAC                         AGACGGGTGGCGTGCGCCCCTTCGGTGTGTCGCTGCTGATGGCGGGCTACG
genomic: GGTGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACACgtgagtgggg ... ctcgctgcagAGACGGGTGGCGTGCGCCCCTTCGGTGTGTCGCTGCTGATGGCGGGCTACG
EST: gi|15373566|gb|BI532992.1|BI532992
EST:     GGTGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACAC                         AGACGGGTGGCGTGCGCCCCTTCGGTGTGTCGCTGCTGATGGCGGGCTACG
genomic: GGTGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACACgtgagtgggg ... ctcgctgcagAGACGGGTGGCGTGCGCCCCTTCGGTGTGTCGCTGCTGATGGCGGGCTACG
EST: gi|161791279|gb|FC081178.1|FC081178
EST:     GGTGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACAC                         AGACGGGTGGCGTGCGCCCCTTCGGTGTGTCGCTGCTGATGGCGGGCTACG
genomic: GGTGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACACgtgagtgggg ... ctcgctgcagAGACGGGTGGCGTGCGCCCCTTCGGTGTGTCGCTGCTGATGGCGGGCTACG
EST: gi|16073596|gb|BI875592.1|BI875592
EST:     GGTGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACAC                         AGACGGGTGGCGTGCGCCCCTTCGGTGTGTCGCTGCTGATGGCGGGCTACG
genomic: GGTGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACACgtgagtgggg ... ctcgctgcagAGACGGGTGGCGTGCGCCCCTTCGGTGTGTCGCTGCTGATGGCGGGCTACG
EST: gi|15368299|gb|BI527725.1|BI527725
EST:     GGGGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACAC                         AGACGGGTGGCGTGCGCCCCTTCGGTGTGTCGCTGCTGATGGCGGGCTACG
genomic: GGTGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACACgtgagtgggg ... ctcgctgcagAGACGGGTGGCGTGCGCCCCTTCGGTGTGTCGCTGCTGATGGCGGGCTACG
EST: gi|161792152|gb|FC077220.1|FC077220
EST:     GGTGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACAC                         AGACGGGTGGCGTGCGCCCCTTCGGTGTGTCGCTGCTGATGGCGGGCTACG
genomic: GGTGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACACgtgagtgggg ... ctcgctgcagAGACGGGTGGCGTGCGCCCCTTCGGTGTGTCGCTGCTGATGGCGGGCTACG
EST: gi|15695486|gb|BI719791.1|BI719791
EST:     GGTGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACAC                         AGACGGGTGGCGTGCGCCCCTTCGGTGTGTCGCTGCTGATGGCGGGCTACG
genomic: GGTGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACACgtgagtgggg ... ctcgctgcagAGACGGGTGGCGTGCGCCCCTTCGGTGTGTCGCTGCTGATGGCGGGCTACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGCGCAAGACTGCGCAGGCGTACTTCCAGACCTACAAGGAGCACATCCCGGTGGCACAGCTCGTGCGTGAGACGGCGGCTGTGATGCAGGAGTTCACACgtgagtggggcaccttgaatgtgcagggcccaatgatggacacggacgatgcctgaacccgattagtgccaagagcgttgcttatcaaacacagcttaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttagtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaca