Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccgcctctcaacatccacgcatccaccaataccttgcagctaaccacgcctcaagtgacccgcctcctgcgcctcctcactccttgtcaccgcctgcagGGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAGCTGCTTGGGCCCAACTACAAAGAGGCCGTGCTCGAGCTCAACGCCTCAG

Basic information

species Chlamydomonas reinhardtii
transcript EDO98380
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO98380 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: LOC_Os04g48060.1 (Oryza sativa), 3'ss of exon 1
-------cccgcctctcaacatccacgcatccaccaataccttgcagctaaccacgcctcaagtgacccgcctcctgcgcctcctcactcct---tgtcaccgcctgcagGGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAGCTGCTTGGGCCCAACTACAAAGAGGCCGTGCTCGAGCTCAACGCCTCAG
       ||     ||| |   ||  ||   | |     | |  || | || ||    |     ||  ||  ||   |   |  |   |  |   | ||     || ||||| ||||||||||| || ||||| || ||||||||||  ||||| ||| ||||||| || || | ||||   |||||||||||||||||||| ||||| |
gtaagcgccatttcctcgaacaccttgcgcgcgctctcgc-taacacccaagcagcagtacgacgaatcgtttctaacctttttttttttttaactatcgttttctacagGGGCCTCCGGGCACCGGGAAGACTACGAGCATCCTGTCGCTGGCACACGAGCTGCTCGGACCTAGCTACCGCGAGGCCGTGCTCGAGCTCAATGCCTCGG
















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|34983941|gb|CF557858.1|CF557858
EST:     GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCG                         GGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG
genomic: GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCGgtgcgtgtcg ... ccgcctgcagGGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG
EST: gi|22058612|gb|BQ813039.1|BQ813039
EST:     GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCG                         GGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG
genomic: GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCGgtgcgtgtcg ... ccgcctgcagGGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG
EST: gi|22058607|gb|BQ813038.1|BQ813038
EST:     GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCG                         GGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG
genomic: GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCGgtgcgtgtcg ... ccgcctgcagGGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG
EST: gi|8287554|gb|BE025113.1|BE025113
EST:     GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCG                         GGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG
genomic: GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCGgtgcgtgtcg ... ccgcctgcagGGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG
EST: gi|16436997|gb|BM002217.1|BM002217
EST:     GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCG                         GGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG
genomic: GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCGgtgcgtgtcg ... ccgcctgcagGGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG
EST: gi|161794755|gb|FC077353.1|FC077353
EST:     GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCG                         GGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG
genomic: GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCGgtgcgtgtcg ... ccgcctgcagGGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG
EST: gi|15697306|gb|BI721611.1|BI721611
EST:     GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCG                         GGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG
genomic: GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCGgtgcgtgtcg ... ccgcctgcagGGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG
EST: gi|15704437|gb|BI728742.1|BI728742
EST:     GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCG                         GGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG
genomic: GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCGgtgcgtgtcg ... ccgcctgcagGGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG
EST: gi|34983940|gb|CF557857.1|CF557857
EST:     GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCG                         GGCCCTCCGGGCACGGGCAAGACCACCA
genomic: GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCGgtgcgtgtcg ... ccgcctgcagGGCCCTCCGGGCACGGGCAAGACCACCA
EST: gi|15698627|gb|BI722932.1|BI722932
EST:     GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCG                         GGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG
genomic: GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCGgtgcgtgtcg ... ccgcctgcagGGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG
EST: gi|15698700|gb|BI723021.1|BI723021
EST:     GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCG                         GGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG
genomic: GGTTACAAGTAATCGCTGAAGAGGGCAACATGCCCAACGTCATCCTCTCGgtgcgtgtcg ... ccgcctgcagGGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacgcctcaagtgacccgcctcctgcgcctcctcactccttgtcaccgcctgcagGGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAGCTGCTTGGGCCCAACTACAAAGAGGCCGTGCTCGAGCTCAACGCCTCAG
                             tcctcac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccgcctctcaacatccacgcatccaccaataccttgcagctaaccacgcctcaagtgacccgcctcctgcgcctcctcactccttgtcaccgcctgcagGGCCCTCCGGGCACGGGCAAGACCACCAGCATCCTGTGCCTGGCCCACCAGCTGCTTGGGCCCAACTACAAAGAGGCCGTGCTCGAGCTCAACGCCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - -acatcca
- - - - - - - - - - - - -accaata
- - - - - - - - - - - - - - - - - - - - - aaccacg