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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagccaaccccacaccgcgacggaccagcaggaaaggccaccgcactcgtaatgccatttgcttatcaacactactactaacaatgacggctgtgtgcagGTGGGCTGCGGCGCGGACGAGCTGATCGACCTGCTCATGCGCTGTGTGCTGGAGCCCGGTGACAAGATCGTGGACTGCCCGCCCACCTTCACCAT

Basic information

species Chlamydomonas reinhardtii
transcript EDP01242
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP01242 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GLYMA16G27220.1 (Glycine max), 3'ss of exon 4
cagccaaccccacaccgcgacggaccagcaggaaaggccaccgcactcgtaatgccatttgcttatcaacactactactaacaatgacggctgtgtgcagGTGGGCTGCGGCGCGGACGAGCTGATCGACCTGCTCATGCGCTGTGTGCTGGAGCCCGGTGACAAGATCGTGGACTGCCCGCCCACCTTCACCAT--------------------------------------------
                          || |  ||   |    | | |    ||   |    |  ||     ||  |  |   |||        |    | |       |    |  ||  |||  || |  |   |    | ||||||||||| || || |||||||| ||||||||||| || |||||||| ||                                            
-----------------------gttagaaccaataccttatgtattttagata--agcctcaaattctttctcttcatgctaattgtcatcatagctacgacaatcaccat-catacatgcttctc-atatatactccagTTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAG
















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|16428804|gb|BI994014.1|BI994014
EST:     TGCGGAGAGCGCTTGCGGAGATGCACAATATCCCGATGGAGAACCTGCTG                         GTGGGCTGCGGCGCGGACGAGCTAATCGACCTGCTCATGCGCTGTGTGCTG
genomic: TGCGGAGAGCGCTTGCGGAGATGCACAACATCCCGATGGAGAACCTGCTGgtgagatatg ... ctgtgtgcagGTGGGCTGCGGCGCGGACGAGCTGATCGACCTGCTCATGCGCTGTGTGCTG
EST: gi|23361878|gb|BU649714.1|BU649714
EST:     TGCGGAGAGCGCTTGCGGAGATGCACAACATCCCGATGGAGAACCTGCTG                         GTGGGCTGCGGCGCGGACGAGCTGATCGACCTGCTCATGCGCTGTGTGCTG
genomic: TGCGGAGAGCGCTTGCGGAGATGCACAACATCCCGATGGAGAACCTGCTGgtgagatatg ... ctgtgtgcagGTGGGCTGCGGCGCGGACGAGCTGATCGACCTGCTCATGCGCTGTGTGCTG
EST: gi|15693220|gb|BI717525.1|BI717525
EST:     TGCGGAGAGCGCTTGCGGAGATGCACAACATCCCGATGGAGAACCTGCTG                         GTGGGCTGCGGCGCGGACGAGCTGATCGACCTGCTCATGCGCTGTGTGCTG
genomic: TGCGGAGAGCGCTTGCGGAGATGCACAACATCCCGATGGAGAACCTGCTGgtgagatatg ... ctgtgtgcagGTGGGCTGCGGCGCGGACGAGCTGATCGACCTGCTCATGCGCTGTGTGCTG
EST: gi|6541204|gb|AV386988.1|AV386988
EST:     TGCGGAGAGCGCTTGCGGAGATGCACAATATCCCGATGGAGAACCTGCTG                         GTGGGCTGCGGCGCGGACGAGCTAATCGACCTGCTCATGCGCTGTGTGCTG
genomic: TGCGGAGAGCGCTTGCGGAGATGCACAACATCCCGATGGAGAACCTGCTGgtgagatatg ... ctgtgtgcagGTGGGCTGCGGCGCGGACGAGCTGATCGACCTGCTCATGCGCTGTGTGCTG
EST: gi|16438059|gb|BM003279.1|BM003279
EST:     TGCGGAGAGCGCTTGCGGAGATGCACAACATCCCGATGGAGAACCTGCTG                         GTGGGCTGCGGCGCGGACGAGCTGATCGACCTGCTCATGCGCTGTGTGCTG
genomic: TGCGGAGAGCGCTTGCGGAGATGCACAACATCCCGATGGAGAACCTGCTGgtgagatatg ... ctgtgtgcagGTGGGCTGCGGCGCGGACGAGCTGATCGACCTGCTCATGCGCTGTGTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgtaatgccatttgcttatcaacactactactaacaatgacggctgtgtgcagGTGGGCTGCGGCGCGGACGAGCTGATCGACCTGCTCATGCGCTGTGTGCTGGAGCCCGGTGACAAGATCGTGGACTGCCCGCCCACCTTCACCAT
                              tactaac  putative branch site (score: 0)
                 ttatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagccaaccccacaccgcgacggaccagcaggaaaggccaccgcactcgtaatgccatttgcttatcaacactactactaacaatgacggctgtgtgcagGTGGGCTGCGGCGCGGACGAGCTGATCGACCTGCTCATGCGCTGTGTGCTGGAGCCCGGTGACAAGATCGTGGACTGCCCGCCCACCTTCACCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - cccacac
- - - - - - - - - - - -accagca
- - - - - - - - - - - - - - - - - - - - - - actcgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaatga