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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTCACCGCGACCTGAAGCCGGAGAACTTCCTGCTGTCGGACCGCTCCGCCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAGgtgcgcgggggtgctcctggcgcatcgggtgaccaatggggcagtgggtttggaagacagcggcaggatgcgtgtttgcaaccgtggcgtgcaaatgtgg...

Basic information

species Chlamydomonas reinhardtii
transcript EDP04678
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP04678 (Chlamydomonas reinhardtii), 5'ss of exon 7
lower sequence: LOC_Os03g48270.1 (Oryza sativa), 5'ss of exon 1
CATTCACCGCGACCTGAAGCCGGAGAACTTCCTGCTGTCGGACCGCTCCGCCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAGgtgcgcgggggtgctcctggcgcatcgggtgaccaatggggcagtgggtttggaagacagcggcaggatgcgtgtttgcaaccgtggcgtgcaaatgtgg-------
    ||||||||||| |||||||||||||||||     | | |    |||  |  |||  ||| ||||| |  || ||||| || ||   ||||||||      |   |  |  |||   |   |       | ||||     |   | ||| |  | |         |      |  |  ||            | | |       
----CACCGCGACCTCAAGCCGGAGAACTTCCTCTACGCCGGCAAGGCCGAGGACGCGCAGCTCAAGGCCATCGATTTCGGCCTCTCCGTCTTCTTCCGACCTGgtcagcttcttcccttcttcttcctctgc-aatgcat--gcacgcttgaacaaaacttttttttttttgcctctcttccccatttaatttttttagaacatat

upper sequence: EDP04678 (Chlamydomonas reinhardtii), 5'ss of exon 7
lower sequence: GRMZM2G311220_T03 (Zea mays), 5'ss of exon 1
CATTCACCGCGACCTGAAGCCGGAGAACTTCCTGCTGTCGGACCGCTCCGCCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAGgtgcgcgggggtgctcctggcgc-atcgggtgaccaatggggcagtgggtttggaagacagcggcag-gatgcgtgtttgcaaccgtggcgtgcaaatgtgg---
    ||||||||||| |||||||||||||||||  |  |  |       |      || |||| ||||| |  ||||||||||| ||   ||||||| | |   |  | |   | ||   ||  |||   |  | |||  ||  |    | ||     |  |  | | |||   || ||  |   |  |    |  |  ||    
----CACCGCGACCTCAAGCCGGAGAACTTCCTCTTCGCCAATAAGAAGGAGAACTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTC-AAGCCTGgtgagtcacaccaaccgagatcctttcccaaattcggacgattttctgcgcatcttcaaccgtgatttctggttttagtgggaggaaacttacttgacgg
















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|161803405|gb|FC088588.1|FC088588
EST:     CCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAG                         GAGGGCCAGGTGTTTACGGACATTGTGGGCAGCGCATACTACGTGGCGCCC
genomic: CCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAGgtgcgcgggg ... tgtgcaacagGAGGGCCAGGTATTTACGGACATTGTGGGCAGCGCATACTACGTGGCGCCC
EST: gi|161814667|gb|FC100431.1|FC100431
EST:     CCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAG                         GAGGGCCAGGTGTTTACGGACATTGTGGGCAGCGCATACTACGTGGCGCCC
genomic: CCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAGgtgcgcgggg ... tgtgcaacagGAGGGCCAGGTATTTACGGACATTGTGGGCAGCGCATACTACGTGGCGCCC
EST: gi|161811928|gb|FC096118.1|FC096118
EST:     CCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAG                         GAGGGCCAGGTGTTTACGGACATTGTGGGCAGCGCATACTACGTGGCGCCC
genomic: CCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAGgtgcgcgggg ... tgtgcaacagGAGGGCCAGGTATTTACGGACATTGTGGGCAGCGCATACTACGTGGCGCCC
EST: gi|161799492|gb|FC086079.1|FC086079
EST:     CCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAG                         GAGGGCCAGGTGTTTACGGACATTGTGGGCAGCGCATACTACGTGGCGCCC
genomic: CCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAGgtgcgcgggg ... tgtgcaacagGAGGGCCAGGTATTTACGGACATTGTGGGCAGCGCATACTACGTGGCGCCC
EST: gi|161814378|gb|FC103730.1|FC103730
EST:     CCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAG                         GAGGGCCAGGTGTTTACGGACATTGTGGGCAGCGCATACTACGTGGCGCCC
genomic: CCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAGgtgcgcgggg ... tgtgcaacagGAGGGCCAGGTATTTACGGACATTGTGGGCAGCGCATACTACGTGGCGCCC
EST: gi|161817487|gb|FC100855.1|FC100855
EST:     CCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAG                         GAGGGCCAGGTGTTTACGGACATTGTGGGCAGCGCATACTACGTGGCGCCC
genomic: CCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAGgtgcgcgggg ... tgtgcaacagGAGGGCCAGGTATTTACGGACATTGTGGGCAGCGCATACTACGTGGCGCCC
EST: gi|14233757|gb|BG852573.1|BG852573
EST:     CCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAG                         GAGGGCCAGGTATTTACGGACATTGTGGGCAGCGCATACTACGTGGCGCCC
genomic: CCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAGgtgcgcgggg ... tgtgcaacagGAGGGCCAGGTATTTACGGACATTGTGGGCAGCGCATACTACGTGGCGCCC
EST: gi|14226566|gb|BG845398.1|BG845398
EST:     CCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAG                         GAGGGCCAGGTATTTACGGACATTGTGGGCAGCGCATACTACGTGGCGCCC
genomic: CCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAGgtgcgcgggg ... tgtgcaacagGAGGGCCAGGTATTTACGGACATTGTGGGCAGCGCATACTACGTGGCGCCC
EST: gi|161800857|gb|FC084103.1|FC084103
EST:     CCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAG                         GAGGGCCAGGTGTTTACGGACATTGTGGGCAGCGCATACTACGTGGCGCCC
genomic: CCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAGgtgcgcgggg ... tgtgcaacagGAGGGCCAGGTATTTACGGACATTGTGGGCAGCGCATACTACGTGGCGCCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTCACCGCGACCTGAAGCCGGAGAACTTCCTGCTGTCGGACCGCTCCGCCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAGgtgcgcgggggtgctcctggcgcatcgggtgaccaatggggcagtgggtttggaagacagcggcaggatgcgtgtttgcaaccgtggcgtgcaaatgtgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgggttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaaat