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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAGgtgggcgaagggactggtgggactggtggtggtggcgtggtggtagcgtgctggtggaggatgcaatccgggagcagtccatgatttggctcggggcgcg...

Basic information

species Chlamydomonas reinhardtii
transcript EDO97202
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO97202 (Chlamydomonas reinhardtii), 5'ss of exon 11
lower sequence: LOC_Os03g18130.3 (Oryza sativa), 5'ss of exon 9
GACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAGg--tgggcgaagggactggtgg-gactggtggtggtggcgtggtgg--tagcgtgctggtggaggatgcaatccgggagcagtccatgatttggctcggggcgcg
                   |  | || |   | ||||| ||||||||||| || ||||| ||||||||||||||||| ||||| ||||  |   |  ||   | |||    | |   |    |  |   |||   |  | |     | |   |   ||   |    | ||  |   | |   |      |  
------------------CACATACTGTACAGGCAGAAAGAGCAGTTCAGTGATGGCGTCGGCTACAACTGGATCGATGGCCTGAAGGCTTTCACCGAGCAGCAGgtactaattaccgaccatttccctgtgtcctgtcctataaatcgcctaattaaattgacccccgtttactctgtcatttcttcag--

upper sequence: EDO97202 (Chlamydomonas reinhardtii), 5'ss of exon 11
lower sequence: GRMZM2G093175_T02 (Zea mays), 5'ss of exon 6
GACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAGgtgggcgaagggactggtgggactggtg--gtggtggcgtggtggtagcgtg----------ctggtggaggat-gcaatccgggagcagtccatgatttggctcggggcgcg
                   |  | ||||   | ||||||||||||||||| |||||||| || |||| ||||||||| ||||| ||||     | |    |   ||  | || ||   |       |   |  | |             ||      ||||    ||||     || | ||  |||||  |   |     
------------------CATATCCTCTACAGACAGAAGGAGCAGTTCAGTGACGGCGTTGGGTACAGCTGGATCGATGGCCTGAAGGCTCATGCAACATCAAATgtaaatgttgccatatcaatttaaggacaactctgtttttttctctctccatggatcatgatccatataca-tacactatttgaatacag-----

upper sequence: EDO97202 (Chlamydomonas reinhardtii), 5'ss of exon 11
lower sequence: GRMZM2G078472_T03 (Zea mays), 5'ss of exon 10
GACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAGgtgggcgaagggactggtgggactggtggtggtggcgtggtggtagcgtgctggtg--gaggatgcaatccgggagcagtccatgatttggctcggggcgcg
                   |  | || |   | ||||| || |||||||| ||||| |||||||||||||||||||| || ||||| |    |  |  ||   |  ||  || |||| || |   |  | ||||   |  | |  || | | |   ||  |  |||                       
------------------CATATTCTGTACAGGCAGAAAGAACAGTTCAGTGACGGAGTGGGCTACAACTGGATCGATGGACTCAAAGCCTTC--ACCGAACAGCAGg-ttgatggtcgtcgt-cgaagttagctaaccagcgctgacgttcccccccatgtccag-----------------------

upper sequence: EDO97202 (Chlamydomonas reinhardtii), 5'ss of exon 11
lower sequence: GRMZM2G078472_T02 (Zea mays), 5'ss of exon 7
GACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAGgtgggcgaagggactggtgggactggtggtggtggcgtggtggtagcgtgctggtg--gaggatgcaatccgggagcagtccatgatttggctcggggcgcg
     |  ||| | || | |  | || |   | ||||| || |||||||| ||||| |||||||||||||||||||| || ||||| |    |  |  ||   |  ||  || |||| || |   |  | ||||   |  | |  || | | |   ||  |  |||                       
----GCATCCTCCGCAGC-ATATTCTGTACAGGCAGAAAGAACAGTTCAGTGACGGAGTGGGCTACAACTGGATCGATGGACTCAAAGCCTTC--ACCGAACAGCAGg-ttgatggtcgtcgt-cgaagttagctaaccagcgctgacgttcccccccatgtccag-----------------------

upper sequence: EDO97202 (Chlamydomonas reinhardtii), 5'ss of exon 11
lower sequence: PP1S410_47V6.1 (Physcomitrella patens), 5'ss of exon 7
GACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAGgtgggcgaagggactggtgggactggtggtggtggcgtggtgg---tagcgtgctggtggaggatg--caatcc-------gggagcagtccatgatttggctcggggcgcg--------------------------------------------------------------------------
                   |  |  | |  |||||||||||||| |||||||| ||||| ||||||| |||||| |||||||||||||     | |  ||    ||  ||||    |    |     |     |  |||   | | |||  ||  |||| |       |  | |||| ||   |||  |    |   |                                                                           
------------------CACATTTTGTATCGCCAGAAGGAGCAATTCAGCGATGGCGTTGGCTACAGCTGGATTGACGGCCTCAAGGCTCATGCACAGAGCCATgt-actgaatctccccgttcattttctcttccgtcaagattgagtttgatcaattctttccacgcaaccagttcaaagtttctcaacagaaactacaaaaccacaaactgctgggactaattcatacctaacaccttcaattgtcctgctcttgtgctgctaacctag

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|161804306|gb|FC092677.1|FC092677
EST:     AGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATTGACGGCCTCAAG                         GCGCACGCGGACAGCCAGGTCAGCGACGACATGATGAAGACGGCCGCGCAT
genomic: AGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAGgtgggcgaag ... tcacctgcagGCGCACGCGGACAGCCAGGTCAGCGACGACATGATGAAGACGGCCGCGCAT
EST: gi|161796812|gb|FC084546.1|FC084546
EST:     GGATTGACGGCCTCAAG                         GCGCACGCGGACAGCCAGGTCAGCGACGACATGATGAAGACGGCCGCGCAT
genomic: GGATCGACGGCCTCAAGgtgggcgaag ... tcacctgcagGCGCACGCGGACAGCCAGGTCAGCGACGACATGATGAAGACGGCCGCGCAT
EST: gi|9210297|gb|BE337212.1|BE337212
EST:     AGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAG                         GCGCACGCGGACAGCCAGGTCAGCGACGACATGATGAAGACGGCCGCGCAT
genomic: AGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAGgtgggcgaag ... tcacctgcagGCGCACGCGGACAGCCAGGTCAGCGACGACATGATGAAGACGGCCGCGCAT
EST: gi|15698263|gb|BI722568.1|BI722568
EST:     AGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAG                         GCGCACGCGGACAGCCAGGTCAGCGACGACATGATGAAGACGGCCGCGCAT
genomic: AGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAGgtgggcgaag ... tcacctgcagGCGCACGCGGACAGCCAGGTCAGCGACGACATGATGAAGACGGCCGCGCAT
EST: gi|161814299|gb|FC102065.1|FC102065
EST:     AGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATTGACGGCCTCAAG                         GCGCACGCGGACAGCCAGGTCAGCGACGACATGATGAAGACGGCCGCGCAT
genomic: AGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAGgtgggcgaag ... tcacctgcagGCGCACGCGGACAGCCAGGTCAGCGACGACATGATGAAGACGGCCGCGCAT
EST: gi|161800664|gb|FC085600.1|FC085600
EST:     AGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATTGACGGCCTCAAG                         GCGCACGCGGACAGCCAGGTCAGCGACGACATGATGAAGACGGCCGCGCAT
genomic: AGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAGgtgggcgaag ... tcacctgcagGCGCACGCGGACAGCCAGGTCAGCGACGACATGATGAAGACGGCCGCGCAT
EST: gi|16430040|gb|BI995266.1|BI995266
EST:     AGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAG                         GCGCACGCGGACAGCCAGGTCAGCGACGACATGATGAAGACGGCCGCGCAT
genomic: AGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAGgtgggcgaag ... tcacctgcagGCGCACGCGGACAGCCAGGTCAGCGACGACATGATGAAGACGGCCGCGCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAGgtgggcgaagggactggtgggactggtggtggtggcgtggtggtagcgtgctggtggaggatgcaatccgggagcagtccatgatttggctcggggcgcg

- - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttggct