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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagaggtcgagacagcggagtaacggccgcggcatcgcggcacgcggcagcagcccgagccggacagtaaggcaggcccatacaacagcggtcggc...

Basic information

species Chlamydomonas reinhardtii
transcript EDO98923
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO98923 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: GRMZM2G152328_T02 (Zea mays), 5'ss of exon 2
---------------ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagaggtcgagacagcggagtaacggccgcggcatcgcggcacgcggcagcagcccgagccggacagtaaggcaggccca--tacaacagcggtcggc---------------------------------
               |||||||||||||||||||||   ||||| |||||||| || |||||||        |      | |      |  |||||   ||  |  |  |  |    |   |   ||   ||| |     |  || |  | |  | || ||| |                                  
GAGAAGATGACCCAGATCATGTTCGAGACCTTCAACACCCCGGCTATGTACGTCGCCATCCAGGCCGT----GCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagc-tgattccgttctctgcttaacaatttccaaatccgatttgctcctgcagtccgttatctctaatatctgtggcttcccctctctcag

upper sequence: EDO98923 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: GLYMA08G15480.1 (Glycine max), 5'ss of exon 3
---------------ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagaggtc----gagacagcggagtaacggccg--cggcatcgcggcacgcggcagcagcccgagccggacagtaaggcaggcccatacaacagcggtcggc-----------
               |||||||| ||||||||||| ||||| |||||||| ||||| |||||||          |      |  || ||    ||  | |    | ||  |  ||   | |   |  |        | | | |    |  |  | |   |        |           
GAAAAGATGACCCAAATCATGTTTGAGACCTTCAATGTGCCTGCCATGTATGTGGCCATCCAGGCTGTTCTCTCCTTGTATGCAAGTGGTCGCACAACTGgtttgtatatcaccatctgtcttgattcattcttttataatcacattgttctttccctgaatcaattccttttaaaacag

upper sequence: EDO98923 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: GLYMA05G32220.1 (Glycine max), 5'ss of exon 2
---------------ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagaggtc----gagacagcggagtaacggccg--cggcatcgcggcacgcggcagcagcccgagccggacagtaa-ggcaggcccatacaacagcggtcggc----------
               |||||||| ||||||||||| ||||| |||||||| ||||| |||||||          |      | ||| ||    ||  | |    | ||     ||   | |   |  |        | | | |   ||  |     |   | |  |              
GAAAAGATGACCCAAATCATGTTTGAGACCTTCAATGTGCCTGCCATGTATGTGGCCATCCAGGCTGTTCTCTCCTTGTATGCCAGTGGTCGCACAACTGgtttgtatattaccatctgtcttgattcattcttttataatcacatcattctttccctgaatcaattcctttcaaaacag

upper sequence: EDO98923 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: GLYMA06G15520.2 (Glycine max), 5'ss of exon 3
---------------ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGg----------------tgagagaggtcgagacagcggagtaacggccgcggcatcgcggcacgcggcagcagcccgagccggacagtaaggcaggcccatacaacagcggtcggc-----
               |||||||| ||||||||||| ||||| |||||||| ||||| |||||||                ||  || |||||  ||| | |  |           |     | |      || |  |     |   ||| |     |  |    |  | | |  |  |      
GAAAAAATGACCCAAATCATGTTTGAGACCTTCAATGTGCCTGCCATGTATGTGGCCATCCAGGCTGTCCTCTCCCTATATGCAAGTGGTCGC-ACAACTGgtttgtacttatttccatctgtcttaattca-ctcctttgtcttcacattgttctatccttgaatcaaatctttttgaatcag

upper sequence: EDO98923 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: GLYMA04G39380.2 (Glycine max), 5'ss of exon 3
---------------ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagag-------aggtcgagacagcggagtaacggccgcggcatcgcggcacgcggcagcagcccg-agccggacagtaaggcaggcccatacaacagcggtcggc------------
               |||||||| ||||||||||| ||||| |||||||| ||||| ||||| |             |  |  |    |  |   ||| |    |   | |   |   | |   ||   |  ||        | |    |  |  | |   |        |            
GAAAAAATGACCCAAATCATGTTTGAGACCTTCAATGTGCCTGCCATGTATGTGGCCATCCAAGCTGTCCTCTCCCTATATGCAAGTGGTCGCACAACTGgtttgtatttgtatccatctgtttcaattcatagttttgtcatcacattgttctttccctgaatcaaatactttctgaaacag

upper sequence: EDO98923 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: PP1S372_48V6.1 (Physcomitrella patens), 5'ss of exon 2
---------------ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagaggtcgagaca-gcggagtaacggccg-cggcatcgcggcacgcg-gcagcagcccgagccggacagtaa-ggcaggcccatacaacagcggtcggc--------------------------------
               |||||||||||||| |||||||||||||| ||||||||||| ||||||| | | |  ||||    | |||      ||  || |||    | ||   | | |  |      |    |||  ||   || |||           |  |  |                                  
GAGAAGATGACGCAGATCATGTTCGAGACGTTCAACGTGCCGGCGATGTACGTGGCGATCCAGGCG-GTGCTGTCGCTGTACGCGAGCGGGCGAACGACGGgtgagtggggagtgagtggtgagggggtggggatggtggtggtaggatgtggaggtgggaggtgattgagaacagatgtggcggtgcgtggaatgcag

upper sequence: EDO98923 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 5'ss of exon 4
---------------ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagaggtcgaga-----cagcggagtaacggccgcggcatcgcggcacgcggcagcagcccgagccggacagtaaggcag--gcccatacaacagcggtcggc----------------------------------------------------------------------------------------
               |||||||||||||| |||||||||||||| ||||||||||| || ||||  || |  |||   |     ||| |||  |||| |||  |  |   || |   ||    ||    |  | |   ||  |   |  ||  |       | |||  |                                                                                         
GAGAAGATGACGCAGATCATGTTCGAGACGTTCAACGTGCCGGCGATGTACGTGGCCATTCAGGC-AGTGCTGTCACTATATGCCAGTGGACGAACGACCGgtgagtgatgggagaaggggtgaggtgaatgcagcatgtgcgttggttgcgaaagtggtggaggtgtgtggagaggtggggtgtttgacatgggaaggtttgtgggtcggggtaagaaactgagagcagttgtggtgatgaatgcaatgcaatgcag

upper sequence: EDO98923 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: EFJ17401 (Selaginella moellendorffii), 5'ss of exon 2
---------------ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagaggtcgagacagcggagtaacggccgcggcatcgcggcacgc----ggcagcagcccgagccggacagtaaggcaggcccatacaacagcggtcggc------------------------------------------------------------------------------------
               |||||||||||||||||||| || ||||||||||||||||| ||||| |  ||     ||     |   ||||    ||     |     ||           |    ||  |  |  ||||  | ||  |   | |    |     |  |                                                                                     
GAGAAGATGACCCAGATCATGTTCGAGACCTTCAATGTCCCGGCCATGTACGTGGCGATCCAAGC-AGTCCTTTCACTCTACGCGAGTGGACGCACTACCGgtatggagtttttttatcccttgcttgttctagacaagatggttgatgcgtgtttcttttcttcgttgcttgcgatagacatgatgcttcaagttggttctacttttgtttttccctctaacacgttgtatgatcgtggtttgtgatcag

upper sequence: EDO98923 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: EFJ35077 (Selaginella moellendorffii), 5'ss of exon 2
---------------ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagag----aggtcgagacagcggagtaacggccgcggcatcgcggcacgcggcagcagcccgagccggacagtaaggcaggcccatacaacagcggtcggc-------------------------------------------------------------------------------------
               |||||||||||||||||||| || ||||||||||||||||| ||||| |          |      |  || |||   ||  |||       |          |    ||  |  |  ||||  | ||  |   | |    |     |  |                                                                                      
GAGAAGATGACCCAGATCATGTTCGAGACCTTCAATGTCCCGGCCATGTACGTGGCAATCCAAGCAGTCCTTTCACTCTACGCGAGTGGACGCACTACCGgtatggagttttttttttcctttgcttgttctagacaagatggttgatgcgtgtttcttttcttcgttgcttgcgatagacatgatgcttcaagttggttctacttttttttcttctctctaacacgttgtatgatcgtggtttgtgatcag

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|10781299|gb|AV637979.1|AV637979
EST:     ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAG                         GCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
genomic: ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagagg ... cgccgtccagGCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
EST: gi|22053164|gb|BQ810620.1|BQ810620
EST:     ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAG                         GCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGNATCGNGCTGGAC
genomic: ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagagg ... cgccgtccagGCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
EST: gi|7687875|gb|AW758521.1|AW758521
EST:     ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAG                         GCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
genomic: ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagagg ... cgccgtccagGCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
EST: gi|10789628|gb|AV626993.1|AV626993
EST:     ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAG                         GCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
genomic: ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagagg ... cgccgtccagGCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
EST: gi|10126118|gb|BE724822.1|BE724822
EST:     ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAG                         GCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
genomic: ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagagg ... cgccgtccagGCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
EST: gi|10777850|gb|AV634530.1|AV634530
EST:     ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAG                         GCCGTGCTGTCCCTGTACGCCAGCGGTCGCACCA
genomic: ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagagg ... cgccgtccagGCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCA
EST: gi|22069702|gb|BQ819234.1|BQ819234
EST:     ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAG                         GCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
genomic: ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagagg ... cgccgtccagGCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
EST: gi|14228289|gb|BG847105.1|BG847105
EST:     ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAG                         GCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
genomic: ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagagg ... cgccgtccagGCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
EST: gi|10127691|gb|BE726395.1|BE726395
EST:     ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAG                         GCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
genomic: ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagagg ... cgccgtccagGCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
EST: gi|161797057|gb|FC085662.1|FC085662
EST:     ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAG                         GCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
genomic: ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagagg ... cgccgtccagGCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
EST: gi|22071637|gb|BQ820975.1|BQ820975
EST:     ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAG                         GCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
genomic: ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagagg ... cgccgtccagGCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
EST: gi|22070013|gb|BQ819473.1|BQ819473
EST:     ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAG                         GCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
genomic: ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagagg ... cgccgtccagGCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
EST: gi|9458838|gb|BE452551.1|BE452551
EST:     ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAG                         GCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
genomic: ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagagg ... cgccgtccagGCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
EST: gi|14240923|gb|BG859739.1|BG859739
EST:     ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAG                         GCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
genomic: ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagagg ... cgccgtccagGCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
EST: gi|8576564|gb|BE129201.1|BE129201
EST:     ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAG                         GCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
genomic: ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagagg ... cgccgtccagGCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
EST: gi|10191366|gb|BE761442.1|BE761442
EST:     ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAG                         GCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
genomic: ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagagg ... cgccgtccagGCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
EST: gi|23362091|gb|BU649911.1|BU649911
EST:     ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAG                         GCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC
genomic: ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagagg ... cgccgtccagGCCGTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagaggtcgagacagcggagtaacggccgcggcatcgcggcacgcggcagcagcccgagccggacagtaaggcaggcccatacaacagcggtcggc

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