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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGCGCTACCCCATTGAGCACGGTATTGTGACCAACTGGGACGACATGGAGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtatttggcacgcacacatgtcccggacatcctcgccacctgcacgcgtcgctgaacttcccttgccgcccctcgcgcctgcctctgcag

Basic information

species Chlamydomonas reinhardtii
transcript EDO98923
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO98923 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: GRMZM2G047055_T04 (Zea mays), 5'ss of exon 3
TCTGCGCTACCCCATTGAGCACGGTATTGTGACCAACTGGGACGACA-TGGAGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtatt-tggcacgcacacatgtc-ccggaca-----tcctcgccacctgc-acgcgtcgctgaacttcccttgccgcccctcgcgc--ctgcctctgcag-----------
         |  | ||| || |      | | |  || ||   ||   ||| || |     | |  |  ||| | ||  ||| |   |||  |   || ||  ||||||  || | | ||   |   |  ||  ||     || ||  || |||  |||    |  |||  ||      | | |||    |  |   ||| |              
---------CATCGTTGGGCGC----CCGCGCCACACCGGTGTGATGGTGGGGATGGGGCAGAAGGATGCCTACGTCGGCGA-CGAGGCGCAGT--CCAAGAGGGGTATCCTGACCctcaagtaccccatcgagcacggaatcgtcagcaactgggacgacatggagaagatctggcatcacaccttctacaacgagctccgtgtggctcccgagg
















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:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
EST: gi|22053164|gb|BQ810620.1|BQ810620
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
EST: gi|7687875|gb|AW758521.1|AW758521
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
EST: gi|10789628|gb|AV626993.1|AV626993
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
EST: gi|10126118|gb|BE724822.1|BE724822
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
EST: gi|10777850|gb|AV634530.1|AV634530
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
EST: gi|22053091|gb|BQ810588.1|BQ810588
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGTGCCCGAG                         GAGCACCCCGTGCTGTTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
EST: gi|22069702|gb|BQ819234.1|BQ819234
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
EST: gi|10127691|gb|BE726395.1|BE726395
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
EST: gi|15370241|gb|BI529667.1|BI529667
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGAGGCCCCCCT
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCT
EST: gi|161797057|gb|FC085662.1|FC085662
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
EST: gi|22071637|gb|BQ820975.1|BQ820975
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
EST: gi|22070013|gb|BQ819473.1|BQ819473
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
EST: gi|9458838|gb|BE452551.1|BE452551
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
EST: gi|49461896|gb|BP089809.1|BP089809
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGAGGTCCCCCTGAACCCCAAGGCCAAACGC
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
EST: gi|14240923|gb|BG859739.1|BG859739
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
EST: gi|8576564|gb|BE129201.1|BE129201
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
EST: gi|49464429|gb|BP092342.1|BP092342
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGATGGCCCCC-TGAACCCCAAGGACAACCG
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGA-GGCCCCCCTGAACCCCAAGGCCAACCG
EST: gi|49469137|gb|BP096998.1|BP096998
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
EST: gi|10191366|gb|BE761442.1|BE761442
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
EST: gi|23362091|gb|BU649911.1|BU649911
EST:     AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAG                         GAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC
genomic: AGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtattt ... gcctctgcagGAGCACCCCGTGCTGCTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGCGCTACCCCATTGAGCACGGTATTGTGACCAACTGGGACGACATGGAGAAGATCTGGCACCACACCTTCTTCAACGAGCTGCGCGTGGCGCCCGAGgtgggtatttggcacgcacacatgtcccggacatcctcgccacctgcacgcgtcgctgaacttcccttgccgcccctcgcgcctgcctctgcag

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