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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACGCGTTCGGCACTGCCCACCGCGCCCACGCCTCCACCGAGGGTGTGACCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagcttagctttaggcgtccgattgttcgtgtatgttgcaaaaagcttcggggggaaggttctcatactggctgccgagggcaatccagctccacgcggccgtttggccgtgctcgacatttccccgacgtccccctgatgcccggcctggttctgacccgtgctccgcccatgcctcccgcgcttacag

Basic information

species Chlamydomonas reinhardtii
transcript EDO98586
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO98586 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: EFJ26420 (Selaginella moellendorffii), 5'ss of exon 3
------CGACGCGTTCGGCACTGCCCACCGCGCCCACGCCTCCACCGAGGGTGTGACCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagcttagctttaggcgtccgattgttcgtgtatgttgcaaaaagcttcggggggaaggttctcatactggctgccgagggcaatccagctccacgcggccgtttggccgtgctcgacatttccccgacgtccccctgatgcccggcctggttctgacccgtgctccgcccatgcctcccgcgcttacag
      ||| || || || || || ||| | || || || || |||||||| |||||||||||||| |||||||||||||| || |||||  |||| ||||      |       |||  | ||     ||| | || |    |  ||||   |    || |   |                                                                                                                                        
CGTGAACGATGCTTTTGGTACCGCTCACAGAGCTCATGCTTCTACCGAGGGCGTGACCAAGTTCCTCAAGCCCTCCGTGGCTGGATTCCTCTTGCAAAAGg------tagattttcttttcctt---tttcccaatgcttccctgagttgacgacgaatttgccag----------------------------------------------------------------------------------------------------------------------------------------

upper sequence: EDO98586 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: EFJ26731 (Selaginella moellendorffii), 5'ss of exon 5
------CGACGCGTTCGGCACTGCCCACCGCGCCCACGCCTCCACCGAGGGTGTGACCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagcttagctttaggcgtccgattgttcgtgtatgttgcaaaaagcttcggggggaaggttctcatactggctgccgagggcaatccagctccacgcggccgtttggccgtgctcgacatttccccgacgtccccctgatgcccggcctggttctgacccgtgctccgcccatgcctcccgcgcttacag
      ||| || || || || || ||| | || || || || |||||||| |||||||||||||| |||||||||||||| || |||||  |||| ||||      |       |||   |||     ||| | || |    |  ||||   |    || |   |                                                                                                                                        
CGTGAACGATGCTTTTGGTACCGCTCACAGAGCTCATGCTTCTACCGAGGGCGTGACCAAGTTCCTCAAGCCCTCCGTGGCTGGATTCCTCTTGCAAAAGg------tagattttctt--ttttctttttcccaatgcttccctgagttgacgacgaatttgccag----------------------------------------------------------------------------------------------------------------------------------------
















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|161823510|gb|FC108510.1|FC108510
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|16431012|gb|BI996238.1|BI996238
EST:     AGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: AGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|10778626|gb|AV635306.1|AV635306
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|161791377|gb|FC077974.1|FC077974
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|161795111|gb|FC078255.1|FC078255
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|161806004|gb|FC089526.1|FC089526
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|161808945|gb|FC094390.1|FC094390
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|161808380|gb|FC098453.1|FC098453
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|161797540|gb|FC086028.1|FC086028
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|161812620|gb|FC099437.1|FC099437
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|161803417|gb|FC093046.1|FC093046
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|161799718|gb|FC085252.1|FC085252
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGGTGCAGAAAGAGCTG                         GACTACCTTGATGGCG
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCG
EST: gi|161792900|gb|FC082154.1|FC082154
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|239842030|gb|GR283887.1|GR283887
EST:     A-GTTCCTGGAGCCCCTCCGTGGCCGGCTTCCTGCTGCCAAAAAGAGCTG                         GACTACTTTGGATTGCGCCCTGGTCCACCCCC
genomic: AAGTTCCTGAAGCCC-TCCGTGGCCGGCTTCCTGCTGC-AGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTG-ATGGCGCCGTG-TCCAACCCC
EST: gi|161812927|gb|FC095129.1|FC095129
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|161822387|gb|FC106808.1|FC106808
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|9028128|gb|BE238168.1|BE238168
EST:     TTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: TTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|161810630|gb|FC094209.1|FC094209
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|161792854|gb|FC082108.1|FC082108
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|161791664|gb|FC078299.1|FC078299
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|161813926|gb|FC104552.1|FC104552
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|161802603|gb|FC089099.1|FC089099
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|161795396|gb|FC078553.1|FC078553
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|161814693|gb|FC102394.1|FC102394
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|161820324|gb|FC105889.1|FC105889
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|7686923|gb|AW757571.1|AW757571
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|9441323|gb|BE441686.1|BE441686
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|10127475|gb|BE726179.1|BE726179
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGAT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGAT
EST: gi|161801398|gb|FC088518.1|FC088518
EST:     CCAAGTTCCTGAAGCCCTCCGTGGGCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|15373411|gb|BI532837.1|BI532837
EST:     CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: CCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
EST: gi|161817186|gb|FC101594.1|FC101594
EST:     GTTCCTGAAGCCTTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTG                         GACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT
genomic: GTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagc ... gcgcttacagGACTACCTTGATGGCGCCGTGTCCAACCCCAAGCGCCCCTTCGTGGCCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGACGCGTTCGGCACTGCCCACCGCGCCCACGCCTCCACCGAGGGTGTGACCAAGTTCCTGAAGCCCTCCGTGGCCGGCTTCCTGCTGCAGAAGGAGCTGgtgagacagcttagctttaggcgtccgattgttcgtgtatgttgcaaaaagcttcggggggaaggttctcatactggctgccgagggcaatccagctccacgcggccgtttggccgtgctcgacatttccccgacgtccccctgatgcccggcctggttctgacccgtgctccgcccatgcctcccgcgcttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT