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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTCCGTCAAGCATGAGCAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAGgtacgcattgggctcacacgcgcattggggtgcgtgtggcgacggttgctgacccttcacctggtgatgttgcacgcgcag

Basic information

species Chlamydomonas reinhardtii
transcript EDP09399
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP09399 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: GLYMA20G23080.2 (Glycine max), 5'ss of exon 3
TTCTCCGTCAAGCATGAGCAGGACCTGGACTGCGGTGGTGGCTACATCAAG-------GTGGTGCCCGCTACCAGgtacgcattgggctcacacgcgcattg-gggtgcgtgtggcgacggttgctgacccttcacctggtgatgttgcacgcgcag-----------------------------------------------
    | ||||||||||| ||| | || |||||||||||||||||||| |||       ||||||      | |||  |   ||| ||     |  | | ||   ||||  |       |   |  |||    |  |    |  || ||   ||                                                   
----CTGTCAAGCATGAACAGAAGCTTGACTGCGGTGGTGGCTACATGAAGTTGCTCAGTGGTGATGTTGATCAGA-AGAAATTTGGTGGGGATACTCCTTACAGgtgatttatatatccccttttgatttgttgctctttcctgatgggtgcctctcatatcgcaaaacacctgaccttttaacatttgttgttctgttgcag

upper sequence: EDP09399 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 3
TTCTCCGTCAAGCATGAGCAGGACCTGGACTGCGGTGGTGGCTACATCAAG-------GTGGTGCCCGCTACCAGgtacgcattgggctcacacgcgcattg-gggtgcgtgtggcgacggttgctg----acccttcacctggtgatgttgcacgcgcag--------------------
    | ||||||||||||||| | || ||||| |||||||||||||| |||       ||| ||      |||||      ||| ||   | || | | ||   |||| || |  ||     |        |  |||||     | |     || ||  |                     
----CTGTCAAGCATGAGCAGAAGCTTGACTGTGGTGGTGGCTACATGAAGTTGCTAAGTGATGATGTTGACCAGACGAA-ATTCGGAGGAGACACTCCTTACAGgtgtgtttttcggttactttcatatcaaacttcaaacattcaaacaccaggcttatctttctttttttatctgcag
















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|15695241|gb|BI719546.1|BI719546
EST:     CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAG                         CGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCCTACTCCATCATGTT
genomic: CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAGgtacgcattg ... gcacgcgcagCGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCCTACTCCATCATGTT
EST: gi|22066094|gb|BQ816759.1|BQ816759
EST:     CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAG                         CGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCCTACTCCATCATGTT
genomic: CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAGgtacgcattg ... gcacgcgcagCGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCCTACTCCATCATGTT
EST: gi|49464355|gb|BP092268.1|BP092268
EST:     GTGCCCGCTA-CAG                         CGAGAAGCAGATGGGCTGAGTTCGGTGGCGACACCCCTTACTCCATCATGT
genomic: GTGCCCGCTACCAGgtacgcattg ... gcacgcgcagCGAGAAGCAGATGGGC-GAGTTCGGTGGCGACACCCCCTACTCCATCATGT
EST: gi|10768396|gb|AV619221.1|AV619221
EST:     CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAG                         CGAGAAGCAGATGGGCGAGTTCGGTGGCGACAC
genomic: CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAGgtacgcattg ... gcacgcgcagCGAGAAGCAGATGGGCGAGTTCGGTGGCGACAC
EST: gi|14240098|gb|BG858914.1|BG858914
EST:     CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAG                         CGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCCTACTCCATCATGTT
genomic: CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAGgtacgcattg ... gcacgcgcagCGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCCTACTCCATCATGTT
EST: gi|49465792|gb|BP093705.1|BP093705
EST:     CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAG                         CGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCC
genomic: CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAGgtacgcattg ... gcacgcgcagCGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCC
EST: gi|6549131|gb|AV394915.1|AV394915
EST:     CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAG                         CGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCTTACTCCATCATGTT
genomic: CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAGgtacgcattg ... gcacgcgcagCGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCCTACTCCATCATGTT
EST: gi|7687751|gb|AW758397.1|AW758397
EST:     CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAG                         CGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCCTACTCCATCATGTT
genomic: CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAGgtacgcattg ... gcacgcgcagCGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCCTACTCCATCATGTT
EST: gi|15702624|gb|BI726929.1|BI726929
EST:     CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAG                         CGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCCTACTCCATCATGTT
genomic: CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAGgtacgcattg ... gcacgcgcagCGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCCTACTCCATCATGTT
EST: gi|161798397|gb|FC083541.1|FC083541
EST:     CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAG                         CGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCCTACTCCATCATGTT
genomic: CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAGgtacgcattg ... gcacgcgcagCGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCCTACTCCATCATGTT
EST: gi|34986390|gb|CF560307.1|CF560307
EST:     CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAG                         CGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCCTACTCCATCATGTT
genomic: CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAGgtacgcattg ... gcacgcgcagCGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCCTACTCCATCATGTT
EST: gi|10769925|gb|AV620750.1|AV620750
EST:     CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAG                         CGAGAAGCAGATG
genomic: CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAGgtacgcattg ... gcacgcgcagCGAGAAGCAGATG
EST: gi|10126041|gb|BE724745.1|BE724745
EST:     CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAG                         CGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCCTACTCCATCATGTT
genomic: CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAGgtacgcattg ... gcacgcgcagCGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCCTACTCCATCATGTT
EST: gi|22068872|gb|BQ818633.1|BQ818633
EST:     CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAG                         CGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCCTACTCCATCATGTT
genomic: CAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAGgtacgcattg ... gcacgcgcagCGAGAAGCAGATGGGCGAGTTCGGTGGCGACACCCCCTACTCCATCATGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTCCGTCAAGCATGAGCAGGACCTGGACTGCGGTGGTGGCTACATCAAGGTGGTGCCCGCTACCAGgtacgcattgggctcacacgcgcattggggtgcgtgtggcgacggttgctgacccttcacctggtgatgttgcacgcgcag

- - - - - - - - - - - - - - - - -  TGGTGG