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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAGgtgagaagacggttgcggggcatgtgggctcggggtagggttttggcaatcggctgacttacgtggcgctttgggcagcatacgagccgcttgcctccaa...

Basic information

species Chlamydomonas reinhardtii
transcript EDP05281
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP05281 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: GLYMA10G00490.1 (Glycine max), 5'ss of exon 5
GTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAGgtgagaagacggt---tgcggggcatgtgggctcggggtagggttttggcaatcggctgacttacgtggcgctttgggcagcatacgagccgcttgcctccaa-------------------------------------------------------
               || || ||||||||||| ||||| ||| |||||||||||||||| || ||||| || ||||| ||  |||||| |   || |   | |   |    | |  |  |   |  | | || |   |   |    | | |   ||| ||    |  |       | || |||   |                                                       
---------------GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattgcgttcaatactttgtgcattgattatgttaaatgatatgtcttgcaatttgtat-cttattgctatgtcatgtgtgttttatgtttccctgtgaatggaagggagtgaacttggtaattaaatgaatgtatgctttctcatttcttcag

upper sequence: EDP05281 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: PP1S136_220V6.1 (Physcomitrella patens), 5'ss of exon 5
GTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAGgtgagaagacggt-tgcggggcatgtgggctcggggtagggttttggcaatcggctgacttacgtggcgctttgggca---gcatacgagccgcttgcctccaa
               || || |||||||||||||||||||| || ||||||||||| || || |||||||||||||| ||  |||||||  ||     | ||     ||| |  |  | | |    ||    ||||  |    | || |      |   | |   | |     ||    ||  | |  
---------------GTTCTCAGCAACACCATCAAGCAGAAACGTAAGGAGAAGGCTGGTAAATGGGAGGTGCCTCTTCCTAAGgtgagccgatatcgtacgaatgctgtagctt--gtgaaactcttgaataatccaccacatcacttaaattgtgaagtacgtgaacggaggcgatgtggtttc--
















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|15698076|gb|BI722381.1|BI722381
EST:     AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAG                         GTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG
genomic: AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAGgtgagaagac ... aacctcacagGTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG
EST: gi|6543378|gb|AV389162.1|AV389162
EST:     AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAG                         GTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG
genomic: AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAGgtgagaagac ... aacctcacagGTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG
EST: gi|10786946|gb|AV643618.1|AV643618
EST:     AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAG                         GTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGC
genomic: AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAGgtgagaagac ... aacctcacagGTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGC
EST: gi|22074959|gb|BQ823735.1|BQ823735
EST:     AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAG                         GTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG
genomic: AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAGgtgagaagac ... aacctcacagGTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG
EST: gi|10778393|gb|AV635073.1|AV635073
EST:     AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAG                         GTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG
genomic: AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAGgtgagaagac ... aacctcacagGTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG
EST: gi|10788677|gb|AV626397.1|AV626397
EST:     AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAG                         GTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG
genomic: AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAGgtgagaagac ... aacctcacagGTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG
EST: gi|6541479|gb|AV387263.1|AV387263
EST:     AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAG                         GTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG
genomic: AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAGgtgagaagac ... aacctcacagGTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG
EST: gi|6541519|gb|AV387303.1|AV387303
EST:     AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAG                         GTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG
genomic: AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAGgtgagaagac ... aacctcacagGTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG
EST: gi|6541845|gb|AV387629.1|AV387629
EST:     AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAG                         GTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG
genomic: AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAGgtgagaagac ... aacctcacagGTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG
EST: gi|10773494|gb|AV624317.1|AV624317
EST:     AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAG                         GTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG
genomic: AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAGgtgagaagac ... aacctcacagGTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG
EST: gi|7687776|gb|AW758422.1|AW758422
EST:     AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAG                         GTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG
genomic: AGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAGgtgagaagac ... aacctcacagGTGCGGCCCATCGCCGAGGACGAGATGTTCAAGGTGATGAAGAGCGGCAAG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAGgtgagaagacggttgcggggcatgtgggctcggggtagggttttggcaatcggctgacttacgtggcgctttgggcagcatacgagccgcttgcctccaa

- - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agggttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catacga