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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtcgaggccaggttcagtggcccgtcagttttgcgtactgtaaatttattgcgatggcgcgtgggtccgggttgttagggaatctgcgggatggctctctggattcgtgtcgacccccttcccgtctggcttttgcagGTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAG

Basic information

species Chlamydomonas reinhardtii
transcript EDP05281
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP05281 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GLYMA10G00490.1 (Glycine max), 3'ss of exon 4
gtgcgtcgaggccaggttcagtggcccgtcagttttgcgtactgtaaatttattgcgatggcgcgtgggtccgggttgttagggaatctgcgggatggctctctggattcgtgtcgacccccttcccgtctggcttttgcagGTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAG
                                                                         |  ||||   |  | ||   ||||| | | ||  |   ||  |||          ||||         |||   |       |||| || ||||||||||| ||||| ||| |||||||||||||||| || ||||| || ||||| ||  ||
-------------------------------------------------------------------------gcatgttcatgtct-tgaaagatggttgtgtgtgtgtttgcagacttgtaagtaatctgat-------ggttttctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAG

upper sequence: EDP05281 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: PP1S136_220V6.1 (Physcomitrella patens), 3'ss of exon 4
gtgcgtcgaggccaggttcagtggcccgtcagttttgcgtactgtaaatttattgcgatggcgcgtgggtccgggttgttagggaatctgcgggatggctctctggattcgtgtcgacccccttcccgtctggcttttgcagGTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAG
                                                 |  |   ||  |    |   |  | | ||  |   | |   ||  |  |     |   ||||| |        | | | | |     || || | | |        |||| || |||||||||||||||||||| || ||||||||||| || || |||||||||||||| ||  ||
------------------------------------------------gtactcctgaaagtttttcattttgcggtgaaaaacatttgccgtcaaagtcacttcatttcgtat------tttccgcctataatactttcatgcgaatt---ttcagGTTCTCAGCAACACCATCAAGCAGAAACGTAAGGAGAAGGCTGGTAAATGGGAGGTGCCTCTTCCTAAG
















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:     ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAG                         GTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
genomic: ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAGgtgcgtcgag ... gcttttgcagGTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
EST: gi|6543378|gb|AV389162.1|AV389162
EST:     ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAG                         GTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
genomic: ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAGgtgcgtcgag ... gcttttgcagGTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
EST: gi|10786946|gb|AV643618.1|AV643618
EST:     ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAG                         GTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
genomic: ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAGgtgcgtcgag ... gcttttgcagGTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
EST: gi|22074959|gb|BQ823735.1|BQ823735
EST:     ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAG                         GTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
genomic: ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAGgtgcgtcgag ... gcttttgcagGTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
EST: gi|10778393|gb|AV635073.1|AV635073
EST:     ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAG                         GTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
genomic: ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAGgtgcgtcgag ... gcttttgcagGTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
EST: gi|10788677|gb|AV626397.1|AV626397
EST:     ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAG                         GTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
genomic: ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAGgtgcgtcgag ... gcttttgcagGTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
EST: gi|10790100|gb|AV627466.1|AV627466
EST:     ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAG                         GTGGACCGCGCCAAGGTCCTGAGCAACA
genomic: ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAGgtgcgtcgag ... gcttttgcagGTGGACCGCGCCAAGGTCCTGAGCAACA
EST: gi|6541479|gb|AV387263.1|AV387263
EST:     ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAG                         GTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
genomic: ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAGgtgcgtcgag ... gcttttgcagGTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
EST: gi|10782152|gb|AV638832.1|AV638832
EST:     ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAG                         GTGGACCGCGCCAAGGTCCTGAGCAACACCATCA
genomic: ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAGgtgcgtcgag ... gcttttgcagGTGGACCGCGCCAAGGTCCTGAGCAACACCATCA
EST: gi|6541519|gb|AV387303.1|AV387303
EST:     ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAG                         GTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
genomic: ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAGgtgcgtcgag ... gcttttgcagGTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
EST: gi|6541845|gb|AV387629.1|AV387629
EST:     ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAG                         GTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
genomic: ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAGgtgcgtcgag ... gcttttgcagGTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
EST: gi|6551579|gb|AV397363.1|AV397363
EST:     ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAG                         GTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
genomic: ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAGgtgcgtcgag ... gcttttgcagGTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
EST: gi|10773494|gb|AV624317.1|AV624317
EST:     ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAG                         GTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG
genomic: ACGGCGCGCCGCAGAATGCTGTGCCGGCCTACCTGCTGGAGCGTGAGCAGgtgcgtcgag ... gcttttgcagGTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcgggatggctctctggattcgtgtcgacccccttcccgtctggcttttgcagGTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAG
                              cccccttcccgtctgg  CT-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtcgaggccaggttcagtggcccgtcagttttgcgtactgtaaatttattgcgatggcgcgtgggtccgggttgttagggaatctgcgggatggctctctggattcgtgtcgacccccttcccgtctggcttttgcagGTGGACCGCGCCAAGGTCCTGAGCAACACCATCAAGCAGAAGCGGAAGGAGAAGGCGGGCAAGTGGGAGGTGCCTCTGCCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA