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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaccacccatctgtccacacacccaagcggcccccactcccgcaccgacgttggcacgctacccccccccccccaatatttaccatggaacctccccagGTGGACGACACGGACGTGATCAACTTCCTGCTGTCCACCGAGATCATCCCGCTGTGCCTGCGCACCATGGAGATCGGCACGGAGCTGTCCAAGACCGTGG

Basic information

species Chlamydomonas reinhardtii
transcript EDP02995
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP02995 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: EFJ05830 (Selaginella moellendorffii), 3'ss of exon 5
acaccacccatctgtccacacacccaagcggcccccactcccgcaccgacgttggcacgctacccccccccccccaatatttaccatg-gaacctccc-cagGTGGACGACACGGACGTGATCAACTTCCTGCTGTCCACCGAGATCATCCCGCTGTGCCTGCGCACCATGGAGATCGGCACGGAGCTGTCCAAGACCGTGG
                                      |     |  |||  |   |   |    |    |   | ||   |  ||   |||||||   ||||| || || || ||||||||||||||||||||||| || || |||||||| || |||||||| || ||||| || ||||  ||||| ||||||||     
-------------------------------------gtaagcaagggactcttctaaagtggttcttttcgtgcgatggatgacacacgaacctcttgcagGTTGATGATACTGACGTGATCAACTTCCTGCTGTCGACTGAAATCATCCCACTTTGCCTGCGTACTATGGAAATGGGCAGCGAGCTCTCCAAGACG----

upper sequence: EDP02995 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: EFJ23499 (Selaginella moellendorffii), 3'ss of exon 5
acaccacccatctgtccacacacccaagcggcccccactcccgcaccgacgttggcacgctacccccccccccccaatatttaccatg-gaacctccc-cagGTGGACGACACGGACGTGATCAACTTCCTGCTGTCCACCGAGATCATCCCGCTGTGCCTGCGCACCATGGAGATCGGCACGGAGCTGTCCAAGACCGTGG
                                      |     | ||||  |   |   |    |    |   | ||   |  ||   |||||||   ||||| || || || ||||||||||||||||||||||| || || |||||||| || |||||||| || |||||||| ||||  ||||| ||||||||     
-------------------------------------gtaagcaagcgactcttctaaagtggttcttttcgtgcgatggatgacacacgaacctcttgcagGTTGATGATACTGACGTGATCAACTTCCTGCTGTCGACTGAAATCATCCCACTTTGCCTGCGTACTATGGAGATGGGCAGCGAGCTCTCCAAGACG----
















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|14231748|gb|BG850564.1|BG850564
EST:     CGAGTACCTGCGCCTGACCCAGCCTGGGCGTGATCGGCGCGCTGGTCAAG                         GGTGGACGACACGGACGTG
genomic: CGAGTACCTGCGCCTGACC-AGCCTGGGCGTGATCGGCGCGCTGGTCAAGgtgagcgacg ... acctccccagG-TGGACGACACGGACGTG
EST: gi|15692949|gb|BI717254.1|BI717254
EST:     TCGAGTACCTGCGCCTGACCAGCCTGGGCGTGATCGGCGCGCTGGTCAAG                         GTGGACGACACGGACGTGATCAACTTCCTGCTGTCCACCGAGATCATCCCG
genomic: TCGAGTACCTGCGCCTGACCAGCCTGGGCGTGATCGGCGCGCTGGTCAAGgtgagcgacg ... acctccccagGTGGACGACACGGACGTGATCAACTTCCTGCTGTCCACCGAGATCATCCCG
EST: gi|6545786|gb|AV391570.1|AV391570
EST:     TCGAGTACCTGCGCCTGACCAGCCTGGGCGTGATCGGCGCGCTGGTCAAG                         GTGGACGACACGGACGTGATCAACTTCCTGCTGTCCACCGAGATCATCCCG
genomic: TCGAGTACCTGCGCCTGACCAGCCTGGGCGTGATCGGCGCGCTGGTCAAGgtgagcgacg ... acctccccagGTGGACGACACGGACGTGATCAACTTCCTGCTGTCCACCGAGATCATCCCG
EST: gi|14231749|gb|BG850565.1|BG850565
EST:     CGAGTACCTGCGCCTGACCAGCCTGGGGCGTGATCGGCGCGCTGGTCAAG                         GTGGACGACACGGACGTGATC
genomic: CGAGTACCTGCGCCTGACCAGCCTGGG-CGTGATCGGCGCGCTGGTCAAGgtgagcgacg ... acctccccagGTGGACGACACGGACGTGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgacgttggcacgctacccccccccccccaatatttaccatggaacctccccagGTGGACGACACGGACGTGATCAACTTCCTGCTGTCCACCGAGATCATCCCGCTGTGCCTGCGCACCATGGAGATCGGCACGGAGCTGTCCAAGACCGTGG
                                              cctcccc  CT-rich tract
                              aatattta  TA-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaccacccatctgtccacacacccaagcggcccccactcccgcaccgacgttggcacgctacccccccccccccaatatttaccatggaacctccccagGTGGACGACACGGACGTGATCAACTTCCTGCTGTCCACCGAGATCATCCCGCTGTGCCTGCGCACCATGGAGATCGGCACGGAGCTGTCCAAGACCGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
acaccac
- - - - - - - -ccacaca
- - - - - - - - - - - - - - - -cccccac
- - - - - - - - - - - - - - - - - - - -cccgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atatttac