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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTTCGTGCAGTTCATCTACGAGCCCATCAAGCAGATCATCGAGCTGGCCATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACGgtgggcatggtgtggtgggtggttcgggccgcggtttgggggttaacggttggtcatggtcaactgactggatcggccggcggcatcggccgggcaactc...

Basic information

species Chlamydomonas reinhardtii
transcript EDO96511
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO96511 (Chlamydomonas reinhardtii), 5'ss of exon 4
lower sequence: EFJ37397 (Selaginella moellendorffii), 5'ss of exon 3
-----------------------GGCTTCGTGCAGTTCATCTACGAGCCCATCAAGCAGATCATCGAGCTGGCCATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACGgtgggcatggtgtggtgggtggttcgggccgcggtttgggggttaacggttggtcatggtcaactgactggatcggccggcggcatcggccgggcaactc
                       || |||||||||||||||||| | || |||||||||||||||||  | ||  |||| |||   | ||||||||| | |   | ||| ||     |   || |   |  |      |    | || | |     ||     |                                                           
CTGGCTCTCCCACTTGTACGCGTGGGTTCGTGCAGTTCATCTACAATCCTATCAAGCAGATCATCGACATCGCGGTGAACGACCAGATGGACAAGCTCTTgt--aagctagattgtttcttcgtttttctagtcacactaatagctttgtgttattgtggacag-----------------------------------------------------------

upper sequence: EDO96511 (Chlamydomonas reinhardtii), 5'ss of exon 4
lower sequence: EFJ33877 (Selaginella moellendorffii), 5'ss of exon 3
-----------------------GGCTTCGTGCAGTTCATCTACGAGCCCATCAAGCAGATCATCGAGCTGGCCATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACGgtgggcatggtgtggtgggtggttcgggccgcggtttgggggttaacggttggtcatggtcaactgactggatcggccggcggcatcggccgggcaactc
                       || |||||||||||||||||| | || |||||||||||||||||  | ||  |||| |||   | ||||||||| | |   | ||| ||     |   || | |    | |  |         | |    | | | | | ||  |                                                       
CTGGCTCTCCCACTTGTACGCGTGGGTTCGTGCAGTTCATCTACAATCCTATCAAGCAGATCATCGACATCGCGGTGAACGACCAGATGGACAAGCTCTTgt--aagctagattgtttcttcgtttgtttcgata-gtcacactaatagctttgtgttattgtggacag------------------------------------------------------
















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|10791866|gb|AV629232.1|AV629232
EST:     CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACG                         TGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
genomic: CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACGgtgggcatgg ... ctacgttcagTGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
EST: gi|49469139|gb|BP097000.1|BP097000
EST:     CCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACG                         TGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
genomic: CCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACGgtgggcatgg ... ctacgttcagTGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
EST: gi|6548651|gb|AV394435.1|AV394435
EST:     CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACG                         TGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
genomic: CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACGgtgggcatgg ... ctacgttcagTGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
EST: gi|10785554|gb|AV642226.1|AV642226
EST:     CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACG                         TGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
genomic: CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACGgtgggcatgg ... ctacgttcagTGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
EST: gi|10791119|gb|AV628485.1|AV628485
EST:     CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACG                         TGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
genomic: CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACGgtgggcatgg ... ctacgttcagTGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
EST: gi|10789530|gb|AV645259.1|AV645259
EST:     CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACG                         TGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
genomic: CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACGgtgggcatgg ... ctacgttcagTGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
EST: gi|10792431|gb|AV629797.1|AV629797
EST:     CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACG                         TGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
genomic: CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACGgtgggcatgg ... ctacgttcagTGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
EST: gi|49469758|gb|BP097619.1|BP097619
EST:     CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACG                         TGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
genomic: CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACGgtgggcatgg ... ctacgttcagTGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
EST: gi|10791837|gb|AV629203.1|AV629203
EST:     CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACG                         TGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
genomic: CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACGgtgggcatgg ... ctacgttcagTGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
EST: gi|10791174|gb|AV628540.1|AV628540
EST:     CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACG                         TGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
genomic: CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACGgtgggcatgg ... ctacgttcagTGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
EST: gi|49467312|gb|BP095225.1|BP095225
EST:     CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACG                         TGATCGGGCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
genomic: CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACGgtgggcatgg ... ctacgttcagTGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
EST: gi|6548641|gb|AV394425.1|AV394425
EST:     CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACG                         TGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
genomic: CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACGgtgggcatgg ... ctacgttcagTGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
EST: gi|10791733|gb|AV629099.1|AV629099
EST:     CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACG                         TGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
genomic: CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACGgtgggcatgg ... ctacgttcagTGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
EST: gi|49469842|gb|BP097703.1|BP097703
EST:     CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACG                         TGATCGGCCGCCTCAAGTCTGACGACAA
genomic: CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACGgtgggcatgg ... ctacgttcagTGATCGGCCGCCTCAAGTCTGACGACAA
EST: gi|10787846|gb|AV644518.1|AV644518
EST:     CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACG                         TGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA
genomic: CATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACGgtgggcatgg ... ctacgttcagTGATCGGCCGCCTCAAGTCTGACGACAAGGAGCTGAGCGGCAAGCCCCTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTTCGTGCAGTTCATCTACGAGCCCATCAAGCAGATCATCGAGCTGGCCATGAAGGACGCCAAGGACAAGCTGTGGCCCATGCTGGAGAAGCTGAACGgtgggcatggtgtggtgggtggttcgggccgcggtttgggggttaacggttggtcatggtcaactgactggatcggccggcggcatcggccgggcaactc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atggtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttggtc