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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAGgtgcgggcgaggaggcggatgacagaggagtgtatggcggcggatgatcgggggagggaagggaaggggcacggtctggaggcggtatcgagcgggcaac...

Basic information

species Chlamydomonas reinhardtii
transcript EDP03835
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP03835 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: LOC_Os06g09290.2 (Oryza sativa), 5'ss of exon 4
GTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAGgtgcgggcgaggaggcgg------atgacagaggagtgtatggcggcggatgatcgggggagggaagggaaggggcacggtctggaggcggtatcgagcgggcaac--------------------
|| ||  | ||||| |||||||||| ||| ||||||||||| || || || |||||||| ||||||||  |   |  |  ||| |        || ||     ||  | |  | | ||| | ||     |   |  | |        ||| |   |  | | |    | |  |                      
GTTGCAAGATGCACAAAGATCATCAGCCCTAACACGGACGATGCTAAATATGTCATCAATGTCAAGCAAATTGCGAAGgtgagtcatgcttttattacttgccagcctttctctgtggaggttcatataaaaaagagtacttctggaggtttatcgctgattttct-ctgatattttatctatgggacattgcag

upper sequence: EDP03835 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 5'ss of exon 4
GTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAGgtg--cgggcgaggaggcggatgacagaggagtgtatgg--cggcggatgatcggggga-----gggaagggaaggggcacggtctggagg--cggtatcgagcgggcaac
|| ||  | || || ||||| |||||| |||| ||||| ||| |||| |||||||||||||| |||||| |   |  |  |  |  | | |     | ||    |  |  |  ||  || |||          |   | |   ||  |  | |||  |    |    | ||||   ||  
GTTGCCAGGTGTACAAAGATAATCAACGCCAATACGGATGACTCCAAATACGTCATCAACGTGAAGCAGATTGCCAAGgtatcataccgtttttgtaagaccaaacagttcatcgcttggtcgttttgtttctgctgatgttgggatcgtgttcttcaaattcaactttgagcattca--
















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|22076975|gb|BQ825751.1|BQ825751
EST:     TCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAG                         ATCGCCAAGTTCGTGGTGGGGCTGGGCGACAAGGTGGCTCCCACCGACATT
genomic: TCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAGgtgcgggcga ... gtcaacgcagATCGCCAAGTTCGTGGTGGGGCTGGGCGACAAGGTGGCTCCCACCGACATT
EST: gi|14226250|gb|BG845066.1|BG845066
EST:     TCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAG                         ATCGCCAAGTTCGTGGTGGGGCTGGGCGACAAGGTGGCTCCCACCGACATT
genomic: TCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAGgtgcgggcga ... gtcaacgcagATCGCCAAGTTCGTGGTGGGGCTGGGCGACAAGGTGGCTCCCACCGACATT
EST: gi|23365334|gb|BU653154.1|BU653154
EST:     TCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAG                         ATCGCCAAGTTCGTGGTGGGGCTGGGCGACAAGGTGGCTCCCACCGACATT
genomic: TCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAGgtgcgggcga ... gtcaacgcagATCGCCAAGTTCGTGGTGGGGCTGGGCGACAAGGTGGCTCCCACCGACATT
EST: gi|22065629|gb|BQ816456.1|BQ816456
EST:     TCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAG                         ATCGCCAAGTTCGTGGTGGGGCTGGGCGA-AAGGTGGCTCCCACCGACAT
genomic: TCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAGgtgcgggcga ... gtcaacgcagATCGCCAAGTTCGTGGTGGGGCTGGGCGACAAGGTGGCTCCCACCGACAT
EST: gi|14228702|gb|BG847518.1|BG847518
EST:     TCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAG                         ATCGCCAAGTTCGTGGTGGGGCTGGGCGACAAGGTGGCTCCCACCGACATT
genomic: TCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAGgtgcgggcga ... gtcaacgcagATCGCCAAGTTCGTGGTGGGGCTGGGCGACAAGGTGGCTCCCACCGACATT
EST: gi|14226251|gb|BG845067.1|BG845067
EST:     TCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAG                         ATCGCCAAGTTCGTGGTGGGGCTGGGCGACAAGGTGGCTCCCACCGACATT
genomic: TCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAGgtgcgggcga ... gtcaacgcagATCGCCAAGTTCGTGGTGGGGCTGGGCGACAAGGTGGCTCCCACCGACATT
EST: gi|22076877|gb|BQ825653.1|BQ825653
EST:     TCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAG                         ATCGCCAAGTTCGTGGTGGGGCTGGGCGACAAGGTGGCTCCCACCGACATT
genomic: TCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAGgtgcgggcga ... gtcaacgcagATCGCCAAGTTCGTGGTGGGGCTGGGCGACAAGGTGGCTCCCACCGACATT

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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAGgtgcgggcgaggaggcggatgacagaggagtgtatggcggcggatgatcgggggagggaagggaaggggcacggtctggaggcggtatcgagcgggcaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtgtat