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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgcagccgcacagcaggggcgatagcagcgtaatgggggcaacttgcgtcgtcatcattgggtggagcccctatcctcagccgcacacgcatgtctcctgctaaacctggtacgctttccgcttcctgcccacagAACAACAACCTGCAGATGATTGTGCGCGCGCACGAGTGCGTGATGGACGGCTTTGAGCGCTTCGCGCAGGGCCATCTGATCACGCTCTTCTCCGCCACCA

Basic information

species Chlamydomonas reinhardtii
transcript EDP09505
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP09505 (Chlamydomonas reinhardtii), 3'ss of exon 12
lower sequence: LOC_Os03g44500.1 (Oryza sativa), 3'ss of exon 18
gtgcgcagccgcacagcaggggcgatagcagcgtaatgggggcaacttgcgt-cgtcatcattgggtggagcccc--tatcctcagccgcacacgcatgtctcctgctaaacctggtacgctttccgcttcctgcccacagAACAACAACCTGCAGATGATTGTGCGCGCGCACGAGTGCGTGATGGACGGCTTTGAGCGCTTCGCGCAGGGCCATCTGATCACGCTCTTCTCCGCCACCA
                     |     |   | |||      |    ||  | |||| ||  |  || || ||||  | | ||| |  ||  ||   ||          | |||| |    ||   |  |  |||    | || ||  | || ||  | |||||||| ||||| ||||| |||||||| |||||||||||||| || || || |                           
---------------------gtttgtgttccctaaccctaaccttctgaattcgtcttccctttgttgaccccctttgttctctgaagctaacatttgctgttcatacagCCTGATCGTGTTATGGAGTTTTGCA---ACAATAATGATCTTCAACTAATTGTGCGAGCGCATGAGTGTGTGATGGATGGCTTTGAGCGCTTTGCTCAAGGTC---------------------------

upper sequence: EDP09505 (Chlamydomonas reinhardtii), 3'ss of exon 12
lower sequence: GRMZM2G028700_T01 (Zea mays), 3'ss of exon 18
gtgcgcagccgcacagcaggggcgatagcagcgtaatgggggcaacttgcgtcgtcatcattgggtggagcccctatcctcagccgcacacgcatgtctcctgctaaacctggtacgctttccgcttcctgcccacagAACAACAACCTGCAGATGATTGTGCGCGCGCACGAGTGCGTGATGGACGGCTTTGAGCGCTTCGCGCAGGGCCATCTGATCACGCTCTTCTCCGCCACCA
                            |||  | ||  |    | |   |  |   |  || | |||  ||| |    |  |      |||    |   |  |  | || |  |   ||   |  | ||||    | |||||  |||||||| |||||||||| || ||||||||||||||||| ||||| ||||| ||||| || || |                           
--------------------------gtcagtatcatctg--ttattca-gctgcttt--ttagctggttcccatggtttatgatcttgacgtgcattgtcaccacagCCCGACAGAGTTATGGAGTTCTGCA---ACAACAATGACCTGCAGTTGATTGTGCGAGCACACGAGTGCGTGATGGATGGCTTCGAGCGTTTCGCTCAAGGTC---------------------------

upper sequence: EDP09505 (Chlamydomonas reinhardtii), 3'ss of exon 12
lower sequence: GRMZM2G009593_T01 (Zea mays), 3'ss of exon 18
gtgcgcagccgcacagcaggggcgatagcagcgtaatggg-ggcaacttgcgtcgtcatca--ttgggtggagcccctatcctcagccgcacacgcatgtctcctgctaaacctggtacgctttccgcttcctgcccacagAACAACAACCTGCAGATGATTGTGCGCGCGCACGAGTGCGTGATGGACGGCTTTGAGCGCTTCGCGCAGGGCCATCTGATCACGCTCTTCTCCGCCACCA
                    | |  || ||   |  |     ||   ||     ||       ||   |||       ||  |  ||   ||| ||||    ||  |  | |||| ||   ||   |  | ||||    | |||||  |||||||| |||||||||| || || ||||| |||||||| ||||||||||| ||||| || || |                           
--------------------gtcagtatcaatatgttattcagccctttattaagttgctggtttccatggtttataaattatgcgcttaacatgcattgtccccac--agCCTGATAGAGTTATGGAGTTCTGCA---ACAACAATGACCTGCAGTTGATTGTGCGAGCACATGAGTGTGTGATGGATGGCTTTGAGCGATTCGCCCAAGGTC---------------------------

upper sequence: EDP09505 (Chlamydomonas reinhardtii), 3'ss of exon 12
lower sequence: PP1S43_56V6.1 (Physcomitrella patens), 3'ss of exon 17
---gtgcgcagccgcacag-----caggggcgatagcagcgtaatgggggcaacttgcg--tcgtc-----atcattgggtggagccccta-----tcctcag---ccgcacacgcatgtctcctgctaaacctggtacgcttt--ccgcttcctg-----cccacagAACAACAACCTGCAGATGATTGTGCGCGCGCACGAGTGCGTGATGGACGGCTTTGAGCGCTTCGCGCAGGGCCATCTGATCACGCTCTTCTCCGCCACCA
       | |||  ||| |     | | |  |||    | | |  ||  |  ||| |||  |||||      ||  ||  || ||  | ||     | ||      ||     | ||| |  |         ||| | |       |||  || ||          | || ||  |||| ||  | |||||||| || || ||||||||||||||||| |||||||| || || || || |                           
gtgagttgtagctccactgattctcggtgttgattcgcgtgaagcggttgtgactcgcgcttcgtctgactgtcgatgattgaagtacgtagggaattctggaattccatttgctcatattcctgatgtggtctgttgcagCCGGACCGTGTCATGGAGTTTTGTAAAAATAATGACCTTCAACTTATTGTGCGGGCACATGAGTGCGTGATGGACGGGTTTGAGCGTTTTGCTCAAGGGC---------------------------

upper sequence: EDP09505 (Chlamydomonas reinhardtii), 3'ss of exon 12
lower sequence: PP1S343_69V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------gtgcgcagccgcacagcaggggcga-tagcagcgta----atgggggcaacttgcgtcgt-catcattgggtggagcccctatcctcag--ccgcacacgcatgtctcctgctaaacctggtacgctttccgcttcctgcccacagAACAACAACCTGCAGATGATTGTGCGCGCGCACGAGTGCGTGATGGACGGCTTTGAGCGCTTCGCGCAGGGCCATCTGATCACGCTCTTCTCCGCCACCA
                                     | |      | | ||| | |  |  |||| | | |     |||||   |   | || |         | ||||| |         | |  | |  |    ||||    ||    | | ||  ||  | | |     |      |||||||| | || ||| |||| ||||| || |||||||||||||||||||| || ||||| |||||||| || |                           
gtaagttggaggtgcggtgttggtgggcgcggggggttacatttgtggaaagcggtgatgggtagcggggcatggagtggggatgataggtgtggcatggggaagagtggaactgggtgtggcggatctgagcgatgatgtggtatgtggcagCCGGATCGGGTGCTGGAGTTTTGTA--AGAACAACGATCTTCAGCTGATCGTGCGTGCACACGAGTGCGTGATGGACGGGTTCGAGCGGTTCGCGCAAGGGC---------------------------

upper sequence: EDP09505 (Chlamydomonas reinhardtii), 3'ss of exon 12
lower sequence: EFJ18258 (Selaginella moellendorffii), 3'ss of exon 18
gtgcgcagccgcacagcaggggcgatagcagcgtaatgggggcaacttgcgtcgtcatcattgggtggagcccctatcctcagccgcacacgcatgtctcctgctaaacctggtacgctttccgcttcctgcccacagAACAACAACCTGCAGATGATTGTGCGCGCGCACGAGTGCGTGATGGACGGCTTTGAGCGCTTCGCGCAGGGCCATCTGATCACGCTCTTCTCCGCCACCA
                                               |  ||| ||    |  | |    ||  |       | |    ||        | |||| | ||||  | | |    |  | ||||    ||||||||||| | ||  | || ||||| || |||||||||||||||||||| |||||||| || || ||||| |                           
----------------------------------------------gtaagtcttc--tgtcagctacttcctgtccgagtggtctgtaacttcctctccttgctcagCCTGACAGGGTGATGGAATTCTGCA---AGAACAACAACTTACAACTAATCGTGCGGGCACACGAGTGCGTGATGGACGGGTTTGAGCGATTTGCACAGGGGC---------------------------

upper sequence: EDP09505 (Chlamydomonas reinhardtii), 3'ss of exon 12
lower sequence: EFJ21999 (Selaginella moellendorffii), 3'ss of exon 18
gtgcgcagccgcacagcaggggcgatagcagcgtaatgggggcaacttgcgtcgtcatcattgggtggagcccctatcct--cagccgcacacgcatgtctcctgctaaacctggtacgctttccgcttcctgcccacagAACAACAACCTGCAGATGATTGTGCGCGCGCACGAGTGCGTGATGGACGGCTTTGAGCGCTTCGCGCAGGGCCATCTGATCACGCTCTTCTCCGCCACCA
                                                  ||    ||          |   ||| |||   | | |||  ||        | |||| | ||||  | | |    |  | ||||    ||||||||||| | ||  | || ||||| || |||||||||||||||||||| |||||||| || || ||||| |                           
--------------------------------------------------gtaagtattccgccagctacttcctgtccgagcggtcgctaacttcctctccttgctcagCCTGACAGGGTGATGGAATTCTGCA---AGAACAACAACTTACAACTAATCGTGCGGGCACACGAGTGCGTGATGGACGGGTTTGAGCGATTTGCACAGGGGC---------------------------

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|161822256|gb|FC110356.1|FC110356
EST:     GCCCCGGCCTGGTCACGTTCGGGCCGGACCGCGTGAAAGAGTTCTGCAAG                         AATAACAACCTGCAGATGATTGTGCGCGCGCACGAGTGCGTGATGGACGGC
genomic: GCCCCGGCCTGGTCACGTTCGGACCGGACCGCGTGAAAGAGTTCTGCAAGgtgcgcagcc ... ctgcccacagAACAACAACCTGCAGATGATTGTGCGCGCGCACGAGTGCGTGATGGACGGC
EST: gi|15697986|gb|BI722291.1|BI722291
EST:     GCCCCGGCCTGGTCACGTTCGGACCGGACCGCGTGAAAGAGTTCTGCAAG                         AACAACAACCTGCAGATGATTGTGCGCGCGCACGAGTGCGTGATGGACGGC
genomic: GCCCCGGCCTGGTCACGTTCGGACCGGACCGCGTGAAAGAGTTCTGCAAGgtgcgcagcc ... ctgcccacagAACAACAACCTGCAGATGATTGTGCGCGCGCACGAGTGCGTGATGGACGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgcacacgcatgtctcctgctaaacctggtacgctttccgcttcctgcccacagAACAACAACCTGCAGATGATTGTGCGCGCGCACGAGTGCGTGATGGACGGCTTTGAGCGCTTCGCGCAGGGCCATCTGATCACGCTCTTCTCCGCCACCA
                  tgctaaa  putative branch site (score: 2)
                                  ctttccgcttcctgcc  putative PPT