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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagcgcgcacgcgggcacgggggcttgatgtggacattgcaaagcggcaaatgcaaaggggtggaatctcgtgggatttccagctgcggaagggggcgccagctcaaccgccgtgggggtgctcatgccgtacagGTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGGCTCAACGAGATTGACCGGTACGCCAGCGAGAACGTGAACAAGCTGCTGG

Basic information

species Chlamydomonas reinhardtii
transcript EDO96600
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO96600 (Chlamydomonas reinhardtii), 3'ss of exon 6
lower sequence: PP1S91_243V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaagcagcgcgcacgcgggcacgggggcttgatgtggacattgcaaag--cggcaaatgcaaaggggtggaatctcgtgggatttccagctgcggaagggggcgccagctcaaccgccgtgggggtgctcatgccgtacagGTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGGCTCAACGAGATTGACCGGTACGCCAGCGAGAACGTGAACAAGCTGCTGG
                                    || |||  ||| |   |||  ||    ||     |   |   |     |   |  ||  ||   ||   |   |  |  | |    |   |  | ||    | ||||| || || |||||||| ||||| ||||||||||||||||| ||||| ||| | ||||| ||||| || ||||||||||||||||| |||||||| || |
------------------------------------ggtcatgtcaatggatggcttatatggagcaaacgggacatatctcggtcttacttg--gattcggattctgacaaagtctc----gtatttgttattgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGGTTGAACGAAATTGATCGATACGCCAGCGAGAACGTAAACAAGCTTCTCG

upper sequence: EDO96600 (Chlamydomonas reinhardtii), 3'ss of exon 6
lower sequence: EFJ23285 (Selaginella moellendorffii), 3'ss of exon 5
gtaagcagcgcgcacgcgggcacgggggcttgatgtggacattgcaaagcggcaaatgcaaaggggtggaatctcgtgggatttccagctgcggaagggggcgccagctcaaccgccgtgggggtgctcatgccgtacagGTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGGCTCAACGAGATTGACCGGTACGCCAGCGAGAACGTGAACAAGCTGCTGG
|||||           |  || | |   |||   |      ||  ||||      ||         | |    |  | |  |||||   |||  |||       |  ||| ||           |  |  |    | ||||| || || || ||||| |||||||| |||||||||||||||||||| |||||||||||||| || || ||||| ||||||||||| |||||||| || |
gtaagttctcttgtttcttgc-cagatccttctcgattcttttttaaagttctcgatttgttcc--tagttctttctagtctttcc--ttgc--aagttcttatcttctcgac-----------tctttgttttct-cagGTTGTCTATGACGTGACCGACCAGGAAAGCTTCAACAACGTCAAGCAATGGCTCAACGAGATCGATCGCTACGCGAGCGAGAACGTAAACAAGCTTCTCG

upper sequence: EDO96600 (Chlamydomonas reinhardtii), 3'ss of exon 6
lower sequence: EFJ26216 (Selaginella moellendorffii), 3'ss of exon 5
gtaagcagcgcgcacgcgggcacgggggcttgatgtggacattgcaaagcggcaaatgcaaaggggtggaatctcgtgggatttccagctgcggaagggggcgccagctcaaccgccgtgggggtgctcatgccgtacagGTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGGCTCAACGAGATTGACCGGTACGCCAGCGAGAACGTGAACAAGCTGCTGG
                                                                   | || ||     |   | ||| |     |   |  |  |  |   ||       |  ||||| |  ||  |||||||| ||||| ||||| |||||||| ||||| |||||||||||||||||||| |||||||| || || ||||| |||||||| ||||||||||| || |
-------------------------------------------------------------------gtaagct-----ggcctacagtttttccacacgatggtaatt---ccctgacacgtttgctcgt-tcgcgcagGTCGTGTACGACGTGACCGACCAGGAAAGCTTTAACAACGTCAAGCAGTGGCTGAACGAGATCGATCGCTACGCGAGCGAGAATGTGAACAAGCTCCTCG

upper sequence: EDO96600 (Chlamydomonas reinhardtii), 3'ss of exon 6
lower sequence: EFJ20286 (Selaginella moellendorffii), 3'ss of exon 5
gtaagcagcgcgcacgcgggcacgggggcttgatgtggacattgcaaagcggcaaatgcaaaggggtggaatctcgtgggatttccagctgcggaagggggcgccagctcaaccgccgtgggggtgctcatgccgtacagGTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGGCTCAACGAGATTGACCGGTACGCCAGCGAGAACGTGAACAAGCTGCTGG
|||||           |  || | |   |||   |      || |||||      ||      |     | |    |    | |     |||  |||       |  ||| ||           |  |  |    | ||||| || || || ||||| |||||||| |||||||||||||||||||| |||||||||||||| || || ||||| ||||||||||| |||||||| || |
gtaagttctcttgtttcttgc-cagatccttctcgattcttttccaaagttctcgattt----gttcctagttctttccagtctttccttgc--aagttcttatcttctcgac-----------tctttgttttct-cagGTTGTCTATGACGTGACCGACCAGGAAAGCTTCAACAACGTCAAGCAATGGCTCAACGAGATCGATCGCTACGCGAGCGAGAACGTAAACAAGCTTCTCG

upper sequence: EDO96600 (Chlamydomonas reinhardtii), 3'ss of exon 6
lower sequence: EFJ14515 (Selaginella moellendorffii), 3'ss of exon 5
gtaagcagcgcgcacgcgggcacgggggcttgatgtggacattgcaaagcggcaaatgcaaaggggtggaatctcgtgggatttccagctgcggaagggggcgccagctcaaccgccgtgggggtgctcatgccgtacagGTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGGCTCAACGAGATTGACCGGTACGCCAGCGAGAACGTGAACAAGCTGCTGG
                                                                   | || ||     |   |  || |     |   |  |  |  |   ||       |  ||||| |  ||  |||||||| ||||| ||||| |||||||| ||||| |||||||||||||||||||| |||||||| || || ||||| |||||||| ||||||||||| || |
-------------------------------------------------------------------gtaagct-----ggcctatagtttttccacacgatggtaatt---ccctgacacgtttgctcgt-tcgcgcagGTCGTGTACGACGTGACTGACCAGGAAAGCTTTAACAACGTCAAGCAGTGGCTGAACGAGATCGATCGCTACGCGAGCGAGAATGTGAACAAGCTCCTCG

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|10779798|gb|AV636478.1|AV636478
EST:     GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATT                         GTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
genomic: GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATTgtaagcagcg ... tgccgtacagGTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
EST: gi|49467422|gb|BP095335.1|BP095335
EST:     GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATT                         GTCGTATACGATGTGAC
genomic: GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATTgtaagcagcg ... tgccgtacagGTCGTATACGATGTGAC
EST: gi|10778347|gb|AV635027.1|AV635027
EST:     GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATT                         GTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
genomic: GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATTgtaagcagcg ... tgccgtacagGTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
EST: gi|161796597|gb|FC082914.1|FC082914
EST:     GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATT                         GTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
genomic: GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATTgtaagcagcg ... tgccgtacagGTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
EST: gi|10771327|gb|AV622150.1|AV622150
EST:     GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATT                         GTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
genomic: GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATTgtaagcagcg ... tgccgtacagGTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
EST: gi|22068890|gb|BQ818649.1|BQ818649
EST:     GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATT                         GTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
genomic: GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATTgtaagcagcg ... tgccgtacagGTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
EST: gi|10776378|gb|AV633058.1|AV633058
EST:     GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATT                         GTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
genomic: GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATTgtaagcagcg ... tgccgtacagGTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
EST: gi|10778045|gb|AV634725.1|AV634725
EST:     GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATT                         GTCGTATACGATGTGACGGACTAGGAGAGCTTCAACAACGTCAAGCAGTGG
genomic: GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATTgtaagcagcg ... tgccgtacagGTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
EST: gi|22063901|gb|BQ815490.1|BQ815490
EST:     GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATT                         GTCGTATACGATGTGAC
genomic: GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATTgtaagcagcg ... tgccgtacagGTCGTATACGATGTGAC
EST: gi|16432961|gb|BI998187.1|BI998187
EST:     GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATT                         GTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
genomic: GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATTgtaagcagcg ... tgccgtacagGTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
EST: gi|6546326|gb|AV392110.1|AV392110
EST:     GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATT                         GTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
genomic: GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATTgtaagcagcg ... tgccgtacagGTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
EST: gi|10777853|gb|AV634533.1|AV634533
EST:     GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATT                         GTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
genomic: GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATTgtaagcagcg ... tgccgtacagGTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
EST: gi|15697029|gb|BI721334.1|BI721334
EST:     GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATT                         GTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
genomic: GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATTgtaagcagcg ... tgccgtacagGTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
EST: gi|16430540|gb|BI995766.1|BI995766
EST:     GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATT                         GTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG
genomic: GCTTCCGGACTATCACCAGCAGCTACTACCGTGGCGCGCACGGCATCATTgtaagcagcg ... tgccgtacagGTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcagcgcgcacgcgggcacgggggcttgatgtggacattgcaaagcggcaaatgcaaaggggtggaatctcgtgggatttccagctgcggaagggggcgccagctcaaccgccgtgggggtgctcatgccgtacagGTCGTATACGATGTGACGGACCAGGAGAGCTTCAACAACGTCAAGCAGTGGCTCAACGAGATTGACCGGTACGCCAGCGAGAACGTGAACAAGCTGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT