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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAGGGTATCTGCAACGCCGTCGGCCTGGCCGTGGCTGAGGCCCACCTGGCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaagttcgtctgttcggcgtagtcctgcttggcatgtgcggggttgctagcttcggggggctagacgcgggcaatgggacatggacagggtcag...

Basic information

species Chlamydomonas reinhardtii
transcript EDP06856
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP06856 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: GRMZM2G033208_T01 (Zea mays), 5'ss of exon 3
---GCCAGGGTATCTGCAACGCCGTCGGCCTGGCCGTGGCTGAGGCCCACCTGGCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgag---tgaagttcgtctgttcggcgtagtcctgcttggcatgt-gcggggttgctagcttcggggggctagacgcgggca-atgggacatggacagggt-cag
   | |||||||||  ||| ||||| ||  ||||  | ||||||   |||||||||||||||||||||||||| |||    ||   ||||| ||||||||||||| |    |  | |    |      ||   |||  ||||    |   |    | |  |||  |  | ||   ||    ||  | |||   | ||||    || |||
TTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAG---ATCGTCGACCACTACACgtaatacttctaataacgccaacgtgcagcgtctcgcttttattacagtcttgcttttagtctgtgtggcacagttttggtaacatgtttcgtggatcctgtacag

upper sequence: EDP06856 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: PP1S120_127V6.1 (Physcomitrella patens), 5'ss of exon 3
---GCCAGGGTATCTGCAACGCCGTCGGCCTGGCCGTGGCTGAGGCCCACCTGGCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag--ttcgtctgttcggcgtagtcctgcttggcatgtgcggggttgctagcttcgggggg----ctagacgcgggcaatgggacatggacagggtcag--------------------------------------------------------------------------------------------
   |||||||||||   |||||||| ||  ||||| |||| || |||||  |||||||||| ||||||||||| |||| ||||   ||||||||||||||||||| || ||    ||    || | |  |   |    || |   ||||   || ||     || || |      || ||     |    |  || |   |    || |                                                                                            
TCGGCCAGGGTATCGCTAACGCCGTTGGTTTGGCCTTGGCCGAAGCCCATTTGGCTGCCCGTTTCAACAAGCCTGACGCCAAG---ATCGTGGACCACTACACgtaagagacacattgcattgctggctgcgctagcactag---tgtgaaaggctggataatttggagtattccctggattgttgtggcgtaacttactctaattccgctcagataatgttagaggctgacttgtgttacagcgctgaagagggttgctgaattgtacgatgatcaatgtggattgttttctcaatgcag

upper sequence: EDP06856 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: PP1S120_164V6.1 (Physcomitrella patens), 5'ss of exon 3
---GCCAGGGTATCTGCAACGCCGTCGGCCTGGCCGTGGCTGAGGCCCACCTGGCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag--ttcgtctgttcggcgtagtcctgcttggcatgtgcggggttgctagcttcggggggc---tagacgcgggcaatgggacatggacagggtcag--------------------------------------------------------------------------------------------
   |||||||||||   |||||||| ||  ||||| |||| || |||||| |||||||||| ||||||||||| |||| ||||   ||||||||||||||||||| || ||    ||    || | |  |   |    || |   ||||   ||  |     | ||||   |   | ||     |    |  || ||  |    || |                                                                                            
TCGGCCAGGGTATCGCTAACGCCGTTGGTTTGGCCTTGGCCGAAGCCCACTTGGCTGCCCGTTTCAACAAGCCTGACGCCAAG---ATCGTGGACCACTACACgtaagagacacattgcattgctggctgcgctagcactag---tgtgaaaggcggtataatccgggtatcccctggattgttgtggcgtaacttgctctaattccgctcatataatgttagaggctgacttgtgttacagcgctgaagaggattgctgaatcgaacgatgaccaatgtggattgttttctcaatgcag

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|22076982|gb|BQ825758.1|BQ825758
EST:     GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGNGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
genomic: GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
EST: gi|10791689|gb|AV629055.1|AV629055
EST:     GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGNGTGACGGCTGCATGATGGA
genomic: GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGCATGATGGA
EST: gi|10788145|gb|AV644817.1|AV644817
EST:     GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGNGTGACGGCTGCATGATGGA
genomic: GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGCATGATGGA
EST: gi|49470897|gb|BP098758.1|BP098758
EST:     GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGGGTGACGGCTGCATGATGGA
genomic: GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGCATGATGGA
EST: gi|10786128|gb|AV642800.1|AV642800
EST:     GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
genomic: GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
EST: gi|10787628|gb|AV644300.1|AV644300
EST:     GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
genomic: GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
EST: gi|49466563|gb|BP094476.1|BP094476
EST:     GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
genomic: GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
EST: gi|239840773|gb|GR282463.1|GR282463
EST:     GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCCACGAGGC
genomic: GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
EST: gi|10789540|gb|AV645269.1|AV645269
EST:     GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
genomic: GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
EST: gi|10787399|gb|AV644071.1|AV644071
EST:     CTGCCCGCTTCAACAATGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
genomic: CTGCCCGCTTCAACAA-GCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
EST: gi|49466622|gb|BP094535.1|BP094535
EST:     GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
genomic: GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
EST: gi|10789066|gb|AV626786.1|AV626786
EST:     GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
genomic: GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
EST: gi|6548055|gb|AV393839.1|AV393839
EST:     GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
genomic: GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
EST: gi|6548544|gb|AV394328.1|AV394328
EST:     GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
genomic: GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
EST: gi|10787836|gb|AV644508.1|AV644508
EST:     GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
genomic: GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
EST: gi|10786495|gb|AV643167.1|AV643167
EST:     GACCACTACAC                         CTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
genomic: GACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
EST: gi|49467668|gb|BP095529.1|BP095529
EST:     GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
genomic: GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
EST: gi|34981503|gb|CF555420.1|CF555420
EST:     GCTGACCGCTTCA-CAAGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGG
genomic: GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGG
EST: gi|10787819|gb|AV644491.1|AV644491
EST:     GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGNGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
genomic: GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGCATGATGGAGGGCATCTCCAACGAGGC
EST: gi|49462565|gb|BP090478.1|BP090478
EST:     GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGGGTGACGGCTGCATGATGGA
genomic: GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGCATGATGGA
EST: gi|22076428|gb|BQ825204.1|BQ825204
EST:     GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACAC                         CTACTGCATCCTGGGTGACGGCTGC
genomic: GCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaag ... cgctcctcagCTACTGCATCCTGGGTGACGGCTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAGGGTATCTGCAACGCCGTCGGCCTGGCCGTGGCTGAGGCCCACCTGGCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGACCACTACACgtgagtgaagttcgtctgttcggcgtagtcctgcttggcatgtgcggggttgctagcttcggggggctagacgcgggcaatgggacatggacagggtcag

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