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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtgccacaagcggtcgcgctagccagctaccagcggtcttggagggcccgcttgcaccattgcccttactgatgtccaccgggccttacgcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCGTAACGCCATCATCAACGCGGCCGAGCTGGCCAGCTACGACCAG

Basic information

species Chlamydomonas reinhardtii
transcript EDP01675
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP01675 (Chlamydomonas reinhardtii), 3'ss of exon 6
lower sequence: EFJ24273 (Selaginella moellendorffii), 3'ss of exon 4
cgtgccacaagcggtcgcgctagccagctaccagcggtcttggagggcccgcttgcaccattgcccttactgatgtccaccgggccttacgcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCGTAACGCCATCATCAACGCGGCCGAGCTGGCCAGCTACGACCAG---------
                                             |    ||   ||  | || | || |  ||  | |   || ||    ||  | ||   |||| ||  ||      || ||||  || ||||| || ||  | || |||||||| |||||||||||||||||||| || ||||| || ||          
---------------------------------------------gtatggcgaacat-actgtcttttc--atcccaagtcggactctt-catct-catacagGAAGGTTTCGCAAAACTTTGGACTGGCCTGGGTCCAAATGTGGCCCGTAACGCTATCATCAACGCGGCCGAGCTCGCTAGCTATGATCAAGTAAAACAG

upper sequence: EDP01675 (Chlamydomonas reinhardtii), 3'ss of exon 6
lower sequence: EFJ35536 (Selaginella moellendorffii), 3'ss of exon 4
cgtgccacaagcggtcgcgctagccagctaccagcggtcttggagggcccgcttgcaccattgcccttactgatgtccaccgggccttacgcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCGTAACGCCATCATCAACGCGGCCGAGCTGGCCAGCTACGACCAG---------
                                         | | |||   | |  ||  |        || | ||||    | |  | |    |  ||   |||| ||  ||      || ||||  || ||||| || ||  | || |||||||| |||||||||||||||||||| || ||||| || ||          
-----------------------------------------gtatggcgaacat--actgtcttttcatctcaagtcc----gactcttca---tctcatacagGAAGGTTTCGCAAAACTTTGGACTGGCCTGGGTCCAAATGTGGCCCGTAACGCTATCATCAACGCGGCCGAGCTCGCTAGCTATGATCAAGTAAAACAG
















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|15367917|gb|BI527343.1|BI527343
EST:     GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCG                         GNGAGGAGGGCATCCTGNGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGC
genomic: GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCGgtgcgtgtcc ... gcacttgcagG-GAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGC
EST: gi|161819692|gb|FC110730.1|FC110730
EST:     GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCG                         GGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
genomic: GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCGgtgcgtgtcc ... gcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
EST: gi|8513770|gb|BE121665.1|BE121665
EST:     GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCG                         GGAGGAGGGCATCCTGNGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
genomic: GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCGgtgcgtgtcc ... gcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
EST: gi|14235024|gb|BG853840.1|BG853840
EST:     GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCG                         GGAGGAGGGCATCCTGNGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
genomic: GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCGgtgcgtgtcc ... gcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
EST: gi|10778258|gb|AV634938.1|AV634938
EST:     GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCG                         GGAGGAGGG-ATCCTGGGCCTGTGGAAGGG
genomic: GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCGgtgcgtgtcc ... gcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGG
EST: gi|9210083|gb|BE336998.1|BE336998
EST:     GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCG                         GGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
genomic: GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCGgtgcgtgtcc ... gcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
EST: gi|10127372|gb|BE726076.1|BE726076
EST:     GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCG                         GGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
genomic: GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCGgtgcgtgtcc ... gcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
EST: gi|15705113|gb|BI729402.1|BI729402
EST:     GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCG                         GGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
genomic: GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCGgtgcgtgtcc ... gcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
EST: gi|49459638|gb|BP087551.1|BP087551
EST:     GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCG                         GGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
genomic: GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCGgtgcgtgtcc ... gcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
EST: gi|9210580|gb|BE337495.1|BE337495
EST:     GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCG                         GGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
genomic: GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCGgtgcgtgtcc ... gcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
EST: gi|10770885|gb|AV621708.1|AV621708
EST:     GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCG                         GGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGGCCCAACATCGCGCG
genomic: GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCGgtgcgtgtcc ... gcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
EST: gi|8400964|gb|BE056598.1|BE056598
EST:     GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCG                         GGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
genomic: GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCGgtgcgtgtcc ... gcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
EST: gi|8933158|gb|BE227919.1|BE227919
EST:     GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCG                         GGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
genomic: GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCGgtgcgtgtcc ... gcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
EST: gi|10125696|gb|BE724400.1|BE724400
EST:     GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCG                         GGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCC-AACATCGCGCG
genomic: GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCGgtgcgtgtcc ... gcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
EST: gi|15373603|gb|BI533029.1|BI533029
EST:     GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCG                         GGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
genomic: GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCGgtgcgtgtcc ... gcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
EST: gi|161812247|gb|FC097815.1|FC097815
EST:     GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCG                         GGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
genomic: GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCGgtgcgtgtcc ... gcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
EST: gi|161810681|gb|FC096834.1|FC096834
EST:     GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCG                         GGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
genomic: GTGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCGgtgcgtgtcc ... gcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCG
EST: gi|15910544|gb|BI816399.1|BI816399
EST:     TGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGCCG                         GGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGC
genomic: TGGCCAAGAAGTACCCCAGCGCCATCGCCGCCTACGGCATCATCGCGC-Ggtgcgtgtcc ... gcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtgccacaagcggtcgcgctagccagctaccagcggtcttggagggcccgcttgcaccattgcccttactgatgtccaccgggccttacgcacttgcagGGAGGAGGGCATCCTGGGCCTGTGGAAGGGTCTGGGCCCCAACATCGCGCGTAACGCCATCATCAACGCGGCCGAGCTGGCCAGCTACGACCAG

- tgccaca
- - - - - - - - - - - - - - - - - - - - - - - - - -cttgcac