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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAATTGAGGAGAAAATCAACAAGGTCCGGTGGTGCCGGAGCTCAAACAACACGCGGATGCTGTTGTCCACCAACGACAAGACCGTGAAGCTATGGAAGgtgaggtttgggttcggtctgggctggcccgcatgcgcattgctcacgttcgctggggtttgcgtgcag

Basic information

species Chlamydomonas reinhardtii
transcript EDO98296
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO98296 (Chlamydomonas reinhardtii), 5'ss of exon 3
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 5'ss of exon 4
GGAAATTGAGGAGAAAATCAACAAGGTCCGGTGGTGCCGGAGCTCAAACAACACGCGGATGCTGTTGTCCACCAACGACAAGACCGTGAAGCTATGGAAGgtgaggtttgggttcggtctgggct---ggcccgcatgcgcattgctcacgttcgctggggtttgcgtgcag----------------------------
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GGAAATTGAGGAGAAAATCAACAAGATTAGATGGTGTCAGACAGCTAACAGCGCACTGTTTCTTCTCTCCACTAATGATAAAACCATCAAATTCTGGAAGgtagggaaaggcatcaattgaactttttgaattttgtgattatcaactgtttttagatagattgaccttgacatcaaatctttttggcatttaattagaa
















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|161819998|gb|FC109684.1|FC109684
EST:     ACACGCGGATGCTGTTGTCCACCAACGACAAGACCGTGAAGCTATGGAAG                         GTCTACGAGAAGAAGGTGTCATGCCTGTCGAACTTCAACTTGGAAGGCCGG
genomic: ACACGCGGATGCTGTTGTCCACCAACGACAAGACCGTGAAGCTATGGAAGgtgaggtttg ... ttgcgtgcagGTCTACGAGAAGAAGGTGTCATGCCTGTCGAACTTCAACTTGGAAGGCCGG
EST: gi|161802583|gb|FC092394.1|FC092394
EST:     ACACGCGGATGCTGTTGTCCACCAACGACAAGACCGTGAAGCTATGGAAG                         GTCTACGAGAAGAAGGTGTCATGCCTGTCGAACTTCAACTTGGAAGGCCGG
genomic: ACACGCGGATGCTGTTGTCCACCAACGACAAGACCGTGAAGCTATGGAAGgtgaggtttg ... ttgcgtgcagGTCTACGAGAAGAAGGTGTCATGCCTGTCGAACTTCAACTTGGAAGGCCGG
EST: gi|8514502|gb|BE122397.1|BE122397
EST:     ACACGCGGATGCTGTTGTCCACCAACGACAAGACCGTTAAGCTATGGAAG                         GTCTACGAGAAGAAGGTGTCATGCCTGTCGAACTTCAACT
genomic: ACACGCGGATGCTGTTGTCCACCAACGACAAGACCGTGAAGCTATGGAAGgtgaggtttg ... ttgcgtgcagGTCTACGAGAAGAAGGTGTCATGCCTGTCGAACTTCAACT
EST: gi|161795145|gb|FC078796.1|FC078796
EST:     ACACGCGGATGCTGTTGTCCACCAACGACAAGACCGTGAAGCTATGGAAG                         GTCTACGAGAAGAAGGTGTCATGCCTGTCGAACTTCAACTTGGAAGGCCGG
genomic: ACACGCGGATGCTGTTGTCCACCAACGACAAGACCGTGAAGCTATGGAAGgtgaggtttg ... ttgcgtgcagGTCTACGAGAAGAAGGTGTCATGCCTGTCGAACTTCAACTTGGAAGGCCGG
EST: gi|16437384|gb|BM002604.1|BM002604
EST:     ACACGCGGATGCTGTTGTCCACCAACGACAAGACCGTGAAGCTATGGAAG                         GTCTACGAGAAGAAGGTGTCATGCCTGTCGAACTTCAACTTGGAAGGCCGG
genomic: ACACGCGGATGCTGTTGTCCACCAACGACAAGACCGTGAAGCTATGGAAGgtgaggtttg ... ttgcgtgcagGTCTACGAGAAGAAGGTGTCATGCCTGTCGAACTTCAACTTGGAAGGCCGG
EST: gi|23363557|gb|BU651377.1|BU651377
EST:     CACGCGGATGCTGTTGTCCACCAACGANCA-GACCGTGAAGCTATGGAAG                         GTCTACGAGAAGAAGGTGTCATGCCTGTCGAACTTCA-CTTGGA-GGCCGG
genomic: CACGCGGATGCTGTTGTCCACCAACGA-CAAGACCGTGAAGCTATGGAAGgtgaggtttg ... ttgcgtgcagGTCTACGAGAAGAAGGTGTCATGCCTGTCGAACTTCAACTTGGAAGGCCGG
EST: gi|15701364|gb|BI725669.1|BI725669
EST:     ACACGCGGATGCTGTTGTCCACCAACGACAAGACCGTGAAGCTATGGAAG                         GTCTACGAGAAGAAGGTGTCATGCCTGTCGAACTTCAACTTGGAAGGCCGG
genomic: ACACGCGGATGCTGTTGTCCACCAACGACAAGACCGTGAAGCTATGGAAGgtgaggtttg ... ttgcgtgcagGTCTACGAGAAGAAGGTGTCATGCCTGTCGAACTTCAACTTGGAAGGCCGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAATTGAGGAGAAAATCAACAAGGTCCGGTGGTGCCGGAGCTCAAACAACACGCGGATGCTGTTGTCCACCAACGACAAGACCGTGAAGCTATGGAAGgtgaggtttgggttcggtctgggctggcccgcatgcgcattgctcacgttcgctggggtttgcgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG