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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAGgtgtgttgtcgtgcgggggcgtgcaggaatcgctcaagccgcaagtctccccgtagcgtgcagcgtaagctggcggggcgcgacaccaggcaaccgcacg...

Basic information

species Chlamydomonas reinhardtii
transcript EDP09161
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP09161 (Chlamydomonas reinhardtii), 5'ss of exon 4
lower sequence: LOC_Os01g16190.1 (Oryza sativa), 5'ss of exon 3
CCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAGgtgtgttgtcgtgcgggggcgt---gcaggaatcgctcaa-gccgcaagtctccc---cgtagcgtgcagcgtaagctggcggggcgcgacaccaggcaaccgcacg
 || || ||||||||||||||||| ||||| || || || || || || ||||| ||||| || ||||||||||| |||||||||  |   | |       | |     | |  | | | || |  |||| | |  |     |  |     |    |  ||  | | |   |||   ||||        
ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgcttattctacctttttataagttttgttaaaaggagcaattgtttcacatttgacaaatggaaacaattgatgtgtccaaacatgtggcac-------

upper sequence: EDP09161 (Chlamydomonas reinhardtii), 5'ss of exon 4
lower sequence: PP1S146_35V6.1 (Physcomitrella patens), 5'ss of exon 3
CCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAGgtgtgttgtcgtgcggg--ggcgtgcaggaatcgctcaagccgcaagtctccccgtagcgtgcagcgtaagctggcggggcgcgacaccaggcaaccgcacg-
 || |||||||| || || ||||| || ||||| || || || ||||||||| |||| |||||||||||||| ||||| |||||   ||   ||    |  | | ||   |   |  |||    |  |   ||    |   |   ||  | |     |    | |||      |  |    |   
GCCTGAGATGGTCGTTGGGTGGTATCATTCACATCCAGGGTTTGGCTGCTGGTTGTCTGGCGTGGATATCAATACGCAACAGgtaatttagggtttcagtagtcttgtttggtactttca---tgtgaccttcgtaattttgaaaagttttaatgcactcttctcgaggtttagtgaataaatct

upper sequence: EDP09161 (Chlamydomonas reinhardtii), 5'ss of exon 4
lower sequence: PP1S46_324V6.1 (Physcomitrella patens), 5'ss of exon 3
CCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAGgtgtgttgtcgtgcgggggcgtgcaggaatcgctcaagccgcaagtctccccgtagcgtgcagcgtaagctggcggggcgcg-acaccaggcaaccgcacg----
 || ||||||||||||||||||||||| || || || || || || |||||| |||| |||||||||||||| || ||||||||   ||    |        |    || |||  |      |  |   |    ||   |  || | ||    |  | || |   | |   |   | ||   |    
ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttaggtttataattaggtttggcatctttt----tgttaaagtggttgttatgaaca-catacaaagatgtggtgaacaaattggtggaacgttggtttt

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|15695776|gb|BI720081.1|BI720081
EST:     ACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAG                         TCTTTCGAGGCGCTGAACAACCGCGCGGTGGCAGTGGTGGTGGATCCAGTG
genomic: ACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAGgtgtgttgtc ... accggcgcagTCTTTCGAGGCGCTGAACAACCGCGCGGTGGCAGTGGTGGTGGATCCAGTG
EST: gi|16431951|gb|BI997177.1|BI997177
EST:     ACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAG                         TCTTTCGAGGCGCTGAACAACCGCGCGGTGGCAGTGGTGGTGGATCCAGTG
genomic: ACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAGgtgtgttgtc ... accggcgcagTCTTTCGAGGCGCTGAACAACCGCGCGGTGGCAGTGGTGGTGGATCCAGTG
EST: gi|15369702|gb|BI529128.1|BI529128
EST:     ACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAG                         TCTTTCGAGGCGCTGAACAACCGCGCGGTGGCAGTGGTGGTGGATCCAGTG
genomic: ACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAGgtgtgttgtc ... accggcgcagTCTTTCGAGGCGCTGAACAACCGCGCGGTGGCAGTGGTGGTGGATCCAGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAGgtgtgttgtcgtgcgggggcgtgcaggaatcgctcaagccgcaagtctccccgtagcgtgcagcgtaagctggcggggcgcgacaccaggcaaccgcacg

- - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaccgc