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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caccaagccgagcagcggctgcggcttcccctcacgcctgcagcccacccacccagcctcacccgctcgcctccctccctccggcctaccaatgcatcagATCCTCAAGTTCTTCTCCTACGAGCACTTCTACGTCATCTACTGCAAGTTCTGGGAGCTGGACCAGGACCACGACTTCCAGCTGGACAAGACAGACCTGG

Basic information

species Chlamydomonas reinhardtii
transcript EDP08306
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP08306 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 7
caccaagccgagcagcggctgcggcttcccctcacgcctgcagcccacccacccagcctcacccgctcgcctccctccctccggcctaccaatgcatcagATCCTCAAGTTCTTCTCCTACGAGCACTTCTACGTCATCTACTGCAAGTTCTGGGAGCTGGACCAGGACCACGACTTCCAGCTGGACAAGACAGACCTGG--------
           | |  | |       |   |   |   ||  |   |   |   ||  |       | ||     |  |  |    | | | |   |  |    | |  | |||||| || ||||| ||||| ||||| |||||||||||||||||||||||   ||| ||||| |||| | | |||||   | | ||          
-----------gtactgacaaaaatatttgcgtgctattgttgt--atttat--agtattgttt--ttgctcatttaacatcacttttctattcactttggcaattagATACTTCTCGTATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGCGATAT

upper sequence: EDP08306 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 6
caccaagccgagcagcggctgcggcttcccctcacgcctgcagcccacccacccagcctcacccgctcgcctccctccctccggcctaccaatgcatcagATCCTCAAGTTCTTCTCCTACGAGCACTTCTACGTCATCTACTGCAAGTTCTGGGAGCTGGACCAGGACCACGACTTCCAGCTGGACAAGACAGACCTGG--------
           | |  | |     |         |   ||  |   |               | ||||   |  |         |     | |    || ||    |  | |||||| || ||||| ||||| ||||| |||||||||||||||||||||||   ||| ||||| |||| | | |||||   | | ||          
-----------gtactgacaaaaacaaatttgtgctattgttgtatatatggt--attgtttctgctcatttaacatgacttttctacttactttggcaaat----agATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT

upper sequence: EDP08306 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: AT1G03960.1 (Arabidopsis thaliana), 3'ss of exon 7
caccaagccgagcagcggct-gcggcttcccctcacgcctgcagcccacccacccagcctcacccgctcgcctccctccctccggcctaccaatgcatcagATCCTCAAGTTCTTCTCCTACGAGCACTTCTACGTCATCTACTGCAAGTTCTGGGAGCTGGACCAGGACCACGACTTCCAGCTGGACAAGACAGACCTGG--------
 | | |   ||| |  ||||     ||||   |  |  ||| | |  |   ||  |      || | |    | ||     |   | |  |  | | |   ||  ||| || ||||||||| |||||||||||||| || |||||||| || ||||| || ||    ||||| || |      | || |||    | ||          
gagctatatgagtattggcttataccttcatattgcttctgtaacaga---actta----tgcctgatt--ttaccatttgcaatcatgtcgtttcttttaattttcagGTACTTCTCCTATGAGCACTTCTACGTGATATACTGCAAATTTTGGGAACTTGATGGTGACCATGATTGTTTTATTGATAAGGACAATCTCATCAAATAT

upper sequence: EDP08306 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 8
caccaagccgagcagcggctgcggcttcccctcacgcctgcagcccacccacccagcctcacccgctcgcctccctccctccggcctaccaatgcatcagATCCTCAAGTTCTTCTCCTACGAGCACTTCTACGTCATCTACTGCAAGTTCTGGGAGCTGGACCAGGACCACGACTTCCAGCTGGACAAGACAGACCTGG--------
 | ||| | |||   |   |||   |     |         ||   | | |   |                 |    || |  | || |     | |||   |  || || ||| || || || |||||||| || || ||||||||||||||||||||||||   || || || |||  | | |||||     | ||          
-aacaa-cagagagacacatgcatatatttgttttattattagattaactagttatttatgatgatgaattgctaggccccatgtcttc----acttcaa--ctgcagGTACTTTTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGACACAGATCATGATTTCTTGATTGACAAAGAGAATCTCATCAGATAT

upper sequence: EDP08306 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: Vv14s0036g00750.t01 (Vitis vinifera), 3'ss of exon 4
caccaagccgagcagcggctgcggcttcccctcacgcctgcagcccac-ccacccagcctcacccgctcgcctccct--ccctccggcctaccaatgcatcagATCCTCAAGTTCTTCTCCTACGAGCACTTCTACGTCATCTACTGCAAGTTCTGGGAGCTGGACCAGGACCACGACTTCCAGCTGGACAAGACAGACCTGG--------
          |   | ||        || | | ||   |  |||     |      |  | |     |   | || |  |  |      |   | |    |    ||  | || |||||| || || |||||||| || || |||||||||||||||||||||||    ||||| || ||   | | || ||     ||||          
---------tatttgtgggaata--ctctcataacatttttagcatgtactgtgtggtattaaaattttaacaccattgcttttttttttttgattatgcccttaccatagGTACTTCTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGATACCGACCATGATTTTTTGATTGATAAAGAGAACCTAATCAGATAT

upper sequence: EDP08306 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: EFJ20642 (Selaginella moellendorffii), 3'ss of exon 7
caccaagccgagcagcggctgcggcttcccctcacgcctgcagcccacccacccagcctcacccgctcgcctccctccctccggcctaccaatgcatcagATCCTCAAGTTCTTCTCCTACGAGCACTTCTACGTCATCTACTGCAAGTTCTGGGAGCTGGACCAGGACCACGACTTCCAGCTGGACAAGACAGACCTGG--------
                                                      || |  |  ||       |  |   |     ||  || ||     ||| || |  |  || |||||||| ||||| ||||| |||||||||||||| |||||||| |||  |||||||||||||    | |||||||| |||||          
---------------------------------------------------gtaagtcctattcgagatatccaatatgtttttgctgacagtg----ggatact-agATATTTTTCCTACGAACACTTTTACGTTATCTACTGCAAGTTTTGGGAGCTTGACACGGACCACGACTTCTTAATCGACAAGACTGACCTTTTGAGATAC

upper sequence: EDP08306 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 7
caccaagccgagcagcggctgcggcttcccctcacgcctgcagcccacccacccagcctcacccgctcgcctccctccctccggcctaccaatgcatcagATCCTCAAGTTCTTCTCCTACGAGCACTTCTACGTCATCTACTGCAAGTTCTGGGAGCTGGACCAGGACCACGACTTCCAGCTGGACAAGACAGACCTGG--------
                                                      || |  |  ||     |    |   |  |  ||  || ||     ||| || |  |  || |||||||| ||||| ||||| |||||||||||||| |||||||| |||  |||||||||||||    | |||||||| |||||          
---------------------------------------------------gtaagtcctattcgagatacaatatgtttttg--ctgacagtg----ggatgct-agATATTTTTCCTACGAACACTTTTACGTTATCTACTGCAAGTTTTGGGAGCTTGACACGGACCACGACTTCTTAATCGACAAGACTGACCTTTTGAGATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacccacccagcctcacccgctcgcctccctccctccggcctaccaatgcatcagATCCTCAAGTTCTTCTCCTACGAGCACTTCTACGTCATCTACTGCAAGTTCTGGGAGCTGGACCAGGACCACGACTTCCAGCTGGACAAGACAGACCTGG
          gcctcac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caccaagccgagcagcggctgcggcttcccctcacgcctgcagcccacccacccagcctcacccgctcgcctccctccctccggcctaccaatgcatcagATCCTCAAGTTCTTCTCCTACGAGCACTTCTACGTCATCTACTGCAAGTTCTGGGAGCTGGACCAGGACCACGACTTCCAGCTGGACAAGACAGACCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
caccaag
- - - - - - - - - - - - - - ccctcac
- - - - - - - - - - - - - - - - - - - - - - -cacccac