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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtgcacccggcgagcgccaattcgtgcatcgtagcataaatggacaattgggctaaccgtgccaaccttttgctggtagGTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCACATCTTCTTCGGCGCGTACCCCAACATGATGAATGTCTTCAAGGAGCTAA

Basic information

species Chlamydomonas reinhardtii
transcript EDP05305
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP05305 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM2G410515_T02 (Zea mays), 3'ss of exon 4
-----gtgagtgtgcacccggc-gagcgccaattcgtgcatcg-tagcataaatggacaattgggctaaccgtgcca--accttttgc----tggtagGTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCACATCTTCTTCGGCGCGTA--CCCCAACATGATGAATGTCTTCAAGGAGCTAA
      | | |     |  | | |    | | |   || || | |  |||  |  |      |   |     |   |  |  ||||      || ||||| ||||| ||||||||||| ||||| || ||||||||||||||  | || ||||| |         |   |    | |   |    ||||||      |  
gtctgataaatacttgcatgactgtttactactctctgaattgctctcattcactgttttcagcatttgttattttatgattttttatgcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTGTAAGTTACAGTTCTGGTCCTTGAGGTCCTCTTCATCATATT--

upper sequence: EDP05305 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 4
-----gtgagtgtgcacccggc-gagcgccaattcgtgcatcg-tagcataaatggacaattgggctaaccgtgcca--accttttgc----tggtagGTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCACATCTTCTTCGGCGCGTACCCCAACATGATGAATGTCTTCAAGGAGCTAA
      | | |     |  | | |    | | |   || || | |  |||  |  |      |   |     |   |  |  ||||      || ||||| ||||| ||||||||||| ||||| || ||||||||||||||  | || ||||| |                                          
gtctgataaatacttgcatgactgtttactactctctgaattgctctcattcactgttttcagcatttgttattttatgattttttatgcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTT------------------------------------------

upper sequence: EDP05305 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GLYMA18G00720.1 (Glycine max), 3'ss of exon 3
-------------gtgagtgtgcacccggcgagcgcca-attcgtgcatcgtagcataaatggacaattgggctaaccgtgccaaccttttgctggt--agGTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCACATCTTCTTCGGCGCGTACCCCAACATGATGAATGTCTTCAAGGAGCTAA
              |||  ||   | | |      | | ||   |  |    | ||    |     |||| | |     | | |   |||   |     |||| ||||||||||| ||  ||||||| |||||||||||||| ||| | |||||||| |                                          
atcatcaggtttgttgaaggttaccacagtatatacaacatatttataataaatcaattttaatgtattgtgttt-ttatactattgtttcattttctaagGTTGCTGCATGGAAAGACAAGGATGGAGACTGGTACGAGACAGGCCTACACATCTTTT------------------------------------------

upper sequence: EDP05305 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 4
--------------------gtgagtgtgcacccggcgagcgccaattcgtgcatcgtagcataaatggacaattgggctaaccgtgccaaccttttgctggtagGTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCACATCTTCTTCGGCGCGTACCCCAACATGATGAATGTCTTCAAGGAGCTAA
                    ||   |||     | |       |||||     ||| ||    | |  || | ||  | |    |||  |    | | |    || | ||||||||||||||||| ||||| |||||||| |||||||| || || || ||||                                          
ttctctggttcttaggttaggttcttgtttgttccgttt-taacaatttacctatcttattggagagcgatatttatgat----gtgatatttgtcttcctccagATAGCTGCATGGAAGGATGAAGATGGGGACTGGTATGAGACTGGTTTACATATTTTCT------------------------------------------

upper sequence: EDP05305 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 4
------gtgagtgtgcacccggcgag---cgccaattcgtgcatcgtagcataaatggacaattg----ggctaaccgtgccaaccttttgctggt--agGTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCACATCTTCTTCGGCGCGTACCCCAACATGATGAATGTCTTCAAGGAGCTAA
       | | |||  |   |          | | ||  |    | |   ||   ||||   ||        ||     | | |   | |  || |  |||| ||||||||||| ||||||||||| |||||||| ||||| ||| | || || ||||                                          
gcaatactaattgtataatagatttaacttcctacttaatttccccttttattgttggaagtttctttcatttagtgaaggctagtctctcttgatatagGTGGCTGCATGGAAAGATGAGGATGGAGACTGGTATGAGACAGGCCTACATATATTCT------------------------------------------

upper sequence: EDP05305 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: PP1S369_27V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------gtgagtgtgcacccggcgagcg-----ccaat-tcgtgc--atcgtagcataaatggacaattgggctaaccgt--gccaaccttttgctg-gtagGTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCACATCTTCTTCGGCGCGTACCCCAACATGATGAATGTCTTCAAGGAGCTAA
                             |  | | |||  | | ||| |      | ||| |   ||  |   || |   | | | ||||    ||  |  |  |  |   || ||    |||||| || |||||||||||  ||||||| || |||||||||||||| ||||||||||| |                                          
gtgataattgtgaacttttgggttaatgtgccattctgcctcagccgaacagaggacgaatattacgctaactataactagactagtcaataatactggctctaagtgatttttctgaaatgtagGTTGCGGCATGGAAGGACAAGGATGGGGATTGGTACGAGACTGGTTTGCACATCTTTT------------------------------------------

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|10793663|gb|AV631029.1|AV631029
EST:     CTGGACACCACCCAATCGTTCTGGAGGGCCGTGACGTGCTCGGTGGCAAG                         GTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCAC
genomic: CTGGACACCACCCAATCGTTCTGGAGGGCCGCGACGTGCTCGGTGGCAAGgtgagtgtgc ... ttgctggtagGTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCAC
EST: gi|16072849|gb|BI874845.1|BI874845
EST:     CTGGACACCACCCAATCGTTCTGGAGGGCCGCGACGTGCTCGGTGGCAAG                         GTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCAC
genomic: CTGGACACCACCCAATCGTTCTGGAGGGCCGCGACGTGCTCGGTGGCAAGgtgagtgtgc ... ttgctggtagGTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCAC
EST: gi|15692428|gb|BI716733.1|BI716733
EST:     CTGGACACCACCCAATCGTTCTGGAGGGCCGCGACGTGCTCGGTGGCAAG                         GTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCAC
genomic: CTGGACACCACCCAATCGTTCTGGAGGGCCGCGACGTGCTCGGTGGCAAGgtgagtgtgc ... ttgctggtagGTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCAC
EST: gi|49470765|gb|BP098626.1|BP098626
EST:     CTGGACACCACCCAATCGTTCTGGAGGGCCGTGACGTGCTCGGTGGCAAG                         GTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCAC
genomic: CTGGACACCACCCAATCGTTCTGGAGGGCCGCGACGTGCTCGGTGGCAAGgtgagtgtgc ... ttgctggtagGTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatcgtagcataaatggacaattgggctaaccgtgccaaccttttgctggtagGTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCACATCTTCTTCGGCGCGTACCCCAACATGATGAATGTCTTCAAGGAGCTAA
                          ggctaac  putative branch site (score: 2)
                                         ccttttgct  putative PPT
           ataaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgtgcacccggcgagcgccaattcgtgcatcgtagcataaatggacaattgggctaaccgtgccaaccttttgctggtagGTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCACATCTTCTTCGGCGCGTACCCCAACATGATGAATGTCTTCAAGGAGCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT