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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggccttgaccgcatcctgggctgtccttgctttgctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC

Basic information

species Chlamydomonas reinhardtii
transcript EDP05803
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
lower sequence: LOC_Os06g44140.1 (Oryza sativa), 3'ss of exon 6
-----gcggtgaccggaaacccat----gctgggtctga-gcactgggtctgagc-gcgaggccttgaccgcatcctgggctgtccttgctttgctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
| | | | || ||| || || || ||| ||| || || ||| || | |||| | | ||||| || | || | |||||| ||||| ||| ||||| ||||| ||||||| |||||||||||||| ||| || ||||| ||||||||||||||| | |||||| ||||||| || |
gtaatgtgtcaaatgccaaatcatttcagccaattcagatgcatacggtgtggttagcttggcatttgctgcattgtttg-tgtccatggtggatgaatg---atatgcagGAGAGCGATATCAAATGGGCGTCGCGGTGGGACAGCTACCTGCTGATGACGGATGATCAGATCCACTGGTTCTCCATCGTGAACTCGCTGATGATCGTGC

upper sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
lower sequence: GRMZM2G006117_T03 (Zea mays), 3'ss of exon 2
--gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgagg-----ccttgaccgcatcctgggctgtccttgctttg---ctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
| ||| || | || | | ||| || | || || | |||| | || | | | || || || | | |||| || |||||| ||||| || |||||||||||||||||| |||||| || || |||||||||||||| || || | ||||| | ||||| || |
gtacaa-gactgggattaagaattgcttattttaactttgtttagctgctagtgtactctttgaatgtttcttttgtcatgattttaatggaacttccactaattttcagGAGAGTGAGATCAAGTGGGCGTCACGCTGGGACACCTACCTGTTGATGACCGATGATCAGATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC

upper sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
lower sequence: GLYMA08G20640.1 (Glycine max), 3'ss of exon 6
gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggccttgaccgcatcc----tgggctgtccttgc---tttgctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
|| | | | ||| | | | | || ||| ||| || || | || |||| |||| | |||| || || ||| ||||| || || |||||||| || || | |||| || || ||||| ||||||||||||||||||||||| |||||||||| |
---------------gtattgctgattaaaatcttggctaccaat---aaactttcacctcatttgttatgatacgttatggcaagtttgttggtact--ttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTCTGATGATTGTTC

upper sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
lower sequence: GLYMA07G01240.1 (Glycine max), 3'ss of exon 6
gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggccttgaccgcatcctgggctgt-ccttgctttgctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
|| | | | | | || || | | | | | || | || | | | || |||| |||| | |||| || || ||| ||||| || || |||||||| || || | |||| || || ||||| ||||||||||||||||||||||| |||||||||| |
---gt-attgctgattaaaatcttggctactcataaattttcacctca-----ttcattatatgatacgttaagccaaagtttgttggtatt--ttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTTTGATGATTGTTC

upper sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
lower sequence: AT1G55130.1 (Arabidopsis thaliana), 3'ss of exon 6
gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggccttgaccgcatcctgggctgtc--cttgctttgctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
| | | | | ||| || | || ||||| | | | || | | | |||||| || | ||| ||||| |||||||||||||| ||| |||| |||| || || || || |||||||| || ||||| |||||| | ||||||||||
------------------------------gtaactaatttactctggagaactc--tttatttatgcgctgtaaacatattatgaagtatgaaatatgcagGAGAGTGTTATCAAATGGGCTTCGCGCTGGGACACATACTTGCTTATGAACGATGATCAAATCCACTGGTTTTCAATCATAAACTCGCTTATGATTGTCC

upper sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
lower sequence: Vv09s0002g02140.t01 (Vitis vinifera), 3'ss of exon 6
gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggccttgaccgcatcctgggctgtccttgctttgctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
| || | | | | | || | ||| | | | | | | ||| |||| || | | | |||| || | ||| ||||| || || ||||| || ||||| || |||| || || ||||| ||||||||||||||||| ||||| ||||||||||||
----------gtaattctttttcgaaatccttgcttg-tcttctcccatgatacggttt---tttttacttgtttttgccttattatt-------ttcagGAAAGTAACATCAAATGGGCTTCACGGTGGGATACATACCTCCTTATGAACGATGATCAGATCCACTGGTTCTCCATCATAAACTCTCTGATGATTGTCC

upper sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
lower sequence: PP1S140_64V6.1 (Physcomitrella patens), 3'ss of exon 6
gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggcc-ttgaccgcatcctgggctgtcc--ttgctttgctggtggcg----acgtgc------agGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
| | | | ||| | |||| || || |||| || || | || || ||| || | ||| || | |||| || || | || ||||| || |||||||| || || || || |||| || | ||||||||||||||||||||||| ||||| | |||||||| |
gtgagaaattcgt-ctcataaccgttctgctcatcatgtgtgaggttgaattaatttttcatgtcttgtgctttcgaatctattttctaacaatattttatgtgcttacgcagTACAGTCATGTCAAATGGGCTTCTCGCTGGGATACATATCTACTCATGACAGATGCGCAGATTCACTGGTTCTCCATCATCAACTCCCTCATGATTGTGC

upper sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
lower sequence: EFJ35060 (Selaginella moellendorffii), 3'ss of exon 6
gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggccttgaccgcatcctgggctgt----ccttgctttgctggtggcgac-gtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
| | || ||| || ||| || | | |||| | || | | ||||| || | | ||||| ||| | ||||| | || || ||| ||||||||||| |||||||| || ||||| |||||| ||||||| ||||
-------------------------------------------gtgaaagtttttggaaaaattctgcgccttgtaactttgcgtgtttgttttcttttatgcagTTGAGTCCAGTGAGATGGGCTTCGAGATGGGATATGTATCTCTACATGTCCGACGACCAGATCCACTGGTTTTCGATCATCAACTCGCTGATGATCGTCC

upper sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
lower sequence: EFJ17419 (Selaginella moellendorffii), 3'ss of exon 6
gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggccttgaccgcatcctgggctgt----ccttgctttgctggtggcgac-gtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
| | || ||| || ||| || | | |||| | || | | ||||| ||| | | ||||| ||| | ||||| | || || ||| ||||||||||| |||||||| || ||||| |||||| ||||||| ||||
-------------------------------------------gtgaaagtttttggaaaaattctgcgccttgtaactttgcgtgtttgttttcttttatgcagTTTAGTCCAGTGAGATGGGCTTCGAGATGGGATATGTATCTCTACATGTCCGACGACCAGATCCACTGGTTTTCGATCATCAACTCGCTGATGATCGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgaggccttgaccgcatcctgggctgtccttgctttgctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC
      ccttgac  putative branch site (score: 4)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggccttgaccgcatcctgggctgtccttgctttgctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC

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