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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCGGCAAGTCCAATCTGCTCTCCCGTTTCACGAGGAATGAGTTCAGCCTCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctatctgcaagagaggatttgactggtcatggccattgacaaaatgcgctgttgctctgagcag

Basic information

species Chlamydomonas reinhardtii
transcript EDP04353
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP04353 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: LOC_Os05g01480.1 (Oryza sativa), 5'ss of exon 1
CGTCGGCAAGTCCAATCTGCTCTCCCGTTTCACGAGGAATGAGTTCAGCCTCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctatctgcaagagaggatttgactggtcatggccattgacaaaatgcgctgttgctctgagcag-------------------------------
||||||||||||||| || ||||||||||||||  | || |||||| |||||||||||||||| ||||| ||||| |||||||| || |||| | | || | | | | ||||   |         |  ||| | |  |   ||  ||  |      | | | || ||| |                               
CGTCGGCAAGTCCAACCTCCTCTCCCGTTTCACCCGCAACGAGTTCTGCCTCGAGTCCAAGTCCACCATCGGCGTCGAGTTCGCCACCCGCACCCTCCATgtatgtccatctttcatctccttccttcctgcttactgtacttaccactagctctagctaccct-agctgcttcgtaattcctttctcaatcaattcaatt

upper sequence: EDP04353 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: LOC_Os03g60870.1 (Oryza sativa), 5'ss of exon 2
CGTCGGCAAGTCCAATCTGCTCTCCCGTTTCACGAGGAATGAGTTCAGCCTCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctatct--gcaagagaggatttgactggtcatggccattga-caaaat-gcgctgttgct--ctgagcag------------------------
|||||||||||||||  | ||||| || |||||  | || |||||| |||||||||||||||| ||||||||||| |||||||| || ||||   | ||||     ||  |   ||  ||       |      ||  | | || |  || ||| |   |||||     |  |||                         
CGTCGGCAAGTCCAACATCCTCTCGCGATTCACCCGCAACGAGTTCTGCCTCGAGTCCAAGTCCACCATTGGCGTCGAGTTCGCCACCCGCACGCTCCAGgtcccccttccctcgcgcgatccatcctcttctctcgcgactatggttcagaatagtagtgttggggatttcgcatgtcaccattgcgttcgatgcattt

upper sequence: EDP04353 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: LOC_Os01g62950.1 (Oryza sativa), 5'ss of exon 1
CGTCGGCAAGTCCAATCTGCTCTCCCGTTTCACGAGGAATGAGTTCAGCCTCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctatctgcaagagaggatttgactggtcatggccattgacaaaatgcgct-gttgctctgagcag-----------------------------------
|||||||||||||||  | |||||||| |||||  | || ||||||  ||||||||||||||| ||||| ||||| |||||||| || |||| | | ||||      || | ||    | |      ||  | |    ||     |   || | || | |    ||  ||                                    
CGTCGGCAAGTCCAACATCCTCTCCCGCTTCACCCGCAACGAGTTCTTCCTCGAGTCCAAGTCCACCATCGGCGTCGAGTTCGCCACCCGCACCCTGCAGg------tacccgcgtacgcgacgcccacccgccccccccccccccctgatccccttgcttgcttgtacaattttgcgattggcgcgcgtcgtgatgtcgcgtcgg

upper sequence: EDP04353 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: GRMZM2G154960_T01 (Zea mays), 5'ss of exon 1
CGTCGGCAAGTCCAATCTGCTCTCCCGTTTCACGAGGAATGAGTTCAGCCTCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctatctgcaag----agaggatttga-ctggtcatggcc--attgacaaaatgcgc--tgttgctctgagcag---------------------
|||||||||||||||  | ||||| || |||||| | || |||||| |||||||||||||||| ||||| ||||| |||||||| || |||| | | |||| |   | ||    |      |        || ||| ||  | ||  ||   |   ||||||   || ||  |  || |                     
CGTCGGCAAGTCCAACATCCTCTCGCGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAGTCCACCATCGGCGTCGAGTTCGCTACCCGCAACCTGCAGgtacccccatacatacacctcaacaaccccgatctgatcgcgccccaatgtgccccatgcgcggcgtggccatttgccgccgtgcatggcgcgtctgttt

upper sequence: EDP04353 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: GRMZM2G473906_T03 (Zea mays), 5'ss of exon 2
CGTCGGCAAGTCCAATCTGCTCTCCCGTTTCACGAGGAATGAGTTCAGCCTCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctatctgcaa--------gagaggatttgactggtcatggccattgaca-----aaatgcgctgttgct-ctgagcag----------------
|||||||||||||||  | |||||||| |||||  | || |||||| |||||||||||||||| ||||| ||||| |||||||| || |||| | | |||| ||  | | | ||||           | | | |   |  | |      ||||||     |||| | |   | ||  |  | |                 
CGTCGGCAAGTCCAACATCCTCTCCCGATTCACCCGCAACGAGTTCTGCCTCGAGTCCAAGTCCACCATCGGCGTCGAGTTCGCCACCCGCACCCTGCAGgtaaacccacccgcaatgatttgaagaacgttctagtttataagtcgttttgacatttgtaaatacacaacttctgttatgtaactagacaaatagtgta

upper sequence: EDP04353 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: GRMZM2G144008_T01 (Zea mays), 5'ss of exon 2
CGTCGGCAAGTCCAATCTGCTCTCCCGTTTCACGAGGAATGAGTTCAGCCTCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat-------ctgcaagagaggatttgactggtcatggccattgacaaaatgcgctgttgctctgagcag---------------------------
|||||||||||||||  | || ||||| |||||  | || |||||| |||||||||||||||| ||||| ||||| |||||||| || |||| | | |||| ||| | |        | ||    ||   | |  || |    ||   | || | | |    | ||||  |  || |                           
CGTCGGCAAGTCCAACATCCTTTCCCGGTTCACCCGCAACGAGTTCTGCCTCGAGTCCAAGTCCACCATCGGCGTCGAGTTCGCCACCCGCACCCTCCAGgtaagcccactccctccccgccctcgaatctctccctagatgagggagtcgagagatt----tattgcattcggcgggttcatactgctggggctggggcgttt

upper sequence: EDP04353 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: Vv06s0004g05550.t01 (Vitis vinifera), 5'ss of exon 1
CGTCGGCAAGTCCAATCTGCTCTCCCGTTTCACGAGGAATGAGTTCAGCCTCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggcta------tctgcaagagaggatttgactggtcatggccattgacaaaatgcgctgtt-gctctgagcag-----------------------
 || || || || ||| |  | ||  | || ||||||||||||||| || | || || |||||||||||||| || ||||||||||| || |   | ||||  |   ||      ||||        | | |   | ||  |  | |||  ||   ||   | ||   ||||  |                         
TGTTGGGAAATCGAATATCTTGTCGAGGTTTACGAGGAATGAGTTCTGCTTGGAATCTAAGTCTACCATTGGAGTTGAGTTCGCGACGCGGACTTTGCAGgtgattttagaatgctctgttcattcagctatattttgtggtctcgattatcattgtgttttttttaatctgttcctgcacgaataatttttaatcagaa

upper sequence: EDP04353 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: PP1S209_94V6.1 (Physcomitrella patens), 5'ss of exon 2
CGTCGGCAAGTCCAATCTGCTCTCCCGTTTCACGAGGAATGAGTTCAGCCTCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgca-----------aggctatc-tgcaa----gagaggatttgactggtcatggccattgacaaaat----gcgctgttgctctgagcag----------
 || || |||||||||||||| ||| | || ||| |||| |||||| |||| ||||| ||||| ||||||||||||||||| || |||||    || |||| |             |||  | |||||    | ||||    |  | |    |||    | | ||      | | |||  ||   |||            
TGTGGGGAAGTCCAATCTGCTTTCCAGATTTACGCGGAACGAGTTCTGCCTGGAGTCGAAGTCGACCATTGGCGTGGAGTTTGCCACTCGATCTATCCAGgtatcgtccggcccgtgctggcatgcaatgtcgtgagggcggggtttggtgcggctgcggtcgaagctgtagaggtgtgactagaagcgagggtccgggg

upper sequence: EDP04353 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: PP1S84_180V6.1 (Physcomitrella patens), 5'ss of exon 2
CGTCGGCAAGTCCAATCTGCTCTCCCGTTTCACGAGGAATGAGTTCAGCCTCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctatctgcaagagaggatttgac-tggtcatggcc-attgacaaaatgcgctgttgctctgagcag-----------------------------
 || || |||||||||||||| ||| | |||||| |||| |||||  | || ||||| ||||| ||||| |||||||||||||| ||||||  |||||||| ||     || |     | | ||   || || || |  |  |||||       ||||| | || |  |  |                             
TGTTGGGAAGTCCAATCTGCTTTCCAGATTCACGCGGAACGAGTTTTGTCTAGAGTCGAAGTCGACCATCGGCGTGGAGTTCGCCACTCGCTCCATTCAGgtaatatcctc-gttcaggggcatgcaacgtgctctttacggattgagctgccacgctggttcttttggtggagaatgtagagcatactttaagagatagt

upper sequence: EDP04353 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: PP1S21_298V6.2 (Physcomitrella patens), 5'ss of exon 2
CGTCGGCAAGTCCAATCTGCTCTCCCGTTTCACGAGGAATGAGTTCAGCCTCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaagg-ctatctgcaagagaggatttgactggtcatggcc--attgacaaaatgcgctgttgctctgagcag----------------------------
 || || |||||||||||||| ||| | || ||  | || |||||| | || ||||||||||| |||||||||||||||||||| ||||||  |||||||| |    |  |||||   ||   || |  |   || ||     |||  |    ||  || || || |     |                            
TGTTGGAAAGTCCAATCTGCTTTCCAGATTTACTCGTAACGAGTTCTGTCTGGAGTCCAAGTCGACCATTGGCGTGGAGTTCGCCACTCGCTCCATTCAGgtatcatccgtctgctgtagtaaatgtaccctttcctgagttaattatcgctgtg-actctttctgtagagggtgttgatgatgcattaggagaggatatt

upper sequence: EDP04353 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: PP1S26_33V6.1 (Physcomitrella patens), 5'ss of exon 2
CGTCGGCAAGTCCAATCTGCTCTCCCGTTTCACGAGGAATGAGTTCAGCCTCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggcta-tctgcaa--gagaggatttgactggtcatggccattgacaaaatgcgctgttgctctgagcag-------------------------------
 ||||| ||||||||||| || ||| | || ||| | ||||||||| | || ||||||||||| |||||||| |||||||| || ||| |    ||||||| |     |  ||||     |  | | |  | |      ||   |||      | ||||||   ||| |                                   
TGTCGGGAAGTCCAATCTACTATCCAGATTTACGCGTAATGAGTTCTGTCTGGAGTCCAAGTCGACCATTGGTGTGGAGTTTGCTACTAGATCTATTCAGgtatcatcaacctgcccctaaatgcaatgtattcactgcggagcttgct----ttcgctgtctttctcattgttaactgtgtttgaaaacgaacgacttgtttt

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|161804362|gb|FC089704.1|FC089704
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|9459748|gb|BE452889.1|BE452889
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|161815543|gb|FC101788.1|FC101788
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|161798278|gb|FC083487.1|FC083487
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|23363628|gb|BU651448.1|BU651448
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|9459215|gb|BE452496.1|BE452496
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|161821621|gb|FC108746.1|FC108746
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|9441236|gb|BE441840.1|BE441840
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|23359663|gb|BU647483.1|BU647483
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|16071620|gb|BI873616.1|BI873616
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|15701542|gb|BI725847.1|BI725847
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|6541367|gb|AV387151.1|AV387151
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|8828268|gb|BE211998.1|BE211998
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|16073328|gb|BI875324.1|BI875324
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTCGGCAAGTCCAATCTGCTCTCCCGTTTCACGAGGAATGAGTTCAGCCTCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctatctgcaagagaggatttgactggtcatggccattgacaaaatgcgctgttgctctgagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG