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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagggcatggacgggaagcttatgtgcgggcagccatgtcaccatgtggcgtatagcatggcggggtgcatggtactggcactggcccgcactacaatgacggtgatttggactcaggcattttgcggccgccaatatgatttctcctcgcgtgcagGACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAG

Basic information

species Chlamydomonas reinhardtii
transcript EDO97202
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO97202 (Chlamydomonas reinhardtii), 3'ss of exon 10
lower sequence: LOC_Os03g18130.3 (Oryza sativa), 3'ss of exon 8
gtgagggcatggacgggaagcttatgtgcgggcagccatgtcaccatgtggcgtatagcatggcggggtgcatggtactggcactggcccgcactacaatgacggtgatttggactcaggcattttgcggc--cgccaatatgatttctcctcgcgtgcagGACCCCT---ACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAG------------------
                                                                                                 |   | ||   ||     |      ||  |  ||   |  ||| |  |   |  ||      |  ||  ||   |    ||  |  |  | || |   | ||||| ||||||||||| || ||||| ||||||||||||||||| ||||| |||                  
-----------------------------------------------------------------------------------------------gtagaaatggcagttcttttttgtttcttcagatgcaatggtaattttgtccgtgttctgaactaatacttctgaaattctccacagCACATACTGTACAGGCAGAAAGAGCAGTTCAGTGATGGCGTCGGCTACAACTGGATCGATGGCCTGAAGGCTTTCACCGAGCAGCAG

upper sequence: EDO97202 (Chlamydomonas reinhardtii), 3'ss of exon 10
lower sequence: GRMZM2G053669_T01 (Zea mays), 3'ss of exon 9
gtgagggcatggacgggaagcttatgtgcgggcagccatgtcaccatgtggcgtatagcatggcggggtgcatggtactggcactggcccgcactacaatgacggtgatttggactcaggcattttgcggccgccaatatgatttct---cctcgcgtgcagG-ACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAG-------------------------------
                                                                   ||  |    |    ||  |  |   | |   |  |   || |||  | | |   |  |    |     | | ||  ||     ||  |    | |  |||  ||||  ||  |  |  | ||||   | ||||| || |||||||| |||||||| ||||||||||||||||| ||||||||                                
-------------------------------------------------------------------gt-taaaacagcaacatcgatcttaattcagagaagcctggttta-atttaattacctccgtgtgttaagtttgcattgcaagccctgaaaactgacacctttaccatccgcagCATATTCTCTACAGGCAGAAAGAACAGTTCAGTGACGGCGTTGGCTACAACTGGATCGATGGCCTCAAATCCTTCACTGAACAGCAGGTGACGGATGAGA

upper sequence: EDO97202 (Chlamydomonas reinhardtii), 3'ss of exon 10
lower sequence: GRMZM2G093175_T02 (Zea mays), 3'ss of exon 5
gtgagggcatggacgggaagcttatgtgcgggcagccatgtcaccatgtggcgtatagcatggcggggtgcatggtactggcactggcccgcactacaatgacggtgatttggactcaggcattttgcggccgccaatatgatttctcctcgcgtgcagGACCCCTACCTGCCCAACGAGGTG--CTCTGGCGCCAGAAGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAG------------------
                                                                                |   | |||  | || |  |   | || ||   ||| |  | |||    |||   | |  ||  |     |        ||        ||||   |    |   ||||   | ||||||||||||||||| |||||||| || |||| ||||||||| ||||| |||                  
--------------------------------------------------------------------------------gtggtagccaac-ctgcgtttcagatgcttct-actgaatc-tttcctagccaaaatttggacgttcagacagacatctgaaaagattttgccttgcagCATATCCTCTACAGACAGAAGGAGCAGTTCAGTGACGGCGTTGGGTACAGCTGGATCGATGGCCTGAAGGCTCATGCAACATCAAAT

upper sequence: EDO97202 (Chlamydomonas reinhardtii), 3'ss of exon 10
lower sequence: GRMZM2G093175_T01 (Zea mays), 3'ss of exon 5
gtgagggcatggacgggaagcttatgtgcgggcagccatgtcaccatgtggcgtatagcatggcggggtgcatggtactggcactggcccgcactacaatgacggtgatttggactcaggcattttgcggccgccaatatgatttctcctcgcgtgcagGACCCCTACCTGCCCAACGAGGTG--CTCTGGCGCCAGAAGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAG------------------
                                                                      || |||  | ||     || ||  | ||  || | |  |   || ||     |||    |||   | |  ||  |     |        ||        ||||   |    |   ||||   | ||||||||||||||||| |||||||| || |||| ||||||||| ||||| |||                  
----------------------------------------------------------------------caaggtggtagc--caacctgcgtttca--gatgcttctactgaatc-----tttcctagccaaaatttggacgttcagacagacatctgaaaagattttgccttgcagCATATCCTCTACAGACAGAAGGAGCAGTTCAGTGACGGCGTTGGGTACAGCTGGATCGATGGCCTGAAGGCTCATGCAACATCAAAT

upper sequence: EDO97202 (Chlamydomonas reinhardtii), 3'ss of exon 10
lower sequence: GRMZM2G078472_T03 (Zea mays), 3'ss of exon 9
gtgagggcatggacgggaagcttatgtgcgggcagccatgtcaccatgtggcgtatagcatggcggggtgcatggtactggcactggcccgcactacaatgacggtgatttggactcaggcattttgcggccgccaatatgatttctcctcgcgtgcagGACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAG------------------
                                                                          |||  | ||     |  ||  | || |  |||  |||   ||| |    | || |    | |   |||  |  |  | | ||    |  | | ||| | || | |  | || |   | ||||| || |||||||| ||||| |||||||||||||||||||| || |||||                   
--------------------------------------------------------------------------gtaaggacat----cttcag-agaaggctggtcgtttac-ctctgtgtctgtgtgttttcaagcctgaactgacgcctc-tgtgccatgcat-cctccgcagC-ATATTCTGTACAGGCAGAAAGAACAGTTCAGTGACGGAGTGGGCTACAACTGGATCGATGGACTCAAAGCCTTCACCGAACAGCAG

upper sequence: EDO97202 (Chlamydomonas reinhardtii), 3'ss of exon 10
lower sequence: GRMZM2G078472_T01 (Zea mays), 3'ss of exon 9
gtgagggcatggacgggaagcttatgtgcgggcagccatgtcaccatgtggcgtatagcatggcggggtgcatggtactggcactggcccgcactacaatgacggtgatttggactcaggcattttgcggccgccaatatgatttctcctcgcgtgcagGACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAG-------------------------------
                                                                          |||  | ||     |  ||  | || |  |||  |||   ||| |    | || |    | |   |||  |  |  | | ||    |  | | ||| | || | |  | || |   | ||||| || |||||||| ||||| |||||||||||||||||||| || |||||                                
--------------------------------------------------------------------------gtaaggacat----cttcag-agaaggctggtcgtttac-ctctgtgtctgtgtgttttcaagcctgaactgacgcctc-tgtgccatgcat-cctccgcagC-ATATTCTGTACAGGCAGAAAGAACAGTTCAGTGACGGAGTGGGCTACAACTGGATCGATGGACTCAAAGCCTTCACCGAACAGCAGGTTGATGGTCGTC

upper sequence: EDO97202 (Chlamydomonas reinhardtii), 3'ss of exon 10
lower sequence: PP1S410_47V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------gtgagggcatggacgggaagcttatgtgcgggcagccatgtcaccatgtgg-cgtatagcatggcggggtgcatggtactggcactggcccgcac---tacaatgacggtgatttggactcaggcat-tttgcggccgccaatatgatttctcctcgcgtgcagGACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAG------------------
                  ||    | | |    |   || | |   |         ||   || ||  |  |     |    | |||  |    |      ||   |   |   |    ||   |    ||||  |  |  |  ||| |  | | | ||  | |    |    | ||  | ||   |  |||  || | |  |  | |  |||||||||||||| |||||||| ||||| ||||||| |||||| ||||||||||||                  
gtgtgtaacccgtttcccgacacaaagaaaatcatttttgtttatcgtggattccttcgagatttgttcacaagatttaaatgcgtgtgtttctcatttggtgcttcatgcgtgtcttttgttaggctgttggtttgggagagattttccccggtcgatgagctgaaactaaacttgttgcacggttttctgtgcagC-ACATTTTGTATCGCCAGAAGGAGCAATTCAGCGATGGCGTTGGCTACAGCTGGATTGACGGCCTCAAGGCTCATGCACAGAGCCAT

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|161804306|gb|FC092677.1|FC092677
EST:     GCCGCATCGAGAAGTACATCCTCCGGAAAGCGTTCGACACCCCCGAG                         GACCCCTACCTGCCCAAGGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGC
genomic: GCCGCATCGAGAAGTACATCCTCCGGAAAGCCTTCGATACCCCCGAGgtgagggcat ... tcgcgtgcagGACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGC
EST: gi|9210297|gb|BE337212.1|BE337212
EST:     GCCGCATCGAGAAGTACATCCTCCGGAAAGCCTTCGATACCCCCGAG                         GACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGC
genomic: GCCGCATCGAGAAGTACATCCTCCGGAAAGCCTTCGATACCCCCGAGgtgagggcat ... tcgcgtgcagGACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGC
EST: gi|15698263|gb|BI722568.1|BI722568
EST:     GCCGCATCGAGAAGTACATCCTCCGGAAAGCCTTCGATACCCCCGAG                         GACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGC
genomic: GCCGCATCGAGAAGTACATCCTCCGGAAAGCCTTCGATACCCCCGAGgtgagggcat ... tcgcgtgcagGACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGC
EST: gi|161814299|gb|FC102065.1|FC102065
EST:     GCCGCATCGAGAAGTACATCCTCCGGAAAGCGTTCGACACCCCCGAG                         GACCCCTACCTGCCCAAGGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGC
genomic: GCCGCATCGAGAAGTACATCCTCCGGAAAGCCTTCGATACCCCCGAGgtgagggcat ... tcgcgtgcagGACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGC
EST: gi|161800664|gb|FC085600.1|FC085600
EST:     GCCGCATCGAGAAGTACATCCTCCGGAAAGCGTTCGACACCCCCGAG                         GACCCCTACCTGCCCAAGGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGC
genomic: GCCGCATCGAGAAGTACATCCTCCGGAAAGCCTTCGATACCCCCGAGgtgagggcat ... tcgcgtgcagGACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGC
EST: gi|16430040|gb|BI995266.1|BI995266
EST:     GCCGCATCGAGAAGTACATCCTCCGGAAAGCCTTCGATACCCCCGAG                         GACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGC
genomic: GCCGCATCGAGAAGTACATCCTCCGGAAAGCCTTCGATACCCCCGAGgtgagggcat ... tcgcgtgcagGACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatttggactcaggcattttgcggccgccaatatgatttctcctcgcgtgcagGACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAG
                                      tttctcctcgc  CT-rich tract
                               aatatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagggcatggacgggaagcttatgtgcgggcagccatgtcaccatgtggcgtatagcatggcggggtgcatggtactggcactggcccgcactacaatgacggtgatttggactcaggcattttgcggccgccaatatgatttctcctcgcgtgcagGACCCCTACCTGCCCAACGAGGTGCTCTGGCGCCAGAAGGAGCAGTTCAGCGACGGCGTGGGCTACAACTGGATCGACGGCCTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG