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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGGGCAGCGTCATGACCAACAAGTACAGCGAGGGCTACCCCGGCGCCCGCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatctggggtccgcaggctgtttagtgggttgcggtgggcgaggggccgtggacgctgaggggcttgctggtggatcttggacctgcgcgggttc...

Basic information

species Chlamydomonas reinhardtii
transcript EDO97448
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO97448 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 4
-------------------------------GGTGGGCAGCGTCATGACCAACAAGTACAGCGAGGGCTACCCCGGCGCCCGCTACTACGGCGGCAACGAGTTCA-TTGACCAGGCAG-AGCGCCTGTGCCAGgtgggaat-ctggggtccgcaggctgtttagtgggttgcggtgggcgaggggccgtggacgctgaggggcttgctggtggatcttggacctgcgcgggttc
                               ||||||   ||||||||||||||||||||||||||| |||||||||||  | |||||||| || ||||||| |  ||||    |    | ||  ||     | |  || |  | ||||    |   |||||| |  |     |    |                                                       
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcag-----------------------------------------------------

upper sequence: EDO97448 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: LOC_Os03g52840.1 (Oryza sativa), 5'ss of exon 4
-------------------------------GGTGGGCAGCGTCATGACCAACAAGTACAGCGAGGGCTACCCCGGCGCCCGCTACTACGGCGGCAACGAGTTCA-TTGACCAGGCAG-AGCGCCTGTGCCAGgtgggaat-ctggggtccgcaggctgtttagtgggttgcggtgggcgaggggccgtggacgctga----ggggcttgctggtggatcttggacctgcgcgggttc--
                               ||||||   ||||||||||||||||||||||||||| |||||||||||  | |||||||| || ||||||| |  ||||    |    | ||  ||     | |  || |  | ||||    |   |||||| |  |     |    |   |     |||  |   |    | |  || ||||||| ||| ||   | |  | || |  
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcagtgcctgatgggagtgaatgatgtgaatttctggtggctctgggttttccttgcgtgcag

upper sequence: EDO97448 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: GRMZM2G135283_T01 (Zea mays), 5'ss of exon 4
-------------------------------GGTGGGCAGCGTCATGACCAACAAGTACAGCGAGGGCTACCCCGGCGCCCGCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTG--CCAGgtgggaatctggg-gtccgcaggc-tgtttagtgggttgcggtgggcgaggggccgtggacgctgaggggcttgctg-gtggatcttggacctgcgcgggttc
                                |||||   ||||||||||||||||||||||||||| ||||| |||||  | |||||||| || || ||||  | || || |    | ||  |||    |  |||    | |  | |    || || ||   | || ||  | ||  | |  |     |      || ||   ||  |  |||  |  | |  |   |       
AGAATTTCACGTCGGTGTCAGTGATGCAGGCAGTGGGTTCCGTCATGACCAACAAGTACAGCGAGGGGTACCCTGGCGCAAGATACTACGGGGGAAATGAgt--actgccctgctctatcggttgtcattctcgtgattgtttcagtggaaacacgcgtgcaaattgagtgactgtctg-ggtgaataatctgaattggggtttttattctgtgtgttcttggtcgcag-------

upper sequence: EDO97448 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: PP1S21_270V6.1 (Physcomitrella patens), 5'ss of exon 4
-------------------------------GGTGGGCAGCGTCATGACCAACAAGTACAGCGAGGGCTACCCCGGCGCCCGCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCT--GTGCCAGgtgggaatctggggtccgcaggctgtttagtgggttgcggtgggcgaggggccgtggacgc-tgaggggcttgctggtggatcttggacctgcgcgggttc
                                |||||    |||||||||||||||||||| ||||| |||||||| || || |||||||| ||||||||||   |   |    |   ||  |   |||  |       |  |            || |||     || |  ||      | || |||  |||  |||   | | |   |       |   | | ||| |    
AAAACTTCACCTCCCTCTCAGTTATGCAGGCAGTGGGGTCAGTCATGACCAACAAGTACAGTGAGGGTTACCCCGGGGCTCGTTACTACGGTGGCAACGAgtatgtcaccttttctctgcttcgtggtgttattacatgacgttaaacttcattactattttccaagt-gtagt--tttggtggtcgtttacgtgtgatcagttgggctgacagcgctacccgtccgcag----

upper sequence: EDO97448 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 4
-------------------------------GGTGGGCAGCGTCATGACCAACAAGTACAGCGAGGGCTACCCCGGCGCCCGCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatctggggtccgcaggctgtttagtgggttgcggtgggcgaggggccgtggacgctgaggggcttgctggtggatcttgga---cctgcgcgggttc--
                                |||||    ||||||||||| |||||||| || || |||||||| || ||||| ||||| |||||||||| | | |           |  || |  |        ||     ||| | |  || |||  |         | |     |     ||  |  |    |  | | | | | || |||      || | |   |    
AGAATTTTACGTCCGTATCAGTTATGCAGGCAGTGGGTTCAGTCATGACCAATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtttctcattttcctctctctctttaaaatataacttgtctgtattctttttcataaacctttattgattgagatttttgctctgttcatgaatagttag-gtatattgacacctctacacaaatgtag

upper sequence: EDO97448 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: EFJ16660 (Selaginella moellendorffii), 5'ss of exon 4
-------------------------------GGTGGGCAGCGTCATGACCAACAAGTACAGCGAGGGCTACCCCGGCGCCCGCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatctggggtccgcaggctgtttagtgggttgcggtgggcgaggggccgtggacgctgaggggcttgctggtggatcttggacctgcgcgggttc
                                |||||   | |||||||||||||||| ||||||||||| || || || || |||||||| || || ||||   | |      |    | |  ||| |   | ||||       |       |  | |||                                                                      
AGAATTTTACTTCAACTTCAGTCATGCAAGCAGTGGGATCCATCATGACCAACAAGTATAGCGAGGGCTATCCAGGAGCTCGTTACTACGGTGGAAATGAgtaggtcgttttttct--tcacaagtgacgtctaggaacgcttaatatttgttcgttctag----------------------------------------------------------------------

upper sequence: EDO97448 (Chlamydomonas reinhardtii), 5'ss of exon 5
lower sequence: EFJ32604 (Selaginella moellendorffii), 5'ss of exon 4
-------------------------------GGTGGGCAGCGTCATGACCAACAAGTACAGCGAGGGCTACCCCGGCGCCCGCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatctggggtccgcaggctgtttagtgggttgcggtgggcgaggggccgtggacgctgaggggcttgctggtggatcttggacctgcgcgggttc
                                |||||   | |||||||||||||||| ||||||||||| || || || || |||||||| || || ||||   | |              ||   | || |  |  ||| ||  | ||    |||||  | | | |   | |                                                         
AGAATTTTACTTCAACTTCAGTCATGCAAGCAGTGGGATCCATCATGACCAACAAGTATAGCGAGGGCTATCCAGGAGCTCGTTACTACGGTGGAAATGAgtaggtcgttt--------tttcttcacaagttacg--tctaggaac-gcttaatgtttgtttgttcgttctag---------------------------------------------------------

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|10781349|gb|AV638029.1|AV638029
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCTAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTC
EST: gi|10126110|gb|BE724814.1|BE724814
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
EST: gi|10126090|gb|BE724794.1|BE724794
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
EST: gi|6550255|gb|AV396039.1|AV396039
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACTCGGCTCAGTGGGGCGTCAAC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
EST: gi|10788776|gb|AV626496.1|AV626496
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
EST: gi|6542140|gb|AV387924.1|AV387924
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
EST: gi|10126692|gb|BE725412.1|BE725412
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
EST: gi|10784593|gb|AV641265.1|AV641265
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
EST: gi|15698243|gb|BI722548.1|BI722548
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
EST: gi|10792084|gb|AV629450.1|AV629450
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
EST: gi|10127493|gb|BE726197.1|BE726197
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
EST: gi|23363367|gb|BU651187.1|BU651187
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
EST: gi|10793828|gb|AV631194.1|AV631194
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
EST: gi|8286884|gb|BE024443.1|BE024443
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAACGTGCGCTGAAGGCATTCCACCTGGGACCCGGCTCAGTGGGG
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGG-ACCCGGCTCAGTGGGG
EST: gi|10769315|gb|AV620140.1|AV620140
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGA
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGA
EST: gi|10790498|gb|AV627864.1|AV627864
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
EST: gi|10792385|gb|AV629751.1|AV629751
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
EST: gi|10793783|gb|AV631149.1|AV631149
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
EST: gi|10788685|gb|AV626405.1|AV626405
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
EST: gi|49470468|gb|BP098329.1|BP098329
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
EST: gi|10771492|gb|AV622315.1|AV622315
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
EST: gi|10792252|gb|AV629618.1|AV629618
EST:     GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAG                         GAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC
genomic: GCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatct ... cgccccgcagGAGCGTGCGCTGAAGGCATTCCACCTGGACCCGGCTCAGTGGGGCGTCAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGGGCAGCGTCATGACCAACAAGTACAGCGAGGGCTACCCCGGCGCCCGCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatctggggtccgcaggctgtttagtgggttgcggtgggcgaggggccgtggacgctgaggggcttgctggtggatcttggacctgcgcgggttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atctggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggatct