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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcacgcgcctcccccaacgccccacagcttcccacggccgcccctgcaaccctcagcgcatctgctaacgctacagcttaaacaacgctacacccgatgtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG

Basic information

species Chlamydomonas reinhardtii
transcript EDO97314
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO97314 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: GRMZM2G007260_T01 (Zea mays), 3'ss of exon 4
gtgagcacgcgcctcccccaacgccccacagcttc-ccacggccgcccctgcaaccctcagcgcatctgctaacgctacagcttaaacaacgctacacccgatgtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG
    | | |   |||     | |      | ||     |    |      |||  ||| ||  ||| ||  ||    |  | || || | |  | |      | |   | |||| |||||||| || ||||| ||  |||||||||| ||||||||||||||||| || ||||| |||||||| ||  |||| || || |||
----gtatgt-tctctttagatgttaaggaactaaattattctcatattggca--cctgagtacat-tgacaata--agtggtttaataccaattc------tttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTCCTATATACGATGTTGCGGCAATATTGACCTCTATTCAG

upper sequence: EDO97314 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: GRMZM2G120674_T01 (Zea mays), 3'ss of exon 3
gtgagcacgcgcctcccccaacgccccacagcttcccacggccgcccctgcaaccctcagcgcatctgctaacgctacagcttaaacaacgctacacccgatgtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG
    | | |   |||     | |      | ||            ||         |   | | |      |   ||||   |||        | |||   | |   | |||| |||||||| || ||||| ||  |||||||||| |||||||||||||| || || || || |||||||| ||  |||| || || |||
----gtatgt-tctctttagatgttaaggaacta-----aattatcctcatg--tattgacacctgaatagat-ttacaa--taagtggtttaataccattttt---ttcagTCTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGCCCTATATATGATGTTGCGGCAATATTGACCTCTATTCAG

upper sequence: EDO97314 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: AT5G62540.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagcacgcgcctcccccaacgccccacagcttcccacggccgcccctgcaaccctcagcgcatctgctaacgctacagcttaaacaacgctac--acccgatgtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG
                                     | | ||   | | ||     || |  |       ||     ||   |  | ||  |    |    |  |  ||||||| ||||| || || ||||||||| |||| ||| | |||||||||||||| ||||||||||||||||| ||  | || || ||||| |||
-----------------------------------gtaagcccaagcattcagtgaacaacatagtaatagaccaattaggaaattcgactttgataattgaactttggtgcagTTTATGCTGATGGAAGCATTTGCTTGGATATCTTGCAAAACCAGTGGAGCCCCATCTACGACGTTGCTGCAGTTCTCACATCAATTCAG

upper sequence: EDO97314 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: AT2G02760.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagcacgcgcctcccccaacgccccacagcttcccacggccgcccctgcaaccctcagcgcatctgctaacgctacagcttaaacaacgctacacccgatgtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG
                             || ||  |||  |      |   || || ||  ||| || | |  | | |||| | ||   |  |      ||||  ||||||| ||||| || ||||| || ||| ||||||| ||||||||||| |||||||| || ||||| || || || || || || || || |||
--------------------gtaagttggagattatcacatcatagtttcttactctgagtacatgtgatca-acgaaagctcacacttggtca------atgt-tgtgcagTTTATGCTGATGGGAGTATATGCTTGGACATTCTCCAAAACCAATGGAGTCCAATATACGATGTCGCTGCTATACTAACCTCCATTCAG

upper sequence: EDO97314 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: AT1G14400.2 (Arabidopsis thaliana), 3'ss of exon 4
gtgagcacgcgcctcccccaacgccccacagcttcccacggccgcccctgcaaccctcagcgcatctgctaacgctacagcttaaacaacgctacacccgatgtgc-gtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG
    | | |    |      |  |  ||  |  |       || ||      |   |||||   | |||     || ||  |  |||     |   | | ||  |  ||| ||| ||||| || ||||| || ||| ||||||| || ||||||||||||||||| ||||| || ||||| || || || || || ||||||
----gtaagt---tatagagatacaacattggattttctatccacctggttgatgttcagct--tttgc-----ctccaatt--aacgttcttctgctctattcgttgtgtagTTTATGCAGATGGGAGTATCTGCTTGGACATTCTACAAAACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAG

upper sequence: EDO97314 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 3'ss of exon 3
gtgagcacgcgcctcccccaacgccccacagcttcccacggccgcccctgcaaccctcagcgcatctgctaacgctacagcttaaacaacgctacacccgatgtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG
        | || |   |  | | |    ||  | |       || | || | |||  ||     | ||    |   | | ||  ||| | ||        ||      |||| || |||||||| ||||| ||| |||| ||  | ||||| ||||||||||||||||||||||| || || |||||||| || || |||
-------ggtgcttgtgctgaggacgtgtagagttct----tggctcgtggatcccggaggcagacagcatgggtccctgttttcaca-cactggtgattgtggcaaatcagTATACGCGGACGGCAGCATCTGCTTGGATATTTTGCAAAATCAGTGGAGTCCCATCTACGACGTGGCAGCGATCCTGACTTCGATTCAG

upper sequence: EDO97314 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 3'ss of exon 3
gtgagcacgcgcctcccccaacgccccacagcttcccacggccgcccctgcaaccctcagcgcatctgctaacgctacagcttaaacaacgctacacccgatgtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG
     |  |||| |      | | |     |  ||||  |||      || | ||   || |   | ||   ||   | |  |  |    |        | || ||   |||| ||||||||||| ||||| ||| | || ||||| ||||| |||||||| || ||||||||||| || || ||  |||| || || |||
-----ctagcgcttgtgttgaggacgtttggagtccctgggcg-----tggagccgagagggacacagcgcgcgtctctgtgtttatgcggtggtgtttg-tg-gcaaacagTATATGCGGACGGTAGCATCTGCTTAGATATCCTGCAAAATCAGTGGAGCCCGATCTACGACGTGGCAGCGATTTTGACTTCGATTCAG

upper sequence: EDO97314 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 3
gtgagcacgcgcctcccccaacgccccacagcttcccacggccgcccctgcaaccctcagcgcatctgctaacgctacagcttaaacaacgctacacccgatgtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG
                                                           |    |  | | |  |      |  | |  |  ||| |     |  |  ||||| ||||| || || |||||||| || |||||||||||||| |||||||| || ||||| || ||||| || || ||||| || ||||||
-----------------------------------------------------------gtaagttcgtttattcgtagtgtctatcttccttacgc-----gctctcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG

upper sequence: EDO97314 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: EFJ23951 (Selaginella moellendorffii), 3'ss of exon 3
gtgagcacgcgcctcccccaacgccccacagcttcccacggccgcccctgcaaccctcagcgcatctgctaacgctacagcttaaacaacgctacacccgatgtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG
                                                           |    |  | | |  |      |  | |  |  ||| |     |  |  ||||| ||||| || || |||||||| || |||||||||||||| |||||||| || || || || ||||| || || ||||| || ||||||
-----------------------------------------------------------gtaagttcgtttattcgtagtgtctatcttccttacgc-----gctctcgcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATTTATGATGTTGCCGCAATACTGACATCGATCCAG

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|16072081|gb|BI874077.1|BI874077
EST:     TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACG                         TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
genomic: TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACGgtgagcacgc ... gtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
EST: gi|9458522|gb|BE452281.1|BE452281
EST:     TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACG                         TGTATGCGGACGGGAGCATTTGCCT
genomic: TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACGgtgagcacgc ... gtgcgtgcagTGTATGCGGACGGGAGCATTTGCCT
EST: gi|10779605|gb|AV636285.1|AV636285
EST:     TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACG                         TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
genomic: TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACGgtgagcacgc ... gtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
EST: gi|15693474|gb|BI717779.1|BI717779
EST:     TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACG                         TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
genomic: TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACGgtgagcacgc ... gtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
EST: gi|161807152|gb|FC089347.1|FC089347
EST:     TAACAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTTCACCCCAACG                         TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
genomic: TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACGgtgagcacgc ... gtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
EST: gi|6544973|gb|AV390757.1|AV390757
EST:     TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACG                         TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
genomic: TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACGgtgagcacgc ... gtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
EST: gi|10770414|gb|AV621239.1|AV621239
EST:     TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACG                         TGTATGCGGACGGGAGCAT
genomic: TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACGgtgagcacgc ... gtgcgtgcagTGTATGCGGACGGGAGCAT
EST: gi|23362539|gb|BU650359.1|BU650359
EST:     TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACG                         TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
genomic: TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACGgtgagcacgc ... gtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
EST: gi|161817678|gb|FC104413.1|FC104413
EST:     TAACAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTTCACCCCAACG                         TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
genomic: TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACGgtgagcacgc ... gtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
EST: gi|10768873|gb|AV619698.1|AV619698
EST:     TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACACCAACG                         TGTATGCGGACGGGA
genomic: TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACGgtgagcacgc ... gtgcgtgcagTGTATGCGGACGGGA
EST: gi|10768871|gb|AV619696.1|AV619696
EST:     TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACG                         TGTATGCGGACGGGAGCATTT
genomic: TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACGgtgagcacgc ... gtgcgtgcagTGTATGCGGACGGGAGCATTT
EST: gi|10773934|gb|AV624757.1|AV624757
EST:     TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACG                         TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
genomic: TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACGgtgagcacgc ... gtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
EST: gi|10769109|gb|AV619934.1|AV619934
EST:     TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACG                         TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGT
genomic: TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACGgtgagcacgc ... gtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGT
EST: gi|15693601|gb|BI717906.1|BI717906
EST:     TTCAAGACGAAGCTGTTCCACCCCAACG                         TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
genomic: TTCAAGACGAAGCTGTTCCACCCCAACGgtgagcacgc ... gtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
EST: gi|16071419|gb|BI873415.1|BI873415
EST:     TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACG                         TGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
genomic: TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACGgtgagcacgc ... gtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTC
EST: gi|15697344|gb|BI721649.1|BI721649
EST:     TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACG                         TGTATGCGGACGGGAGCA
genomic: TAATAAGGCGCCCACTGTCAAGTTCAAGACGAAGCTGTTCCACCCCAACGgtgagcacgc ... gtgcgtgcagTGTATGCGGACGGGAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcgcatctgctaacgctacagcttaaacaacgctacacccgatgtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG
         tgctaac  putative branch site (score: 1)
                        ttaaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcacgcgcctcccccaacgccccacagcttcccacggccgcccctgcaaccctcagcgcatctgctaacgctacagcttaaacaacgctacacccgatgtgcgtgcagTGTATGCGGACGGGAGCATTTGCCTGGACATCCTCCAAAACCAGTGGAGTCCCATCTACGACGTTGCGGCCATCCTGACGTCAATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG