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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattattgcctacaacaatctgaattttcctttcaatatgatcaaattcatatgcttatttgtgattatactttgctttgattcagGAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAACTTCAACAAGAGGGAATATGTGGTTCAGGTGTTGATGAAGGTAATACCC

Basic information

species Arabidopsis thaliana
transcript AT1G68660.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G68660.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G09880.1 (Glycine max), 3'ss of exon 2
---------gtattattgcctacaacaatctgaattttcctttcaatatgat-caaattcatatgcttatttgtga---ttatactttgctttgattcagGAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAACTTCAACAAGAGGGAATATGTGGTTCAGGTGTTGATGAAGGTAATACCC
          | |  |||  ||   |  ||| | ||   |      ||| |  ||||     ||| | | |  | |   | ||    || |||    |||||||||   ||| | | | ||||| ||| | ||  | || ||||||||||||||||||||| | |||||||| || || |||||||||||||| ||||| 
ctgactcttctctctttgtttattcctgtctcatttcatcgcatgttataaaacaaaagagaatgatcaatccttaacttcatgacatgttttctgccagGAAATCGCGGAAAACATCCCCACCCTACCGAGTTTTGCTGCACAATGACAACTTCAACAAGCGAGAATATGTTGTGCAAGTGTTGATGAAGGTGATACCA

upper sequence: AT1G68660.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G31940.1 (Glycine max), 3'ss of exon 2
----------gtattattgcctacaacaatctgaattttcc---tttcaatatgat-caaattcatatgcttatttgtgattatactttgctttgattcagGAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAACTTCAACAAGAGGGAATATGTGGTTCAGGTGTTGATGAAGGTAATACCC
           | |  |||  ||   |  ||| | ||   |   | | | ||| |  |||| |   ||| | |    |  | ||    || |||    |||||||||   ||| | | | ||||||||| | ||  | || ||||||||||||||||||||| | |||||||| || || |||||||||||||| ||||| 
ttgttggctcttctctttgtttattcctgtctcatttcatcacatgttactataaagcaaaatagaatgatgaaacctt-tcatgacatgttttctgccagGAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAACTTCAACAAGCGAGAATATGTTGTGCAAGTGTTGATGAAGGTGATACCT
















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|125220852|gb|EL234937.1|EL234937
EST:     CCAATTATAGAG-AAACCACTCCTGGTCGTGAATCCGAGTTTGATTTAAG                         GAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGA
genomic: CCAATTATAGAGAAAACCACTCCTGGTCGTGAATCCGAGTTTGATTTAAGgtattattgc ... tttgattcagGAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGA
EST: gi|116477619|gb|EG520211.1|EG520211
EST:     CCAATTATAGAGAAAACCACTCCTGGTCGTGAATCCGAGTTTGATTTAAG                         GAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAA
genomic: CCAATTATAGAGAAAACCACTCCTGGTCGTGAATCCGAGTTTGATTTAAGgtattattgc ... tttgattcagGAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAA
EST: gi|125010124|gb|EL082393.1|EL082393
EST:     TATAGAGAAAACCACTCCTGGTCGTGAATCCGAGTTTGATTTAAG                         GAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAA
genomic: TATAGAGAAAACCACTCCTGGTCGTGAATCCGAGTTTGATTTAAGgtattattgc ... tttgattcagGAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAA
EST: gi|86077088|gb|DR372845.1|DR372845
EST:     CCAATTATAGAGAAAACCACTCCTGGTCGTGAATCCGAGTTTGATTTAAG                         GAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAA
genomic: CCAATTATAGAGAAAACCACTCCTGGTCGTGAATCCGAGTTTGATTTAAGgtattattgc ... tttgattcagGAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAA
EST: gi|47828580|gb|CK118264.1|CK118264
EST:     CCAATTATAGAGAAAACCACTCCTGGTCGTGAATCCGAGTTTGATTTAAG                         GAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAA
genomic: CCAATTATAGAGAAAACCACTCCTGGTCGTGAATCCGAGTTTGATTTAAGgtattattgc ... tttgattcagGAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAA
EST: gi|124717609|gb|EH809011.1|EH809011
EST:     CCAATTATAGAGAAAACCACTCCTGGTCGTGAATCCGAGTTTGATTTAAG                         GAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAA
genomic: CCAATTATAGAGAAAACCACTCCTGGTCGTGAATCCGAGTTTGATTTAAGgtattattgc ... tttgattcagGAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAA
EST: gi|116477612|gb|EG520204.1|EG520204
EST:     CCAATTATAGAGAAAACCACTCCTGGTCGTGAATCCGAGTTTGATTTAAG                         GAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAA
genomic: CCAATTATAGAGAAAACCACTCCTGGTCGTGAATCCGAGTTTGATTTAAGgtattattgc ... tttgattcagGAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAA
EST: gi|125158269|gb|EL186943.1|EL186943
EST:     GTGAATCCGAGTTTGATTTAAG                         GAAACCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAA
genomic: GTGAATCCGAGTTTGATTTAAGgtattattgc ... tttgattcagGAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAA
EST: gi|125228398|gb|EL242483.1|EL242483
EST:     CCAATTATAGAGAAAACCACTCCTGGTCGTGAATCCGAGTTTGATTTAAG                         GAAATCAAAGAAGATAGCTCCACCTTACAGGGT
genomic: CCAATTATAGAGAAAACCACTCCTGGTCGTGAATCCGAGTTTGATTTAAGgtattattgc ... tttgattcagGAAATCAAAGAAGATAGCTCCACCTTACAGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaatatgatcaaattcatatgcttatttgtgattatactttgctttgattcagGAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAACTTCAACAAGAGGGAATATGTGGTTCAGGTGTTGATGAAGGTAATACCC
                                            ctttgat  putative branch site (score: 5)
                                       ctttgcttt  CT-rich tract
                        ttatttgtgattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattattgcctacaacaatctgaattttcctttcaatatgatcaaattcatatgcttatttgtgattatactttgctttgattcagGAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAACTTCAACAAGAGGGAATATGTGGTTCAGGTGTTGATGAAGGTAATACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG