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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacttcagtccacgacaagattgacatatggttttgtgaattgactttgagattttgaagagaattcgaatttttgtttccagAAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACCGGAAATACCCAAACGGGTCGAGACCAAACCGGGCAGCTGGAACCGGTTA

Basic information

species Arabidopsis thaliana
transcript AT5G63790.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G63790.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g34830.1 (Oryza sativa), 3'ss of exon 1
gtaaaacttcagtccacgacaagattgacatatggttttgtgaattgactttgagattttgaagagaattcgaatttttgtttccagAAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACCGGAAATACCCAAACGGGTCGAGACCAAACCGGGCAGCTGGAACCGGTTA
        |  |||     ||       | |       ||  || | |     |   ||    ||   | |     |   |   ||| ||||||| ||||||| ||||| || |||||||||||||| | | | ||||| || ||||| ||||||||| | || ||||| || || ||  |||| ||
-------gtacgtctcttccatctccctcctccatccatgcaaacttatagctactgttcatcgatcgtccatgactccatg--cagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA

upper sequence: AT5G63790.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g34830.2 (Oryza sativa), 3'ss of exon 1
-------gtaaaacttcagtccacgacaagattgacatatggttttgtga-----attgactttgagattttgaagagaattcga--atttttgtttccagAAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACCGGAAATACCCAAACGGGTCGAGACCAAACCGGGCAGCTGGAACCGGTTA
         |   | ||   | |  ||     |  ||| |   |     |         ||||  || |  ||   |    |||   ||   |   | ||| ||||||| ||||||| ||||| || |||||||||||||| | | | ||||| || ||||| ||||||||| | || ||||| || || ||  |||| ||
gttcgatccatggcatctcccaagtacgtctcttccatctccctcctccatccatgcaaacttatagctactgttcatcgatcgtccatgactccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA

upper sequence: AT5G63790.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g66120.1 (Oryza sativa), 3'ss of exon 1
-----------gtaaaacttcagtccacga--caagattgacat--atggttttgtgaattgactttgagattttgaagagaattcgaatttttgtttccagAAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACCGGAAATACCCAAACGGGTCGAGACCAAACCGGGCAGCTGGAACCGGTTA
            |    || ||  |  | |  ||  |    |||  | |   | ||||||||| |    ||||| |    || ||     | |||| |  ||  |||||| ||||||| ||||| || |||||||||||||| |   ||||||| || ||||| ||||||||| | || ||||| || || ||  | || ||
gtacgataatcctcctcctccatcctcccaatcatcaccaccatcaacgccgtcgtgaattgattgattgattt-ggtttgatttgttggtgttgtgt--agGGATGGCGCTGTACGGAGAGAAGGAGTGGTACTTCTTCTCCCCGCGAGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCGGGGTA

upper sequence: AT5G63790.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G32850.1 (Glycine max), 3'ss of exon 1
-----------------------------------------------gtaaaacttcagtccacgacaagattgacatatggttttgtgaattgactttgagattttgaagagaattcgaatttttgtttccagAAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACCGGAAATACCCAAACGGGTCGAGACCAAACCGGGCAGCTGGAACCGGTTA
                                                |  || |||| |        |  |  ||      |||| |   |  || || |  |  |    |  |||    ||||| | | |||| |||||  | |||||||||||||| |||||||| ||||| | | ||||||| |||||||||||||| |||||||| |||||||| || |||| ||| ||
gtacctttttttcttttctcactctagtctctgtattcttttgccttttttaatttcattagggtcttaattctactacattttttttctctccaccttaaagtcct----attatttatgtttttatgtacagAGATGGCTCTTTACGGTGAGAAAGAGTGGTACTTTTTCTCTCCTCGAGACCGAAAATACCCAAACGGTTCGAGACCGAACCGGGCTGCCGGAAGCGGGTA

upper sequence: AT5G63790.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 1
gtaaaacttcagtccacgacaagattgacatatggttttgtgaatt--gactttgagattttg-------aagagaattcgaatttttgtttccagAAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACCGGAAATACCCAAACGGGTCGAGACCAAACCGGGCAGCTGGAACCGGTTA
       || |||     |   | ||    |   ||      ||||   | | |    ||| |        |  || |  || ||  |   | ||||||| |  || ||||| |||||||||||||||||||| || | | | |||||||||||||| ||||| ||  | || ||||| || || |||| ||| ||
--gttcgtttagtttcttatgggtttcgttttgtgtgaaaccaattccaattgtatcgtttagttcaattgattgattatgagttggtcaatgcagAAATTGGTTTTTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGACCGGAAATACCCGAACGGTTCACGGCCGAACCGCGCCGCCGGAAGCGGCTA

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|116415196|gb|EG457788.1|EG457788
EST:     GGTTATCGCAGAGATTGACTTGTACAAATTCAATCCATGGGAGCTTCCAG                         AAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACC
genomic: GGTTATCGCAGAGATTGACTTGTACAAATTCAATCCATGGGAGCTTCCAGgtaaaacttc ... ttgtttccagAAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACC
EST: gi|164042556|gb|ES089892.1|ES089892
EST:     TTCAATCCATGGGAGCTTCCAG                         AAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACC
genomic: TTCAATCCATGGGAGCTTCCAGgtaaaacttc ... ttgtttccagAAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACC
EST: gi|116445706|gb|EG488298.1|EG488298
EST:     GGTTATCGCAGAGATTGACTTGTACAAATTCAATCCATGGGAGCTTCCAG                         AAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACC
genomic: GGTTATCGCAGAGATTGACTTGTACAAATTCAATCCATGGGAGCTTCCAGgtaaaacttc ... ttgtttccagAAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACC
EST: gi|116445702|gb|EG488294.1|EG488294
EST:     GGTTATCGCAGAGATTGACTTGTACAAATTCAATCCATGGGAGCTTCCAG                         AAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACC
genomic: GGTTATCGCAGAGATTGACTTGTACAAATTCAATCCATGGGAGCTTCCAGgtaaaacttc ... ttgtttccagAAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACC
EST: gi|116474563|gb|EG517155.1|EG517155
EST:     GGTTATCGCAGAGATTGACTTGTACAAATTCAATCCATGGGAGCTTCCAG                         AAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACC
genomic: GGTTATCGCAGAGATTGACTTGTACAAATTCAATCCATGGGAGCTTCCAGgtaaaacttc ... ttgtttccagAAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACC
EST: gi|116411311|gb|EG453903.1|EG453903
EST:     GGTTATCGCAGAGATTGACTTGTACAAATTCAATCCATGGGAGCTTCCAG                         AAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACC
genomic: GGTTATCGCAGAGATTGACTTGTACAAATTCAATCCATGGGAGCTTCCAGgtaaaacttc ... ttgtttccagAAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttttgtgaattgactttgagattttgaagagaattcgaatttttgtttccagAAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACCGGAAATACCCAAACGGGTCGAGACCAAACCGGGCAGCTGGAACCGGTTA
          aattgac  putative branch site (score: 3)
                                          tttttgtttcc  putative PPT
                                        aatttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaacttcagtccacgacaagattgacatatggttttgtgaattgactttgagattttgaagagaattcgaatttttgtttccagAAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACCGGAAATACCCAAACGGGTCGAGACCAAACCGGGCAGCTGGAACCGGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA