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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaggctcaagtctttatatcttcaagttcagcttgtcttgattaatttgcttatactgtgtcaatttctccccttttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAG

Basic information

species Arabidopsis thaliana
transcript AT3G01310.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 11
---------gtgagaggc--tca--agtctttat-atcttcaagttcagcttgtct-tgattaatttgcttatactgtgtcaatttctcccct-tttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAG
          | | |  |  |||  | | ||||| |  ||  | || ||||  |   |  ||||| | ||   | ||  || |||  ||   | ||||||||| |||||||| ||||| || ||| |||||||||| |||||||||||||| ||| | || || || || ||
agACAAAACTTAAAAATCCTTCAGTAATGTTTATTAATTTTTATTTGAGCTACTGAATTCTTAATCTTCTGTGATTG-ATCTATTGGTCTTGTGTTTGCAGACAAAACTTAAAAGTGCTGTTCAGCTGCAAGATCTGTTAGATGCCACAAGGATGCTGGTGCCTCGCACTAG

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 14
---------gtgagaggc--tca--agtctttat-atcttcaagttcagcttgtcttgattaatttgcttatactgtgtcaatttctcccct-tttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAG
          | | || |  |||  ||| ||||| |  ||  | || ||||  |      | | |    | |  |   || |||  ||   | ||||||||| |||||||| ||||| || ||| |||||||||| |||||||||||| | ||| | || || || || ||
agACAAAACTTAAAAGTCCTTCAGTAGTGTTTATTAATTTTTATTTGAGCTACTGAAATCTTAATCTTCTGTGATTGATCTATTGATCTTATGTTTGCAGACAAAACTTAAAAGTGCTGTTCAGCTGCAAGATCTGTTAGATGCCACACGGATGCTGGTGCCTCGCACTAG

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 11
----------------gtgagaggctcaagtctttatatcttca--agttcagcttg--tcttgattaatttgcttatactgtgtcaatttctccccttttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAG
                |||  |   | |  | | |  |  || |   | ||  || |  | ||  || |  |  ||    ||  | |||         ||||||||| |||||||| ||||| || ||  | |||||||| |||||||||||| | ||| ||||||| ||||| ||
gtgatattattttctagtgctaatgtaatatttgtcaacttttatttgatccactggattttttttttacctcttttgtttgatttaatgatcttttgtttgcagACAAAACTTAAAAGTGCTGTTCAACTTCAAGATCTGTTAGATGCCACACGCATGCTAGTTCCTCGTACCAG

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 13
----------------------gtgagaggctcaagtctttatatct--tcaagttcagcttgtcttgattaatttgcttatactgtgtcaatttctccccttttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAG
                      |||  |   |    |  || ||| |  ||   |  |  || | ||  || |  |  ||    ||  | |||         ||||||||| |||||||| ||||| || ||  | |||||| | |||||||||||| ||||| ||||||| ||||| ||
gtgatattattttctagtgtttgtgtaatatttgtctacttttatttgatcttctggattttttttttttttacctcttttgcttgatttaatgatcttttgtttgcagACAAAACTTAAAAGTGCTGTTCAACTTCAAGATTTGTTAGATGCCACACGAATGCTAGTTCCTCGTACCAG

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 13
----------------------gtgagaggctcaagtctttatatcttcaa-gttcagcttgtcttgattaatttgcttatactgtgtcaatttct--ccccttttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAG
                       |       |    |  || |||  ||||  |||   ||    | ||   ||     ||  ||  |   ||  |   | ||||||||||| ||||| ||||||||  |||||||||||||| | || ||||||||| | ||| | || || || |||||
gtgcttactttcccttcatctttttctcattttgttttattgtattgtcaatattcttatttatgtaatcgcttattagatggtgcatttgttgatgatctcttttgcagACAAAACTCAAGAGTGCTATCCAGTTGCAAGATTTGTTGGATGCCACACGGATGCTTGTACCACGCACAAG

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|124793068|gb|EH882747.1|EH882747
EST:     ACTATTAAACCTAATGTTGAAGTTACAATGGTGGAAAGCCAAGAGCTGAG                         ACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATG
genomic: ACTATTAAACCTAATGTTGAAG-TACAATGGTGGAAAGCCAAGAGCTGAGgtgagaggct ... ccttttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATG
EST: gi|19874907|gb|AU235738.1|AU235738
EST:     AACTATTAAACCTAATGTTGAAGTACAATGGTGGAAAGCCAAGAGCTGAG                         ACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGA
genomic: AACTATTAAACCTAATGTTGAAGTACAATGGTGGAAAGCCAAGAGCTGAGgtgagaggct ... ccttttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagcttgtcttgattaatttgcttatactgtgtcaatttctccccttttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAG
             gattaat  putative branch site (score: 3)
                                  tcaatttctccccttt  putative PPT
              attaatttgcttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaggctcaagtctttatatcttcaagttcagcttgtcttgattaatttgcttatactgtgtcaatttctccccttttgcagACCAAACTTAAGAGTGCCGTCCAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA