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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgggatgttgatgattgtcaggcttgctatgttgtgttttggggaaaacttcagctagtaacatcttttgtggtttggtatctttgcttctatgccagAAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGTGGTTTAAGCAATCTTATGGTTCTTGGTTCTTGGGAGATTACATATCTGA

Basic information

species Arabidopsis thaliana
transcript AT4G20325.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G20325.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G08230.3 (Glycine max), 3'ss of exon 3
gtaatgggatgttgatgattgtcaggcttgctatgttgtgttttggggaaaacttcagctagtaacatcttttgtggttt---ggtatctttgcttctatgccagAAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGTGGTTTAAGCAATCTTATGGTTCTTGGTTCTTGGGAGATTACATATCTGA
  | | | ||||      || |   | |     | | ||  ||   |      || |    ||    ||| |||   |||     | | ||  ||| | || ||| ||||| ||||   |  || |||   ||||  |||||||| |||||||||||||||||| | |  ||||| |||||||| ||||||||||| ||| ||||
--atttgaatgtgttcagtttt---gttaatactatcgtacttattgaggcttttgaatgtgtgctctctcttggctttttcatatgttttcacttgtttgacagGAAATGCAACACAATATCTGTTTGTAAATGGAATGCTTCAGGAACTTCAGTGGTTTAAGAACTTGTATGGATCTTGGTTTTTGGGAGATTATATAACTGA

upper sequence: AT4G20325.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0008g03180.t01 (Vitis vinifera), 3'ss of exon 3
--gtaatgggatgttgatgattgtcaggcttgctatgttgtgttttggggaaaacttcagctagtaacatcttttgtggtttggtatc-tttgcttctatgccagAAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGTGGTTTAAGCAATCTTATGGTTCTTGGTTCTTGGGAGATTACATATCTGA
    | |  |   ||  |   ||| | | | |   ||  || ||||||   | || | |  |   ||      ||| | | |  |||  ||  ||| | |  ||| ||| |  ||||| |  || ||||| |||| ||  || ||||||||| | ||||||||||||||||| || ||||||||| | || |||||  | | |||
tgccattttgtcatttttatatgttaagataggcttgg-gtcttttggcacatacataaattttcaag----cttgggatattatattgttcacttgtttcacagGAAAAGCGACATGTTATCTCTTTAAAAATGGGACACTCCAAGAACTTAATTGGTTTAAGCAATCTTACGGGTCTTGGTTCCTCGGGGATTATGTCTGTGA
















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|116459190|gb|EG501782.1|EG501782
EST:     TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAG                         AAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGT
genomic: TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAGgtaatgggat ... tctatgccagAAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGT
EST: gi|116411164|gb|EG453756.1|EG453756
EST:     TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAG                         AAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGT
genomic: TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAGgtaatgggat ... tctatgccagAAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGT
EST: gi|116411167|gb|EG453759.1|EG453759
EST:     TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAG                         AAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGT
genomic: TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAGgtaatgggat ... tctatgccagAAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGT
EST: gi|116459202|gb|EG501794.1|EG501794
EST:     TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAG                         AAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGT
genomic: TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAGgtaatgggat ... tctatgccagAAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGT
EST: gi|116411166|gb|EG453758.1|EG453758
EST:     TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAG                         AAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGT
genomic: TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAGgtaatgggat ... tctatgccagAAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGT
EST: gi|116459198|gb|EG501790.1|EG501790
EST:     TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAG                         AAAATGGAACATGCTTCCTTTTTTAATAATGAGATGCTTCAAGAACTTCAG
genomic: TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAGgtaatgggat ... tctatgccagAAAATGGAACATGCTTCC-TTTTTAATAATGAGATGCTTCAAGAACTTCAG
EST: gi|116411176|gb|EG453768.1|EG453768
EST:     TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAG                         AAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGT
genomic: TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAGgtaatgggat ... tctatgccagAAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGT
EST: gi|116411168|gb|EG453760.1|EG453760
EST:     TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAG                         AAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGT
genomic: TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAGgtaatgggat ... tctatgccagAAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGT
EST: gi|116459191|gb|EG501783.1|EG501783
EST:     TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAG                         AAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGT
genomic: TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAGgtaatgggat ... tctatgccagAAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGT
EST: gi|116411162|gb|EG453754.1|EG453754
EST:     TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAG                         AAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGT
genomic: TGGCGGAAACAAACCCGGAGAACTGTTAACACTCCGCCATCCAAAATCAGgtaatgggat ... tctatgccagAAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaacttcagctagtaacatcttttgtggtttggtatctttgcttctatgccagAAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGTGGTTTAAGCAATCTTATGGTTCTTGGTTCTTGGGAGATTACATATCTGA
            tagtaac  putative branch site (score: 1)
                                     tctttgcttct  putative PPT
                   atctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgggatgttgatgattgtcaggcttgctatgttgtgttttggggaaaacttcagctagtaacatcttttgtggtttggtatctttgcttctatgccagAAAATGGAACATGCTTCCTTTTTAATAATGAGATGCTTCAAGAACTTCAGTGGTTTAAGCAATCTTATGGTTCTTGGTTCTTGGGAGATTACATATCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT