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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAGgttagtgtgattctatttcggtattcagctccaatgtttaaaagatagatgaatgatagattgtttcaacttgtgtattgtggtgaag

Basic information

species Arabidopsis thaliana
transcript AT2G47470.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G47470.3 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os01g23740.2 (Oryza sativa), 5'ss of exon 2
GTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAGgttagtgtgattctatttcggtattcagctccaatgtttaaaagatagatgaatgatagattgtttcaacttgtgtattgtggtgaag---------------------------------------------------------------------------------------------------------------
|||||||||||||||||| ||||| || |||||||||||||| || ||||| |||||||| || || ||||| || |||||||||||  ||     || | |||  ||       | |||  ||     || | |  |  |||  || |     |     |  |     || |                                                                                                               
GTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAGgtatgttc---tcaagttcaatacctg---ctaattatttgggcattgcttgaaaatattttctcatctccatcctgctactcagaggtggtcagaaaatggttagaacatgcatattcatgaaatgtgttgccatcctcattttgatttggtttgataaaattaaggattctcacttcaactctatttctcgctttag

upper sequence: AT2G47470.3 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G128171_T04 (Zea mays), 5'ss of exon 2
GTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAGgttagtgtgattctatt-tcggtattcagctccaa--tgtttaaaagatagatgaatgat---agattgtttcaac-ttgtgtattgtggtgaag-----
|||||||||||||||||| |||||||| ||||||||||  || || ||||| || ||||| ||||| ||||| |||||||| |||||   |||   ||| |  |    ||  ||    ||  || ||        |||||||        |||  ||  |  || | | |  |  |         
GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAGTTTTAAGAAAGCTAAATCTGTCTTGATTGCTAAGgtatatgtatatctgtcatacacatgaagaattaaattggttctctacctgatgaatctctcagcattacttagatattatatgtccttttattccacta

upper sequence: AT2G47470.3 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G159369_T01 (Zea mays), 5'ss of exon 2
GTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAGgttagtgtgattctatttcggtattcagctccaatgtttaaaagatagatg----aatgatagattgtttcaacttgtgtattgtggtgaag--------------------------------------------------------------------------
|||||| |||||||| || ||||| || ||||||||||| || || || ||||||||||||||||| |||||  |||| ||||||||   | | |   | ||| |     |      ||||||   |    |   |     || ||  |        | || | ||| ||   |||                                                                           
GTGTGGCCACTGCAAAAAGCTTGCCCCCGAGTATGAAAAACTTGGCGCCAGCTTCAAGAAGGCTAAATCTGTACTGATAGCAAAGgtacatctcaccttgtttagtctccccaggggaatgttggtattgcaacagttttcatcatttacatcccacaattttctatggtatcgaaacttgttctgaatatctaattacatttctttgctgcaatgaattaactgttttcctttttgtatctactacctag

upper sequence: AT2G47470.3 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA10G01820.1 (Glycine max), 5'ss of exon 3
GTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAGgttagtgtgattctatttcggtattcagctccaatgt----ttaaaagatagatgaatgatagattgtttcaacttgtgtattgtgg---tgaag-----
|||||| |||||||| || ||||||||||| ||||||||||| ||    ||||||||||| || || ||||| || ||||  ||||| ||     |  | ||||  |    | ||| ||| |    |||  |  |   ||  |  |  ||  |||    | || | || ||    | | |     
GTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcaccctggtgtttctttcagaacctctaatattattttaccatttttctgtttacttaataatttgttgtggtattttttgagcttcaggcattt

upper sequence: AT2G47470.3 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA02G01750.1 (Glycine max), 5'ss of exon 2
GTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAGgttagtg---tgat-tctatttcggtattcagctccaatgtttaaaagatagatgaatgataga---ttgtttcaacttgtgtattgtggtgaag-----
|||||| |||||||| || ||||||||||| ||||||||||| ||    ||||||||||| || || ||||| || || |  ||||| ||     || | | | ||||   |||  |    |   |||| ||  |   ||  |  |  |   || |||     | | | ||  | |  ||     
GTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcaccttggtgtttctttcaaaatttcgaataatgttttacaatttttctgtttactttatattttttttgtggtattttttaagtttcaggcatt

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|124986678|gb|EL059182.1|EL059182
EST:     AAGGCTAAGTCTGTGTTGATTGCAAAG                         GTTGATTGTGATGAGCAAAAGAGTGTCTGTACTAA
genomic: AAGGCTAAGTCTGTGTTGATTGCAAAGgttagtgtga ... tgtggtgaagGTTGATTGTGATGAGCAAAAGAGTGTCTGTACTAA
EST: gi|164114123|gb|ES038307.1|ES038307
EST:     GAAGGCTAAGTCTGTGTTGATTGCAAAG                         GTTGATTGTGATGAGCAAAAGAGTGTCTGTACTAAATATGGTGCTAGTGGA
genomic: GAAGGCTAAGTCTGTGTTGATTGCAAAGgttagtgtga ... tgtggtgaagGTTGATTGTGATGAGCAAAAGAGTGTCTGTACTAAATATGGTGTTAGTGGA
EST: gi|163983893|gb|ES156765.1|ES156765
EST:     CTAAGTCTGTGTTGATTGCAAAG                         GTTGATTGTGATGAGCAAAAGAGTGTCTGTACTAAATATGGTGTTAGTGGA
genomic: CTAAGTCTGTGTTGATTGCAAAGgttagtgtga ... tgtggtgaagGTTGATTGTGATGAGCAAAAGAGTGTCTGTACTAAATATGGTGTTAGTGGA
EST: gi|164096433|gb|ES104240.1|ES104240
EST:     AAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAG                         GTTGATTGTGATGAG
genomic: AAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAGgttagtgtga ... tgtggtgaagGTTGATTGTGATGAG
EST: gi|116441306|gb|EG483898.1|EG483898
EST:     AAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAG                         GTTGATTGTGATGAGCAAAAGAGTGTCTGTACTAAATATGGTGTTAGTGGA
genomic: AAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAGgttagtgtga ... tgtggtgaagGTTGATTGTGATGAGCAAAAGAGTGTCTGTACTAAATATGGTGTTAGTGGA
EST: gi|124812664|gb|EH897530.1|EH897530
EST:     AAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAG                         GTTGATTGTGATGAGCAAAAAGAGTGT
genomic: AAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAGgttagtgtga ... tgtggtgaagGTTGATTGTGATGAGCAAAA-GAGTGT
EST: gi|301501187|gb|HO206727.1|HO206727
EST:     AAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAG                         GTTGATTGTGATGAGCAAAAGAGTGTCTGTACTAAATATGGTGTTAGTGGA
genomic: AAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAGgttagtgtga ... tgtggtgaagGTTGATTGTGATGAGCAAAAGAGTGTCTGTACTAAATATGGTGTTAGTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAGgttagtgtgattctatttcggtattcagctccaatgtttaaaagatagatgaatgatagattgtttcaacttgtgtattgtggtgaag

- - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG