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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggagaaaattgagtcgccattcttttatctggtttacgatttgattgatggattgtcccatgttagctgacatatgtgtaatgtttttcttgtgcatttatctttttcagAAAAGTTCCATGAGATATACAACTTTGCTTTTGGGTGGGCGAAAGAGAAG

Basic information

species Arabidopsis thaliana
transcript AT3G12760.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G12760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os06g12690.3 (Oryza sativa), 3'ss of exon 7
--------------------------------------------gtaaggagaaaattgagtcgccattcttttatctg-gtttacgatttga--ttga---tggattgtcccatgtta--gctgacatatgtgtaatgtttttcttgtgcatttatctttt------tcagAAAAGTTCCATGAGATATACAACTTTGCTTTTGGGTGGGCGAAAGAGAAG
                                            ||||    | | || |||   || | | | | |    |  | ||  |||  | ||   || || |    |  | |  ||   | | | | | || | |    ||||   |||   |||      ||||| || |||| |||||||||||||||||||||||  ||||| |  || |||
gtatgtgttttctttgtgtgaagttggattttctctatgttgaagtaacactacattttagtttacaatttgtgaccaatatgaaggaactgaaatagaatgtgtatggaaggaattcaatgccatcttttatttgatatctaatctgtgtggttactctttcctcactcagATAAATTCCGTGAGATATACAACTTTGCTTTTGCTTGGGCTAGGGAAAAG

upper sequence: AT3G12760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G41570.2 (Glycine max), 3'ss of exon 7
----------------gtaaggagaaaattgagtcgccattcttttatctggtttacgatttgattg-----atggattgtccc-----atgttagctgacatatgtgtaatgtttttcttgtgcatttatctttttcagAAAAGTTCCATGAGATATACAACTTTGCTTTTGGGTGGGCGAAAGAGAAG
                  |    | |  |  |  |    ||   | ||    ||||  |||   |||     |   ||| || |     || || | | |  |   || ||| | ||   |||   |||   || | |||| || ||||  |||||||| |||||||||||||| ||||| |||||||||
gtatgggcaacagtattcagactgcagctcaaaactagttttagtcatacaatttataattcacttgtcactagaaattatctccagcaatttttgataagctccctgaaatatattcactgt---ttttgattgtccagAGAAATTCCGCGAGATATATAACTTTGCTTTTGGCTGGGCAAAAGAGAAG

upper sequence: AT3G12760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G17580.1 (Glycine max), 3'ss of exon 7
----------------gtaaggagaaaattgagtcgccattcttttatctggtttacgatttgattgatggattgtcccatgttagctgacatatgtgtaatgtttttcttgtgcatttatcttttt--------cagAAAAGTTCCATGAGATATACAACTTTGCTTTTGGGTGGGCGAAAGAGAAG
                 ||      | ||  |  |    ||   | ||    ||||  |||   |||      |     || |      | || |   |||  |   |    |  ||| ||  ||||        |||| || |||| ||||||||| || ||||||||||| ||||| |||||||||
gtatgggcaacagtatttagattacagatcaaaactagttttagtcatacaatttataattcacttgtcactataaattatctccagcaatattttgataagctccctgaaatatattcattgtttttgattgtccagAGAAATTCCGTGAGATATATAATTTTGCTTTTGGCTGGGCAAAAGAGAAG

upper sequence: AT3G12760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv19s0085g00630.t01 (Vitis vinifera), 3'ss of exon 7
gtaaggagaaaattgagtcgccattcttttatctggtt--tacgatttgattgatggattgtcccatgttagctgacatatgtgtaatgtttttcttgtgcatttatctttttcagAAAAGTTCCATGAGATATACAACTTTGCTTTTGGGTGGGCGAAAGAGAAG
                 | |  ||  ||| || || |   |||  |  || | || |||||  |  | || |        ||  | |  | ||   |||   ||  | | || |||||||||||| |||||||||||||||||||||||| ||||| ||||| |||
-------------cttttggtaatagtttgatttgatcagtactgtgagaataatagattgaac--ttttggtcttttcttgc-tgaaatgttgtctgtttcttactatattccagAAAAGTTCCGTGAGATATACAACTTTGCTTTTGGCTGGGCTAAAGAAAAG

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|125057045|gb|EL126447.1|EL126447
EST:     GTTCTGAGCTTAAAGATGAAC                         AAAAGTTCCATGAGATATACAACTTTGCTTTTGGGTGGGCGAAAGAGAAG
genomic: GTTCTGAGCTTAAAGATGAACgtaaggagaa ... tctttttcagAAAAGTTCCATGAGATATACAACTTTGCTTTTGGGTGGGCGAAAGAGAAG
EST: gi|86078707|gb|DR374464.1|DR374464
EST:     GAAGTTGCAGGAAAAGCTGCCATTTATGCGTTCTGAGCTTAAAGATGAAC                         AAAAGTTCCATGAGATATACAACTTTGCTTTTGGGTGGGCGAAAGAGAAG
genomic: GAAGTTGCAGGAAAAGCTGCCATTTATGCGTTCTGAGCTTAAAGATGAACgtaaggagaa ... tctttttcagAAAAGTTCCATGAGATATACAACTTTGCTTTTGGGTGGGCGAAAGAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcccatgttagctgacatatgtgtaatgtttttcttgtgcatttatctttttcagAAAAGTTCCATGAGATATACAACTTTGCTTTTGGGTGGGCGAAAGAGAAG
         agctgac  putative branch site (score: 3)
                                       catttatctttttc  putative PPT
                                        atttatctttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggagaaaattgagtcgccattcttttatctggtttacgatttgattgatggattgtcccatgttagctgacatatgtgtaatgtttttcttgtgcatttatctttttcagAAAAGTTCCATGAGATATACAACTTTGCTTTTGGGTGGGCGAAAGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA