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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttattcttaaactccctccctcttcttctcaagctttcttcttcactgaaccaagaatattgattttgattcctgtgtctgcagAGGAAATGGACTGGGACAAGAACGGAATGGTGAACTTCAAAGAGTTTCTCTTCGCATTTACGCAGTGGGTTGGGATAGATGAGAATGAAGAAGAAGAAGA

Basic information

species Arabidopsis thaliana
transcript AT4G26470.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26470.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g40720.1 (Oryza sativa), 3'ss of exon 4
---------gtttattcttaaactccctccctcttcttctcaagctttcttcttcactgaa-ccaagaatattgattttgattcctgtgtctg----cagAGGAAATGGACTGGGACAAGAACGGAATGGTGAACTTCAAAGAGTTTCTCTTCGCATTTACGCAGTGGGTTGGGATAGATGAGAATGAAGAAGAAGAAGA
            || ||| ||| |  ||   |   |   ||        |||   | | |  || |  || |     ||  ||  | ||  ||    ||||||||||||||||||||||||| |||||||||| ||||||||| ||||| || ||||| || |  ||||||||||| || || ||||| || ||  | ||
atttctctatagtaatctaaaaatttctagattgacaattcccatcagtttcagaattaagtcctaacatgtaacactttctttttttgcatggcaccagAGGAAATGGACTGGGACAAGAATGGAATGGTGACCTTCAAAGAATTTCTGTTTGCATTCACTCGCTGGGTTGGGATTGACGAAAATGAGGACGACAATGA

upper sequence: AT4G26470.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g10470.1 (Oryza sativa), 3'ss of exon 4
------gtttattcttaaactccctccctcttcttctcaagctttct-tcttcactga-accaagaatattgattttgattcctg-tgtctgcagAGGAAATGGACTGGGACAAGAACGGAATGGTGAACTTCAAAGAGTTTCTCTTCGCATTTACGCAGTGGGTTGGGATAGATGAGAATGAAGAAGAAGAAGA
       ||  || ||    |  |  |       || || |    |  |   |||||| |   |   |  | ||      |  || ||    ||||||||||||| ||||||||||| |||| ||||| |||||| ||||| |||||||| ||||| |  ||||| ||||| ||||| || ||||| || || ||
gtaagttttcttttttgtggtatcgtcacaaatctcacatgaacacagtacacactgacaatgatggtcctaatacactcttttggtggtcccagAGGAAATGGATTGGGACAAGAATGGAACGGTGACCTTCAAGGAGTTCCTCTTCGCTTTTACTCGTTGGGTGGGGATTGATGATAACGAAGATGACGACGA

upper sequence: AT4G26470.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G006790_T01 (Zea mays), 3'ss of exon 3
-------------gtttattcttaaactccctccctcttcttctcaagctttcttct--tcactgaaccaagaatattgattttgattcctgtgtctgcagAGGAAATGGACTGGGACAAGAACGGAATGGTGAACTTCAAAGAGTTTCTCTTCGCATTTACGCAGTGGGTTGGGATAGATGAGAATGAAGAAGAAGAAGA
              |  |  || | | | |||    ||  || | || ||| | ||   ||     |      |  || |  ||  ||    || |   |||||||||||||||||||||||||||||||||||  ||||| ||||| || || || || || |  ||||| || || ||||| ||||| || ||||| ||
gaagtataaaaacttgcacactcataattcctgttactgttt-tgaaacttgcgtcccatcttcccagtcctgacgtttacctttctttacatggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGTTTGCCTTCACTCGCTGGGTAGGAATTGATGAAAATGAGGATGAAGATGA

upper sequence: AT4G26470.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G155822_T01 (Zea mays), 3'ss of exon 4
---------gtttattcttaaactccctc-----cctcttcttctcaa-gctttcttcttcactgaaccaagaatattgattttgattcctgtgtctgcagAGGAAATGGACTGGGACAAGAACGGAATGGTGAACTTCAAAGAGTTTCTCTTCGCATTTACGCAGTGGGTTGGGATAGATGAGAATGAAGAAGAAGAAGA
         |  ||||    |   | ||      ||  | ||  | |   | |  || |  | |   ||    ||||| | ||   ||  || |  ||||||||| ||||||||||||||||| |||| ||||| |||||| || || || ||||| || || || ||||| |||||  || |  | ||||| || || ||
tcctagattgcctattacagagacctcttagattccagtcctggttattacctgtttatatatttcccctgatatatttacttcatttggtg-gaatgcagAGGAGATGGACTGGGACAAGAATGGAACGGTGACCTTCAAGGAATTCCTTTTCGCTTTCACTCACTGGGTGGGGATCAATAATGAAGAAGACGAGGACGA

upper sequence: AT4G26470.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G16060.1 (Glycine max), 3'ss of exon 5
-----------------gtttattcttaaactccctccctcttcttctcaagctttcttcttcactgaaccaagaatattgattttgattcctgtgtctgcagAGGAAATGGACTGGGACAAGAACGGAATGGTGAACTTCAAAGAGTTTCTCTTCGCATTTACGCAGTGGGTTGGGATAGATGAGAATGAAGAAGAAGAAGA
                   | |  |||    |   |   ||||| |  | ||  || || || ||| |   ||| || ||| |||   | |     |||||||| |||||||| ||||| || || ||||||||||||||||| |||||||| || || ||||| |  |||||||| || |||||   ||| || || ||| |
atacagtagcaactctaaatcaaccttctctttgttttttcttcctagctagtatt-ttatttactaa--taagtattttgttttctctgcaaaattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGAGGACGAGGAAAA

upper sequence: AT4G26470.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0015g01200.t01 (Vitis vinifera), 3'ss of exon 4
------------gttt--attcttaaactccctccctcttcttctcaagctttcttcttcactgaaccaagaatattgattttgattcctgtgtctgcagAGGAAATGGACTGGGACAAGAACGGAATGGTGAACTTCAAAGAGTTTCTCTTCGCATTTACGCAGTGGGTTGGGATAGATGAGAATGAAGAAGAAGAAGA
            |||   |   || |       | |       ||| |  ||| |||   | | | | |      |||   |    |  | |   ||||||||| ||||| ||||| || || ||||||||||||||||| |||||||| || || || || |  ||||||||||| || || | ||| || ||||||||
tgccagtagatggttagaagctttgatgatttcctcgaacaggctccaatttttttccataataatctatttcacttggcctcttgttttattattgcagAGGAGATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTTTTTGCTTTCACCCGTTGGGTTGGGATTGACGATATTGAGGATGAAGAAGA

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|125096941|gb|EL153566.1|EL153566
EST:     TGATGAATCAGGAGAACGATCCTCCGGGCGGATTGCAATGAAGAGATTTG                         AGGAAATGGACTGGGACAAGAACGGAATGGTGA
genomic: TGATGAATCAGGAGAACGATCCTCCGGGCGGATTGCAATGAAGAGATTTGgtttattctt ... gtgtctgcagAGGAAATGGACTGGGACAAGAACGGAATGGTGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagctttcttcttcactgaaccaagaatattgattttgattcctgtgtctgcagAGGAAATGGACTGGGACAAGAACGGAATGGTGAACTTCAAAGAGTTTCTCTTCGCATTTACGCAGTGGGTTGGGATAGATGAGAATGAAGAAGAAGAAGA
                                        ttcctgt  CT-rich tract
                          aatattgattttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttattcttaaactccctccctcttcttctcaagctttcttcttcactgaaccaagaatattgattttgattcctgtgtctgcagAGGAAATGGACTGGGACAAGAACGGAATGGTGAACTTCAAAGAGTTTCTCTTCGCATTTACGCAGTGGGTTGGGATAGATGAGAATGAAGAAGAAGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG