Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacaattttctactttactttgctaactacaacgtttaattttgatttgctgaaacttggctttggtttatgctttttatgataatctttttttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAAAACTGCTTCCTGAATCCTACAAGCAGAAAG

Basic information

species Arabidopsis thaliana
transcript AT3G52880.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52880.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G07820.1 (Glycine max), 3'ss of exon 3
gtaagacaattttctactttactttgctaactacaacgtttaattttgatttgctgaaacttggctttggtttatgctttttatgataatctttttttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAAAACTGCTTCCTGAATCCTACAAGCAGAAAG
 |  |    |  |||   ||   ||    | || ||  || ||| |    ||||      |    | |  |  ||  ||    ||||     ||   | ||||||   ||||||||||||| || ||||||  ||||||||| ||||| |||||||   |||||||||| |  ||||   ||||||
-tgggcttttcatctctgttgaattctccattataat-ttaaatatcagcttgccttggttg---tctcatgaatatttaccttgatgtcaattggattttgcagCCCCTGCTAGACTTCCTGGGTTCCATGTCTGTGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAG
















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|86038366|gb|DR334121.1|DR334121
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038353|gb|DR334108.1|DR334108
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038384|gb|DR334139.1|DR334139
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038379|gb|DR334134.1|DR334134
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038373|gb|DR334128.1|DR334128
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038364|gb|DR334119.1|DR334119
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038359|gb|DR334114.1|DR334114
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038370|gb|DR334125.1|DR334125
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038368|gb|DR334123.1|DR334123
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038365|gb|DR334120.1|DR334120
EST:     TAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: TAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038377|gb|DR334132.1|DR334132
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|152033821|gb|BP816817.2|BP816817
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038378|gb|DR334133.1|DR334133
EST:     GGCTCCATATGAACGCCCTGCACTTMGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038374|gb|DR334129.1|DR334129
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038367|gb|DR334122.1|DR334122
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038380|gb|DR334135.1|DR334135
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038376|gb|DR334131.1|DR334131
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTMCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038355|gb|DR334110.1|DR334110
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038356|gb|DR334111.1|DR334111
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038354|gb|DR334109.1|DR334109
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038381|gb|DR334136.1|DR334136
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038383|gb|DR334138.1|DR334138
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038357|gb|DR334112.1|DR334112
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGCAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038369|gb|DR334124.1|DR334124
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038361|gb|DR334116.1|DR334116
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038362|gb|DR334117.1|DR334117
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038382|gb|DR334137.1|DR334137
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTMCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|301501396|gb|HO206936.1|HO206936
EST:     GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA
EST: gi|86038375|gb|DR334130.1|DR334130
EST:     GGCTCCATATGAACGCMCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAG                         GGGCTGCTAGACTTCCAGGTTTCCATTGSTGTGTTGGTAGTGGTGGAGAAA
genomic: GGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAAGgtaagacaat ... tttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctgaaacttggctttggtttatgctttttatgataatctttttttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAAAACTGCTTCCTGAATCCTACAAGCAGAAAG
                                       tctttttttgttgc  CT-rich tract
                    tttatgctttttatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagacaattttctactttactttgctaactacaacgtttaattttgatttgctgaaacttggctttggtttatgctttttatgataatctttttttgttgcagGGGCTGCTAGACTTCCAGGTTTCCATTGCTGTGTTGGTAGTGGTGGAGAAAAACTGCTTCCTGAATCCTACAAGCAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA