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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttatcttcttctacattgcggaagattagatcatattaagaaagttagtgctggtcttgtgattgttaaatgtgcttgaattctttgtcagGTTGTTGAAATTAGCAAAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAG

Basic information

species Arabidopsis thaliana
transcript AT2G18230.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G37790.1 (Glycine max), 3'ss of exon 3
gtaagttttatcttcttctacattgcggaagattagatcatattaagaaagttagtgctg-----gtcttgtgattgttaaatgtgcttgaattctttgtcagGTTGTTGAAATTAGCAAAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAG
   |  |   |     |||  |   |  ||  ||| ||  |    | | || |  | |        ||||||   |    ||     |||| |||  || ||||| ||||||||| |||||||  | ||||||||||| ||||| |||||||  ||||| ||||| |||
---aaatcactagcagtctgaaactccaaatcttacattttgcctacatagattattccatttaactcttgtttctagagaaataaattgatttccatggcagGTGGTTGAAATTGGCAAAGGCAGTAAGGTTAAGTATGAGCTGGACAAGACAAGTGGACTTATAAAG

upper sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G07530.2 (Glycine max), 3'ss of exon 3
--gtaagtttta-tcttcttctacattgcggaagattagatcatattaagaaagttagtgctggtcttgtgattgttaaatgtgcttgaattctttgtcagGTTGTTGAAATTAGCAAAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAG
   | | |   | |||    || ||   |  |   || |     ||| |  |    | ||    ||||||   |    ||     | || |||  || ||||| ||||||||| |||||||  | ||||||||||| ||||| |||||||  ||||| ||||| |||
aaatcactagcagtctgaaacttcaaatcttacattttgccttcattgattattccattga-actcttgtttctagggaaataaatcgatttcaatggcagGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACAAGTGGACTTATAAAG

upper sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G07530.4 (Glycine max), 3'ss of exon 2
----------------------gtaagttttatcttcttctacattgcggaagattagatcatattaagaaagttagtgctggt-----cttgtgattgttaaatgtgcttgaattctttgtcagGTTGTTGAAATTAGCAAAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAG
                      |  |  |   |     |||  |      ||  ||| ||  |      |  | |  | |   |     |||||   |    ||     | || |||  || ||||| ||||||||| |||||||  | ||||||||||| ||||| |||||||  ||||| ||||| |||
attgaggttctgcttaaataaggagaaatcactagcagtctgaaacttcaaatcttacattttgccttcattgattattccattgaactcttgtttctagGGAAATAAATCGATTTCAATGGCAGGTGGTTGAAATTGGCAAAGGAAGTAAGGTTAAGTATGAGCTGGACAAGACAAGTGGACTTATAAAG

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|116390031|gb|EG432623.1|EG432623
EST:     GTCCAGAAGCTCCTACTGTTTTCAACTGT                         GTTGTTGAAATTAGCAAAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAAC
genomic: GTCCAGAAGCTCCTACTGTTTTCAACTGTgtaagtttta ... tctttgtcagGTTGTTGAAATTAGCAAAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAAC
EST: gi|116390040|gb|EG432632.1|EG432632
EST:     GTCCAAAAGCTCCTACTGTTTTCAACTGT                         GTTGTTGAAATTAGCAAAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAAC
genomic: GTCCAGAAGCTCCTACTGTTTTCAACTGTgtaagtttta ... tctttgtcagGTTGTTGAAATTAGCAAAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAAC
EST: gi|116443161|gb|EG485753.1|EG485753
EST:     GTCCAGAAGCTCCTACTGTTTTCAACTGT                         GTTGTTGAAATTAGCAAAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAAC
genomic: GTCCAGAAGCTCCTACTGTTTTCAACTGTgtaagtttta ... tctttgtcagGTTGTTGAAATTAGCAAAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAAC
EST: gi|116390041|gb|EG432633.1|EG432633
EST:     GTCCAGAAGCTCCTACTGTTTTCAACTGT                         GTTGTTGAAATTAGCAAAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAAC
genomic: GTCCAGAAGCTCCTACTGTTTTCAACTGTgtaagtttta ... tctttgtcagGTTGTTGAAATTAGCAAAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAAC
EST: gi|116451434|gb|EG494026.1|EG494026
EST:     GTCCAGAAGCTCCTACTGTTTTCAACTGT                         GTTGTTGAAATTAGCAAAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAAC
genomic: GTCCAGAAGCTCCTACTGTTTTCAACTGTgtaagtttta ... tctttgtcagGTTGTTGAAATTAGCAAAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAAC
EST: gi|116451435|gb|EG494027.1|EG494027
EST:     GTCCAGAAGCTCCTACTGTTTTCAACTGT                         GTTGTTGAAATTAGCAAAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAAC
genomic: GTCCAGAAGCTCCTACTGTTTTCAACTGTgtaagtttta ... tctttgtcagGTTGTTGAAATTAGCAAAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagaaagttagtgctggtcttgtgattgttaaatgtgcttgaattctttgtcagGTTGTTGAAATTAGCAAAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAG
                                            ttctttgtc  CT-rich tract
                         attgttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttatcttcttctacattgcggaagattagatcatattaagaaagttagtgctggtcttgtgattgttaaatgtgcttgaattctttgtcagGTTGTTGAAATTAGCAAAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC