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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatttttcacttactatctttcagccagatccccgatagctacaaatgcaagcaagaacagcctccaaattgtgtctgagaaatccgaaagatcagtgagaattttgtttctggacttgttacagGATTACATAGATAGTATGGAAGGAGCAACATTATCAGGGAGACAAGCTTCGTCATACATCTGTGATGCTGGTGAAGAACTAGCAGAGCTAAACAAGAAGC

Basic information

species Arabidopsis thaliana
transcript AT3G04870.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G04870.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA20G37170.1 (Glycine max), 3'ss of exon 13
gtaacatttttcacttactatctttcagccagatccccgatagctacaaatgcaagcaagaacagcctccaaattgtgtctgagaaatccgaaagatcagtgagaattttgtttctggacttgttacagGATTACATAGATAGTATGGAAGGAGCAACATTATCAGGGAGACAAGCTTCGTCATACATCTGTGATGCTGGTGAAGAACTAGCAGAGCTAAACAAGAAGC
  | || ||      |  | | ||    |||| |   |   ||     | || ||            |  || |||  |  | |            ||| |   | | || ||  |    ||||| ||||| |||||||| || |||||||| ||||| || || || |||||||||||| | || ||||||||||| || |||| | |||  |   |    |||||||
--agcaattgctgtatgttgttttct--ccagttttactgcagt----agtgaaa------------tttaagttgcattggtgttgc--------tcacttttattattattgttatttttgtt-cagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCGGCCTATATCTGTGATGCAGGGGAAGGATTAGTGGCATTGCGGAAGAAGC

upper sequence: AT3G04870.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv14s0030g01740.t01 (Vitis vinifera), 3'ss of exon 13
--------------------------------------------------------gtaacatttttcacttactatct--ttcagccagatc-----cccgatagctacaaatgcaagcaagaacagcctccaaattgtgtctgagaaatccgaaagatcagtgagaattttgtttctggacttgttacagGATTACATAGATAGTATGGAAGGAGCAACATTATCAGGGAGACAAGCTTCGTCATACATCTGTGATGCTGGTGAAGAACTAGCAGAGCTAAACAAGAAGC
                                                        ||      ||||    |  || |  ||     |||       |   || | |  | || ||  |   |  |||        ||  | |   |    | |   |||| || ||  | |||||  || ||||| |||||||||||| || |||||||||||||||||  | ||||| || ||| ||||  | || || || || || || |||||| ||||||  ||  | || ||||
gtaatttttgccttaacttcatccactcactgataatactgtttggttaccaaactgtcctgcatttccaccagcatttaatttgaaaagaaaaatgacataatggattaatatacattcttaataagctagttgggtggctttctcattcacaattcatcattgggacatgtgttt--gggcttgt-acagGATTACATTGACAGTATGGAAGGAGCAACCCTGTCAGGCAGGCAAACTTCAGCCTATATTTGCGACGCGGGGGAAGAATTAGCAGCACTGCAGAAAAAGC
















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|86077676|gb|DR373433.1|DR373433
EST:     AGAAGACGCCCATAAAGAATTTCTTCCTCGCCGGTTCATACACAAAGCAG                         GATTACATAGATAGTATGGAAGGAGCAACATTATCAGGGAGACAAGCTTCG
genomic: AGAAGACGCCCATAAAGAATTTCTTCCTCGCCGGTTCATACACAAAGCAGgtaacatttt ... cttgttacagGATTACATAGATAGTATGGAAGGAGCAACATTATCAGGGAGACAAGCTTCG
EST: gi|124973947|gb|EL047540.1|EL047540
EST:     GAAGTACGCCCATAAGGAATTTCTTCCTCGCCGGTTCATACACAAAGCAG                         GATTACATAGATAGTATGGAAGGAGCAACA
genomic: GAAG-ACGCCCATAAAGAATTTCTTCCTCGCCGGTTCATACACAAAGCAGgtaacatttt ... cttgttacagGATTACATAGATAGTATGGAAGGAGCAACA
EST: gi|125090460|gb|EL148438.1|EL148438
EST:     CTTCCTTCGCCGGTTCATACACAAAGCAG                         GATTACATAGATAGTATGGAAGGAGCAACATTATCAGGGAG
genomic: CTTCC-TCGCCGGTTCATACACAAAGCAGgtaacatttt ... cttgttacagGATTACATAGATAGTATGGAAGGAGCAACATTATCAGGGAG
EST: gi|124811019|gb|EH895885.1|EH895885
EST:     AGAAGACGCCCATAAAGAATTTCTTCCTCGCCGGTTCATACACAAAGCAG                         GATTACATAGATAGTATGGAAGGAGCAACA
genomic: AGAAGACGCCCATAAAGAATTTCTTCCTCGCCGGTTCATACACAAAGCAGgtaacatttt ... cttgttacagGATTACATAGATAGTATGGAAGGAGCAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtctgagaaatccgaaagatcagtgagaattttgtttctggacttgttacagGATTACATAGATAGTATGGAAGGAGCAACATTATCAGGGAGACAAGCTTCGTCATACATCTGTGATGCTGGTGAAGAACTAGCAGAGCTAAACAAGAAGC
                              aattttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacatttttcacttactatctttcagccagatccccgatagctacaaatgcaagcaagaacagcctccaaattgtgtctgagaaatccgaaagatcagtgagaattttgtttctggacttgttacagGATTACATAGATAGTATGGAAGGAGCAACATTATCAGGGAGACAAGCTTCGTCATACATCTGTGATGCTGGTGAAGAACTAGCAGAGCTAAACAAGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC