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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcattagggaatatgaaaagtgctctcaagatccatgctttaatgtcattgtgggattagaattgaggatatcttgtttttgttgttttgtttgaatcagTGTGATAGACAATAATGGGTTACATAGGAGCTCATGGTGTAGCAGCTCTTCATAGGTACAAATACAGTGGAGTGGATCACTCTTATCTTGCCAAATACGT

Basic information

species Arabidopsis thaliana
transcript AT1G13560.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G13560.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 1
gcattagggaatatgaaaagtgctctcaagatccatgctttaatgtcattgtgggattagaattgag-gatatcttgtttttgttgttttgtttgaatcagTGT------------GATAGACAATAATGGGTTACATAGGAGCTCATGGTGTAGCAGCTCTTCATAGGTACAAATACAGTGGAGTGGATCACTCTTATCTTGCCAAATACGT
   | |  |  | ||  |  |    | | |     || ||| |  ||  ||     |  ||||  |  ||| | | ||     ||| ||   ||  | |||| |            || ||  || |||| | ||||||||| | ||||| |||||||| || ||||  ||||| |||||||||||||||||||| ||| |            
-tttcattggttttgcgatttttctttatgggttttgattttagatccatgattcgtgggaatgaattgatttttggtgcaaattggttgaatttgagcagTTTCTGTTGAGAACTGAGAGCAAAAAATGAGGTACATAGGATCCCATGGAGTAGCAGCGCTGCATAAATACAAGTACAGTGGAGTGGATCACTCGTATGT------------
















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|86070079|gb|DR365836.1|DR365836
EST:     CACTCGAGACGAGAAAGGCTCGTATCTGATTTTACCGCCACCGGACCATC                         TGTGATAGACAATAATGGGTTACATAGGAGCTCATGGTGTAGCAGCTCTTC
genomic: CACTCGAGACGAGAAAGGCTCGTATCTGATTTTACCGCCACCGGACCATCgtaagtactc ... tttgaatcagTGTGATAGACAATAATGGGTTACATAGGAGCTCATGGTGTAGCAGCTCTTC
EST: gi|86070083|gb|DR365840.1|DR365840
EST:     CACTCGAGACGAGAAAGGCTCGTATCTGATTTTACCGCCACCGGACCATC                         TGTGATAGACAATAATGGGTTACATAGGAGCTCATGGTGTAGCAGCTCTTC
genomic: CACTCGAGACGAGAAAGGCTCGTATCTGATTTTACCGCCACCGGACCATCgtaagtactc ... tttgaatcagTGTGATAGACAATAATGGGTTACATAGGAGCTCATGGTGTAGCAGCTCTTC
EST: gi|86070078|gb|DR365835.1|DR365835
EST:     CACTCGAGACGAGAAAGGCTCGTATCTGATTTTACCGCCACCGGACCATC                         TGTGATAGACAATAATGGGTTACATAGGAGCTCATGGTGTAGCAGCTCTTC
genomic: CACTCGAGACGAGAAAGGCTCGTATCTGATTTTACCGCCACCGGACCATCgtaagtactc ... tttgaatcagTGTGATAGACAATAATGGGTTACATAGGAGCTCATGGTGTAGCAGCTCTTC
EST: gi|152034149|gb|BP868711.2|BP868711
EST:     CACTCGAGACGAGAAAGGCTCGTATCTGATTTTACCGCCACCGGACCATC                         TGTGATAGACAATAATGGGTTACATAGGAGCTCATGGTGTAGCAGCTCTTC
genomic: CACTCGAGACGAGAAAGGCTCGTATCTGATTTTACCGCCACCGGACCATCgtaagtactc ... tttgaatcagTGTGATAGACAATAATGGGTTACATAGGAGCTCATGGTGTAGCAGCTCTTC
EST: gi|86070080|gb|DR365837.1|DR365837
EST:     CACTCGAGACGAGAAAGGCTCGTATCTGATTTTACCGCCACCGGACCATC                         TGTGATAGACAATAATGGGTTACATAGGAGCTCATGGTGTAGCAGCTCTTC
genomic: CACTCGAGACGAGAAAGGCTCGTATCTGATTTTACCGCCACCGGACCATCgtaagtactc ... tttgaatcagTGTGATAGACAATAATGGGTTACATAGGAGCTCATGGTGTAGCAGCTCTTC
EST: gi|86070077|gb|DR365834.1|DR365834
EST:     CACTCGAGACGAGAAAGGCTCGTATCTGATTTTACCGCCACCGGACCATC                         TGTGATAGACAATAATGGGTTACATAGGAGCTCATGGTGTAGCAGCTCTTC
genomic: CACTCGAGACGAGAAAGGCTCGTATCTGATTTTACCGCCACCGGACCATCgtaagtactc ... tttgaatcagTGTGATAGACAATAATGGGTTACATAGGAGCTCATGGTGTAGCAGCTCTTC
EST: gi|86070082|gb|DR365839.1|DR365839
EST:     CACTCGAGACGAGAAAGGCTCGTATCTGATTTTACCGCCACCGGACCATC                         TGTGATAGACAATAATGGGTTACATAGGAGCTCATGGTGTAGCAGCTCTTC
genomic: CACTCGAGACGAGAAAGGCTCGTATCTGATTTTACCGCCACCGGACCATCgtaagtactc ... tttgaatcagTGTGATAGACAATAATGGGTTACATAGGAGCTCATGGTGTAGCAGCTCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattgtgggattagaattgaggatatcttgtttttgttgttttgtttgaatcagTGTGATAGACAATAATGGGTTACATAGGAGCTCATGGTGTAGCAGCTCTTCATAGGTACAAATACAGTGGAGTGGATCACTCTTATCTTGCCAAATACGT
                                        ttttgttt  CT-rich tract
          attagaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcattagggaatatgaaaagtgctctcaagatccatgctttaatgtcattgtgggattagaattgaggatatcttgtttttgttgttttgtttgaatcagTGTGATAGACAATAATGGGTTACATAGGAGCTCATGGTGTAGCAGCTCTTCATAGGTACAAATACAGTGGAGTGGATCACTCTTATCTTGCCAAATACGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - atgaaaa
- - - - - - - - - - - ctctcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg