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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctggttttacacaacaaaaagctgacttgttcttattctagtgcatttgcttggtgctacaataacctagacttgtcgatttccagACAATCAACGACTGGTATGATAGAGATATCGACGCAATTAATGAGCCATATCGTCCAATTCCATCTGGAGCAATATCAGAGCCAGAG

Basic information

species Arabidopsis thaliana
transcript AT3G51820.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G51820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g28200.1 (Oryza sativa), 3'ss of exon 5
------------------gtctggttttacacaacaaaaagctgacttg-----ttcttattctagtgcat----------ttgc-ttggtgcta-caataacctagacttgtcgatttcc--------agACAATCAACGACTGGTATGATAGAGATATCGACGCAATTAATGAGCCATATCGTCCAATTCCATCTGGAGCAATATCAGAGCCAGAG
                  |    |||||| ||    |    ||  |||      ||| |||| |  |||||          ||||  || ||||| |||  |  |   |||    || | |        ||||||| ||||||||||||||| ||||||| || || || ||||| || || ||||| ||||| || || || ||||||||    |||
gtttgctgttaggacttggatatgttttatacttttatcgactctcttcataacttcatattatgctgcatggagaactttttgcactgctgctaacaaatatgtcagctttcaaatgttcctgactgtagACAATTAACGACTGGTATGATCGAGATATAGATGCGATAAATGAACCTTACCGTCCTATTCCTTCAGGCGCTATATCAGAAAATGAG

upper sequence: AT3G51820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G162672_T01 (Zea mays), 3'ss of exon 5
gtctggttttacacaacaaaaagctgactt-gttcttat-tctagtgcatttgcttgg--------tgctac-aataac--------ctagacttgtcgatttccagACAATCAACGACTGGTATGATAGAGATATCGACGCAATTAATGAGCCATATCGTCCAATTCCATCTGGAGCAATATCAGAGCCAGAG
|| |  ||||| |          | | |||  ||  ||  |  || |    ||| |||        | |||| |||||         | | || |      ||  ||||| | || |||||||||||| |||| || || |||||||||||||| ||||| || |||||||| || || ||||||||       
gtttacttttaaattctctttgtcagccttcatttataccttcagagatgctgcgtgggagactatttctactaataagtatgtcagCCAAACATTCTTGCTTGTAGACACTTAATGACTGGTATGATCGAGACATTGATGCAATTAATGAGCCTTATCGGCCTATTCCATCAGGTGCTATATCAGA-------

upper sequence: AT3G51820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G162672_T02 (Zea mays), 3'ss of exon 5
gtctggttttacacaacaaaaagctgactt-gttcttattct-agtgcatttgcttgg--------tgctac-aataac--------ctagacttgtcgatttccagACAATCAACGACTGGTATGATAGAGATATCGACGCAATTAATGAGCCATATCGTCCAATTCCATCTGGAGCAATATCAGAGCCAGAG
|| |  ||||| |          | | |||  ||  ||   | || |    ||| |||        | |||| |||||         | | || |      ||  ||||| | || |||||||||||| |||| || || |||||||||||||| ||||| || |||||||| || || ||||||||    |||
gtttacttttaaattctctttgtcagccttcatttataccttcagagatgctgcgtgggagactatttctactaataagtatgtcagccaaacattcttgcttgtagACACTTAATGACTGGTATGATCGAGACATTGATGCAATTAATGAGCCTTATCGGCCTATTCCATCAGGTGCTATATCAGAAAACGAG

upper sequence: AT3G51820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0105g00590.t01 (Vitis vinifera), 3'ss of exon 5
--gtctggttttacacaacaaaaagctgacttgttctt------attctagtgcatttgcttggtgcta----caataacctagacttgtcgatttccagACAATCAACGACTGGTATGATAGAGATATCGACGCAATTAATGAGCCATATCGTCCAATTCCATCTGGAGCAATATCAGAGCCAGAG
    |    |  || ||| |     ||  | | | |||      || ||   | ||||| ||  ||  |       |      | |   |    ||  ||||| |||| || ||||||||| |||| || || ||||||||||| || |||||||| ||||| || || |||||||| ||    |||
actcccaaatgcactcaaaattgttcttgcctttgcttgaaaggatgcttaagaatttgattaatgtaaatttttgtgcttgtgtcaccttttcttttagACACTCAATGATTGGTATGATCGAGAGATTGATGCAATTAATGAACCTTATCGTCCTATTCCTTCAGGGGCAATATCCGAAAATGAG

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|125199514|gb|EL214468.1|EL214468
EST:     CGATTCTTTGCATGATGATGTCTGGTCCTTGTCTTACTGGCTATACACAG                         ACAATCAACGACTGGTATGATAGAGATATCGACG
genomic: CGATTCTTTGCATGATGATGTCTGGTCCTTGTCTTACTGGCTATACACAGgtctggtttt ... cgatttccagACAATCAACGACTGGTATGATAGAGATATCGACG
EST: gi|124778033|gb|EH867976.1|EH867976
EST:     CGATTCTTTGCATGATGATGTCTGGTCCTTGTCTTACTGGCTATACACAG                         ACAATCAAACGACTGGTATGATAGAGATATCG
genomic: CGATTCTTTGCATGATGATGTCTGGTCCTTGTCTTACTGGCTATACACAGgtctggtttt ... cgatttccagACAATCAA-CGACTGGTATGATAGAGATATCG
EST: gi|124863751|gb|EH948188.1|EH948188
EST:     CGATTCTTTGCATGATGATGTCTGGTCCTTGTCTTACTGGCTATACACAG                         ACAATCAACGACTGGTATGATAGAG
genomic: CGATTCTTTGCATGATGATGTCTGGTCCTTGTCTTACTGGCTATACACAGgtctggtttt ... cgatttccagACAATCAACGACTGGTATGATAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttattctagtgcatttgcttggtgctacaataacctagacttgtcgatttccagACAATCAACGACTGGTATGATAGAGATATCGACGCAATTAATGAGCCATATCGTCCAATTCCATCTGGAGCAATATCAGAGCCAGAG
                            caataac  putative branch site (score: 2)
                                                tttcc  putative PPT
                          tacaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctggttttacacaacaaaaagctgacttgttcttattctagtgcatttgcttggtgctacaataacctagacttgtcgatttccagACAATCAACGACTGGTATGATAGAGATATCGACGCAATTAATGAGCCATATCGTCCAATTCCATCTGGAGCAATATCAGAGCCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA