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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaatttgattctcattccatatataggagaagaatgatggcaaaatcggttttgatgtgacctagttgggatttccttgcttctattagagtgtcaaaatttggttgatccaggataagactgactcctattttgtgatctgtagGTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAG

Basic information

species Arabidopsis thaliana
transcript AT5G16440.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g36190.1 (Oryza sativa), 3'ss of exon 2
gtaagtgaatttgattctcattccatatataggagaagaatgatggcaaaatcggttttgatgtgacctagttgggatttccttgcttctattagagtgtcaaaatttggttgatccaggataagact-gactcctattttgtgatctgtagGTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAG
                                             | ||     ||| |  ||   |    ||   ||   | ||   | |  |   | |  ||  || |||  |   | |  | ||| ||||    |  | |||     ||| |||||||||||||| || ||| |||| ||| ||||||| || ||||||||||| ||  | |||||||| || |||||  | || ||||||
---------------------------------------------gtaagtgttgttatc-tgcatctctattcaaat---cctgtgcccaacattcttttgaa--ttagttatt--ggaacgatacttgacttgattcatttgac--acagGCCATCTGATGGAAAAAATCGAATCTGAAAATCTACTTCATAGGGCTTTCAGTGTATTCCTGTTCAACTCAAAATATGAACTCCTACTCCAG

upper sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G133082_T03 (Zea mays), 3'ss of exon 2
gtaagtgaatttgattctcattccatatataggagaagaatgatggcaaaatcggttttgatgtgacctagttgggatttccttgcttctattagagtgtcaaaatttggttgatccaggataagactgac--tcctattttgtga---tctgtagGTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAG--------
                                                 |||   || |||     | ||     || |||     |   |||  ||||||| | ||| | |  |     |      |     || || ||  | |     | |||| ||||| ||||| ||||| |||||||  |||   || ||||||||||||||||| ||  | ||||||||||| ||||||||||| || |||        
-----------------------------------------------ttaatgacttgtgac----cttaacccagagttc-----taacattgaagtgtcagattttagctactattacacttttttattcatcatacttgatcaataattatagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGCCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTGCAGGTATTCAC

upper sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G133082_T01 (Zea mays), 3'ss of exon 2
gtaagtgaatttgattctcattccatatataggagaagaatgatggcaaaatcggttttgatgtgacctagttgggatttccttgcttctattagagtgtcaaaatttggttgatccaggataagactgac--tcctattttgtga---tctgtagGTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAG
                                                 |||   || |||     | ||     || |||     |   |||  ||||||| | ||| | |  |     |      |     || || ||  | |     | |||| ||||| ||||| ||||| |||||||  |||   || ||||||||||||||||| ||  | ||||||||||| ||||||||||| || |||
-----------------------------------------------ttaatgacttgtgac----cttaacccagagttc-----taacattgaagtgtcagattttagctactattacacttttttattcatcatacttgatcaataattatagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGCCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTGCAG

upper sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G145029_T01 (Zea mays), 3'ss of exon 2
gtaagtgaatttgattctcattccatatataggagaagaatgatggcaaaatcggttttgatgtgacctagt-tgggatttccttgcttctattagagtgtcaaaatttggttgat------ccaggataagactgactcctattttgtgatctgtagGTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAG
                                                         ||||||     || | |   |      | ||   | |  ||||||| | ||| | || |      |  |  ||  | | |  | |  |   | || | |||| ||||| ||||| ||||| |||||||  ||| | || ||||||||||||||||| ||  | ||||||||||| ||||| ||||| || |||
---------------------------------------------------------ttgatgacttgtaatcttaaaccagagttctaacagtgaagtgtcagattttagctgctatcacacttgtttattaatcatacttgatcaataattt-tagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG

upper sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 2
gtaagtgaatttgattctcattccatatataggagaagaatgatggcaaaatcggttttgatgtgacctagttgggatttccttgcttctattagagtgtcaaaatttggttgatccaggataagactgactcctattttgtgatctgtagGTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAG-
                                           |    | |||   |||   ||   || ||||  |||    | || |  |  |  |      |  ||||| ||  |  ||  ||         ||||| |      |||||||  |||||||||||||||||||||||||||| || || |||||||||||||| ||  | |||||||| ||||||||||||||||| ||| 
------------------------------------------ctttagatatcaagtttt-cgttttct-gttgttattgtgctcctccgttctgcctac--ggacctggttaatttattatttgagctttaataattttat------taggTCACTTGATGGAAAAGATTGAAGCTGAGAATTTGCTGCATAGAGCTTTCAGTGTATTCCTGTTCAACTCTAAGTATGAGTTGCTTCTTCAGG

upper sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G38550.1 (Glycine max), 3'ss of exon 2
gtaagtgaatttgattctcattccatatataggagaagaatgatggcaaaatcggttttgatgtgacctagttgggatttccttgcttctattagagtgtcaaaatttggttgatccaggataagactgactcctattttgtgatctgtagGTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAG
                                    |  || ||  |||  |    |||  |||       ||| | | | | | ||  |  || ||       |  ||||| ||  |  ||        |    ||||| |      |||||||  |||||||||||||||||||||||||||| || || |||||||||||||| ||  | |||||||| ||||||||||||||||| |||
-----------------------------------tatcattatatcaagttttccttttctgttgtt--attgtgctcttcct-ctcttgctacag-------acctggttaatttattattttgtgctccaaaattttat------tagGTCACTTGATGGAAAAGATTGAAGCTGAGAATTTGCTGCATAGAGCTTTCAGTGTATTCCTGTTCAACTCAAAGTATGAGTTGCTTCTTCAG

upper sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0023g00600.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtgaatttgattctcattccatatataggagaagaatgatggcaaaatcggttttgatgtgacctagttgggatttccttgcttctattagagtgtcaaaat-ttggttgatccaggataagactgactcctattttgtgatctgtagGTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAG
                                              ||     |  ||  |      | |  ||  ||    ||| |  | | |  || |  | || |||||| |  ||  ||        || ||  |     || || ||||||| ||||||||||||||||| |||||||||| || ||||||||||||||||| ||| | || ||||| || | ||| || || || |||
-------------------------------------------ccacatgcatgaattgcactca--caatgtgacatcagattgatgtt-tcaatgtatggatatcttggtttactcatcattcag--agctactgctc----atttgcagGTCATTTGATGGAAAAGATTGAATCTGAGAATTTGCTGCACAGAGCTTTCAGTGTATTTCTGTTTAACTCGAAATTTGAATTACTCCTTCAG

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|86024853|gb|DR320606.1|DR320606
EST:     TATCGTTGATGAAAATGATCGTGTGGTGGGACATGACACTAAGTATAACT                         GTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCA
genomic: TCTCGTTGATGAAAATGATCGTGTGGTGGGACATGACACTAAGTATAACTgtaagtgaat ... tgatctgtagGTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCA
EST: gi|86024858|gb|DR320611.1|DR320611
EST:     TCTCGTTGATGAAAATGATCGTGTGGTGGGACATGACACTAAGTATAACT                         GTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCA
genomic: TCTCGTTGATGAAAATGATCGTGTGGTGGGACATGACACTAAGTATAACTgtaagtgaat ... tgatctgtagGTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCA
EST: gi|86024851|gb|DR320604.1|DR320604
EST:     TATCGTTGATGAAAATGATCGTGTGGTGGGACATGACACTAAGTATAACT                         GTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCA
genomic: TCTCGTTGATGAAAATGATCGTGTGGTGGGACATGACACTAAGTATAACTgtaagtgaat ... tgatctgtagGTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCA
EST: gi|86024854|gb|DR320607.1|DR320607
EST:     TCTCGTTGATGAAAATGATCGTGTGGTGGGACATGACACTAAGTATAACT                         GTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCA
genomic: TCTCGTTGATGAAAATGATCGTGTGGTGGGACATGACACTAAGTATAACTgtaagtgaat ... tgatctgtagGTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCA
EST: gi|86024862|gb|DR320615.1|DR320615
EST:     TCTCGTTGATGAAAATGATCGTGTGGTGGGACATGACACTAAGTATAACT                         GTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCA
genomic: TCTCGTTGATGAAAATGATCGTGTGGTGGGACATGACACTAAGTATAACTgtaagtgaat ... tgatctgtagGTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCA
EST: gi|86024861|gb|DR320614.1|DR320614
EST:     TCTCGTTGATGAAAATGATCGTGTGGTGGGACATGACACTAAGTATAACT                         GTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCA
genomic: TCTCGTTGATGAAAATGATCGTGTGGTGGGACATGACACTAAGTATAACTgtaagtgaat ... tgatctgtagGTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCA
EST: gi|86024856|gb|DR320609.1|DR320609
EST:     TCTCGTTGATGAAAATGATCGTGTGGTGGGACATGACACTAAGTATAACT                         GTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCA
genomic: TCTCGTTGATGAAAATGATCGTGTGGTGGGACATGACACTAAGTATAACTgtaagtgaat ... tgatctgtagGTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtcaaaatttggttgatccaggataagactgactcctattttgtgatctgtagGTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAG
                            gactgac  putative branch site (score: 2)
     aaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgaatttgattctcattccatatataggagaagaatgatggcaaaatcggttttgatgtgacctagttgggatttccttgcttctattagagtgtcaaaatttggttgatccaggataagactgactcctattttgtgatctgtagGTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT