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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatatactctccatgtgtcaattttaaaggattgacctacctgaagtttctaatggttcttttgctaaaaattcttgttcatgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG

Basic information

species Arabidopsis thaliana
transcript AT2G44350.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 13
------------gtatgtatatactctccatgtgtcaattttaaaggattgacctacctgaagtttctaatggttcttttgctaaaaattcttgttcatgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG
            |   | |  | | |||  | | ||  | |   | || | | |||   | | |  |   |   |    |||| |  ||  |   | |   ||||||| ||||| || |||||||| ||||| || |||||||||||| | |||||||||||||| ||  | || ||  |||||||||||
ttattttcttttgctggcaattgc-ctctctctctctctctctcatgactcatctatgggcactgacctcttcattccgtgctcatgatattcaattac--agGTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCGTTGCACGGCCTGGCTAATCAG

upper sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
-gtatgtatatactctccatgtgtcaattttaaaggat------tgacctacctgaagtttctaatggttcttttgctaaaaattcttgttca--tgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG
  |||   | |  | | | | |||      |     ||      ||||  | ||   |   ||||    |   |  |  |    |  | ||||  |  ||||||| ||||| || ||||| || ||||| || |||||||||||| | |||||||||||||| ||| | || ||  |||||||||||
gatatactttttttttacttttgttggccattgcctatctctcatgactcatctctgggcactaacctcttcatcccatacttgtgatattcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG

upper sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 14
--------gtatgta-tatactctccatgtgtcaattttaaaggattgacctacctgaagtttctaatggttcttttgctaaaaattcttgttca--tgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG
        |  || |   | ||  | |  |||   ||||      |   | |  |    | ||  | |  | ||| |||| |   | ||  | ||  || ||||||| ||||| || ||||| || ||||| || || ||||| ||  ||||||| |||||||||||||| |||||  | || ||||||
ctttaattgcttgcaacctgctagctac-tgttttttttgccatgtgaccatgtccttgggtttgacttat-cttctgctcatggtactcatccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG

upper sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA15G42300.2 (Glycine max), 3'ss of exon 13
---------------------------------------------------------------------------------------------------gtatgtatatactctccatgtgtcaattttaaaggattgacctacctgaagtttctaatggttcttttgctaaaaattcttgttcatgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG
                                                                                                   || | | |||  | |  || | |  || |  |   ||  |  ||  |  |  |  |||||  | || | ||     |||  ||      |||||| |||| | || ||||| || |||||  ||||||||||||| || ||||| ||||||||||| || ||||||||||| ||||||
gtaagttacttcctttaatcaagccctttccattctgtcataatttagaattgtaaaacattaaaaaggattttttaatatatattgtggtaaaggcctgtgtttttattatatatatatatatatatatatatatatatatatatatatatattaatg--tattgtactgtgtgttcccgtc-----agGTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAATGGGTTAGCTGGGCCCCTGCATGGTTTGGCCAATCAG

upper sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 13
--------------------------------------------------------------------------------------------------------gtatgtat-atactctccatgtgtcaattttaaaggattgacctacc-tgaagtttctaatggt-tcttttgctaaaaattcttgttcatgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG
                                                                                                         ||||  | ||| | ||  |  ||   |||   |  ||| |   | | |||||     |||| | ||| |||    | ||| |  |  ||  |||||| ||||||| |  |||| || || || |||||||||||||||||||||||| ||||||| |||||||||||||||||||| |||
gtaagtgagcctagattcgttctaattagttaaatggaaatgtgtaattttgttgtatttccgagggtaaagtcattattttatcctgaagttatttaatggaattatggctcatattttcagtcagtgtgtttgttattatttagtgatcatgaagag--gaatgttctctattgactgatattatgctcaattcagGTTGCTAGTGCATTGGCAGATCCTTACCTTTCATTTGCAGCTGCATTAAATGGTCTAGCTGGCCCACTCCATGGTTTGGCTAACCAG

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|116471055|gb|EG513647.1|EG513647
EST:     TGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG                         GTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAAT
genomic: TGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTGgtatgtatat ... gttcatgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAAT
EST: gi|164140704|gb|ES206886.1|ES206886
EST:     GCTCACACTGGTCACCTG                         GTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAAT
genomic: GCTCACACTGGTCACCTGgtatgtatat ... gttcatgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAAT
EST: gi|47832067|gb|CK121751.1|CK121751
EST:     TGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG                         GTTGGTAGTGCACTTTCAGACCCATATCTGTCA
genomic: TGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTGgtatgtatat ... gttcatgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCA
EST: gi|116453292|gb|EG495884.1|EG495884
EST:     TGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG                         GTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAAT
genomic: TGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTGgtatgtatat ... gttcatgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAAT
EST: gi|164010800|gb|ES076008.1|ES076008
EST:     GTTAGTGCTCACACTGGTCACCTG                         GTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAAT
genomic: GTTAGTGCTCACACTGGTCACCTGgtatgtatat ... gttcatgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAAT
EST: gi|301502837|gb|HO208377.1|HO208377
EST:     TGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG                         GTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAAT
genomic: TGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTGgtatgtatat ... gttcatgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAAT
EST: gi|124942076|gb|EL018374.1|EL018374
EST:     GTGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG                         GTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCA
genomic: GTGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTGgtatgtatat ... gttcatgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacctacctgaagtttctaatggttcttttgctaaaaattcttgttcatgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG
                               tgctaaa  putative branch site (score: 2)
                                        ttcttgttc  putative PPT
                            ttttgctaaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatatactctccatgtgtcaattttaaaggattgacctacctgaagtttctaatggttcttttgctaaaaattcttgttcatgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC