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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacgacttctctttttcacttatactatatctctttttatttgattgaaattttttgacgaaaatattagagcgttgcaactaatccctccttatgactttccggtgtaatatatgaaccttgtctgaatttcaaagttgcccgttttaccatacagCGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAG

Basic information

species Arabidopsis thaliana
transcript AT2G21170.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os09g36450.1 (Oryza sativa), 3'ss of exon 4
gttacgacttctctttttcacttatactatatctctttttatttgattgaaattttttgacgaaaatattagagcgttgcaactaatccctccttatgactttccggtgtaatatatgaaccttgtctgaatttcaaagttgcccgttttaccatacagCGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAG
                                             |||    |   ||      ||| |||       ||||  |     |  ||     ||   | | | | |  || |  || | |   |||||      ||     |  | || || | ||| ||  |    ||| |||||||| | ||||| |||||||||||||| || || ||||||||||| || ||| | ||| ||
---------------------------------------------attatggtagctttg----aattttaagcaagcgcaaaaagataatttttt--gtttcttgttttcacac-tggagtttttatatgtttca------cctaaaatgtc-tatagTGCGGAGCAATTGGTGGACATTGGCTGCCAATGGGTTATTCTTGGGCATTCAGAGCGTAGACATGTCATTGGTGAAGATGATCAG

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G06740.1 (Glycine max), 3'ss of exon 4
gttacgacttctctttttcacttatactatatctctttttatttgattgaaattttttgacgaaaatattagagcgttgcaactaatccctccttatgactttccggtgtaatatatgaaccttgtctgaatttcaaagttgcccgttttaccatacagCGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAG
                                             |||    ||||   | |  |   | |   |  |   | |  | ||| ||| ||  | |  |    |||  |     ||||  |  | ||| |  |  | | |||        || ||||| || || ||||||||||||||||||||||| |||||||| ||||| || || |||||||| || |||||||| ||||||
---------------------------------------------attatggttttg-aatgtgatgttcaagccaattatattgttaccttcttgtggttctttgaacaaattca-----cttggttacacttccatctgactctttt--------agTGTGGAGCAACTAAAAGACCTTGGCTGCAAGTGGGTTATTCTTGGACATTCTGAGCGAAGACATGTAATTGGAGAAAATGATGAG

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 4
gttacgacttctctttttcacttatactatatctctttttatttgattgaaattttttgacgaaaatattagagcgttgcaactaatccctccttatgactttccggtgtaatatatgaaccttgtctgaatttcaaagttgcccgttttaccatacagCGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAG
                                                     ||||  | |  |   | |   |  |     |  | ||| ||| ||  | |  |    | |  |     ||||| |  | || |      || |  |    |   || ||||| || || ||||||||||||||||||||||| |||||||| ||||| || || |||||||| || |||||||| ||||||
--------------------------------------------------cggttttgaatgtgatgttcaagccaattatgttgttaccttcttgtggttctttgaacaagttca-----cttgtttacactt-acttccacctgactcttta---agTGTGGAGCAACTAAAAGACCTTGGCTGCAAGTGGGTTATTCTTGGACATTCTGAGCGAAGACATGTAATTGGAGAAAATGATGAG

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G34300.1 (Glycine max), 3'ss of exon 4
gttacgacttctctttttcacttatactatatctctttttatttgattgaaattttttgacgaaaatattagagcgttgcaactaatccctccttatgactttccggtgtaatatatgaacc--ttgtctgaatttcaaagttgcccgttttaccatacagCGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAG
                                                      ||    | || || |||      |     |  |        |  |   | |  ||||| |    |  |  |  | |   | | ||| |  |   || |    |  |||| |||||| || ||||| ||||| |||||||||||  ||||||| ||||| || || |||||||| || |||||||| ||||||
------------------------------------------------------ttacaccaaatatgttactattattttg-tggtggtcatcaactatgctacaatgtaacaagctattcagtcatttagttattaaaat--ctgattct----tgtagCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG

upper sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G36990.2 (Glycine max), 3'ss of exon 4
gttacgacttctctttttcacttatactatatctctttttatttgattgaaat-tttttgacgaaaatattagagcgttgcaactaatccctccttatgactttccggtgtaatatatgaaccttgtctgaatttcaaagttgcccgttttaccatacagCGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAG
                                              | |   | || |||| |  | | |  ||   ||| | | |||       ||  | ||   |   ||||  |   || | ||      || |||  || |  |||        |||| |||||| || ||||| ||||| |||||||||||  ||||||| ||||| || || |||||| | || |||||||| ||||||
----------------------------------------------tcgtgttgttcttgatgtgattct--gatgtttgaaccaaatgttatactacaatttaatgagttaattcagtcacttagtta----ttaaaacctgactcttt--------agCGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAG

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|125319164|gb|EL333249.1|EL333249
EST:     GGTCAGAACTCTTGGGTTGGGAAAGGTGGAGCCTTCACTGGTGAAATCAG                         CGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTG
genomic: GGTCAGAACTCTTGGGTTGGGAAAGGTGGAGCCTTCACTGGTGAAATCAGgttacgactt ... taccatacagCGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTG
EST: gi|47828644|gb|CK118328.1|CK118328
EST:     GGTCAGAACTCTTGGGTTGGGAAAGGTGGAGCCTTCACTGGTGAAATCAG                         CGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTC
genomic: GGTCAGAACTCTTGGGTTGGGAAAGGTGGAGCCTTCACTGGTGAAATCAGgttacgactt ... taccatacagCGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTC
EST: gi|164170692|gb|ES185221.1|ES185221
EST:     GGTGAAATCAG                         CGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTC
genomic: GGTGAAATCAGgttacgactt ... taccatacagCGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTC
EST: gi|47831761|gb|CK121445.1|CK121445
EST:     GGTCAGAACTCTTGGGTTGGGAAAGGTGGAGCCTTCACTGGTGAAATCAG                         CGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTC
genomic: GGTCAGAACTCTTGGGTTGGGAAAGGTGGAGCCTTCACTGGTGAAATCAGgttacgactt ... taccatacagCGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTC
EST: gi|116463095|gb|EG505687.1|EG505687
EST:     GGTCAGAACTCTTGGGTTGGGAAAGGTGGAGCCTTCACTGGTGAAATCAG                         CGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTC
genomic: GGTCAGAACTCTTGGGTTGGGAAAGGTGGAGCCTTCACTGGTGAAATCAGgttacgactt ... taccatacagCGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTC
EST: gi|125014999|gb|EL087268.1|EL087268
EST:     GGTCAGAACTCTTGGGTTGGGAAAGGTGGAGCCTTCACTGGTGAAATCAG                         CGTGGAACAGCTCAAAGACCTTGGCTGC
genomic: GGTCAGAACTCTTGGGTTGGGAAAGGTGGAGCCTTCACTGGTGAAATCAGgttacgactt ... taccatacagCGTGGAACAGCTCAAAGACCTTGGCTGC
EST: gi|116454376|gb|EG496968.1|EG496968
EST:     GGTCAGAACTCTTGGGTTGGGAAAGGTGGAGCCTTCACTGGTGAAATCAG                         CGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTC
genomic: GGTCAGAACTCTTGGGTTGGGAAAGGTGGAGCCTTCACTGGTGAAATCAGgttacgactt ... taccatacagCGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTC
EST: gi|124889702|gb|EH968604.1|EH968604
EST:     GGTCAGAACTCTTGGGTTGGGAAAGGTGGAGCCTTCACTGGTGAAATCAG                         CGTGGAACAGCTCAAAGAACCTTGGCTGCAAGTGGGTCATTCTTGG
genomic: GGTCAGAACTCTTGGGTTGGGAAAGGTGGAGCCTTCACTGGTGAAATCAGgttacgactt ... taccatacagCGTGGAACAGCTCAAAGA-CCTTGGCTGCAAGTGGGTCATTCTTGG
EST: gi|125006765|gb|EL079034.1|EL079034
EST:     GGTCAGAACTCTTGGGTTGGGAAAGGTGGAGCCTTCACTGGTGAAATCAG                         CGTGGAACAGCTCAAAGACCTTGG
genomic: GGTCAGAACTCTTGGGTTGGGAAAGGTGGAGCCTTCACTGGTGAAATCAGgttacgactt ... taccatacagCGTGGAACAGCTCAAAGACCTTGG
EST: gi|124997723|gb|EL069992.1|EL069992
EST:     TGGTGAAATCAG                         CGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTC
genomic: TGGTGAAATCAGgttacgactt ... taccatacagCGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggtgtaatatatgaaccttgtctgaatttcaaagttgcccgttttaccatacagCGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAG
                                      cccgtttt  CT-rich tract
     taatatatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacgacttctctttttcacttatactatatctctttttatttgattgaaattttttgacgaaaatattagagcgttgcaactaatccctccttatgactttccggtgtaatatatgaaccttgtctgaatttcaaagttgcccgttttaccatacagCGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG