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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaacagatttacaagctaggagctgcaacagttcttttgtatcttttgttaaactggaacccaccatttgcatttgtgttacagCTTGATGACGTTATCGATCTTGTGATCCCAAGAGGAAGCAACAAGCTTGTTACTCAGATAAAAAATACTACAAAAATCCCTGTGCTAGGTCATGCTG

Basic information

species Arabidopsis thaliana
transcript AT2G39800.4
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G39800.4 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
gtaagaacagatttacaagctaggagctgcaacagttcttttgtatcttttgttaaactggaacccaccatttgcatttgtgttacagCTTGATGACGTTATCGATCTTGTGATCCCAAGAGGAAGCAACAAGCTTGTTACTCAGATAAAAAATACTACAAAAATCCCTGTGCTAGGTCATGCTG
           | | |||      |  | |||     | ||  ||       ||   ||  |||||   ||   |   ||||   ||||||||||| || || |||||||| || ||||||||||| || ||||||||  |||| || ||     | || || || ||||| || || |||||||
------gtgtgtatgcaattctatattttcaaag---cgttgatactaccaatttggcta-aacccgtaatacac---tgtg---cagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG

upper sequence: AT2G39800.4 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA02G41850.1 (Glycine max), 3'ss of exon 9
gtaagaacagatttacaagctaggagctgcaacagttcttttgtatcttttgttaaactggaacccacca--tttgcatttgtgttacagCTTGATGACGTTATCGATCTTGTGATCCCAAGAGGAAGCAACAAGCTTGTTACTCAGATAAAAAATACTACAAAAATCCCTGTGCTAGGTCATGCTG
          | | |  ||   ||||||  ||      |||  || |  |  | |   |         ||  |||  ||||   || ||||| ||||| || |||||||| ||||| |||||||| |||||||| |||||| ||||||| || | | | || ||||| |||||  ||||||||||||
------gtgaactaatcagt--ggagct-taatttcagtttcataaccctgttcaccttaagcattggcacctttctatttaaatttcagCTGGATGATGTAATCGATCTGGTGATTCCAAGAGGCAGCAACAAACTTGTTTCTCAGATCAAGAGTTCCACTAAAATTCCTGTTTTAGGTCATGCTG

upper sequence: AT2G39800.4 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 12
-------------gtaagaacagat-ttacaagctaggagctgcaacagttcttttgtatcttttgttaaactgga-------acccaccatttgcattt-gtgttacagCTTGATGACGTTATCGATCTTGTGATCCCAAGAGGAAGCAACAAGCTTGTTACTCAGATAAAAAATACTACAAAAATCCCTGTGCTAGGTCATGCTG
              | ||||      ||   || ||  | |      | ||      |     |    ||| ||||       || ||  ||||   ||| ||| | ||||||||||| || ||||| ||||| ||||||||||| ||||| || |||||| |||| |||||  || | |||||||| ||||| || || |||||||
gtgagctgatgtgctgagaatgatcattgatagttaaaaacatttgaactttcagaatggtgatatgaaaaatggatgttcacactcagtatttttgttttgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG

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|116479708|gb|EG522300.1|EG522300
EST:     CAAGAGAAGAGATTCCTGATTTGCTTAAAG                         CTTGATGACGTTATCGATCTTGTGATCCCAAGAGGAAGCAACAAGCTTGT
genomic: CAAGAGAAGAGATTCCTGATTTGCTT-AAGgtaagaacag ... tgtgttacagCTTGATGACGTTATCGATCTTGTGATCCCAAGAGGAAGCAACAAGCTTGT
EST: gi|116452373|gb|EG494965.1|EG494965
EST:     AACTCATTGGACTTGTGACTTCAAGAGAAGAGATTCCTGATTTGCTTAAG                         CTTGATGACGTTATCGATCTTGTGATCCCAAGAGGAAGCAACAAGCTTGTT
genomic: AACTCATTGGACTTGTGACTTCAAGAGAAGAGATTCCTGATTTGCTTAAGgtaagaacag ... tgtgttacagCTTGATGACGTTATCGATCTTGTGATCCCAAGAGGAAGCAACAAGCTTGTT
EST: gi|47832219|gb|CK121903.1|CK121903
EST:     AACTCATTGGACTTGTGACTTCAAGAGAAGAGATTCCTGATTTGCTTAAG                         CTTGATGACGTTATCGATCTTGTGATCCCAAGAGGAAGCAACAAGCTTGTT
genomic: AACTCATTGGACTTGTGACTTCAAGAGAAGAGATTCCTGATTTGCTTAAGgtaagaacag ... tgtgttacagCTTGATGACGTTATCGATCTTGTGATCCCAAGAGGAAGCAACAAGCTTGTT
EST: gi|86060515|gb|DR356272.1|DR356272
EST:     AACTCATTGGACTTGTGACTTCAAGAGAAGAGATTCCTGATTTGCTTAAG                         CTTGATGACGTTATCGATCTTGTGATCCCAAGAGGAAGCAACAAGCTTGTT
genomic: AACTCATTGGACTTGTGACTTCAAGAGAAGAGATTCCTGATTTGCTTAAGgtaagaacag ... tgtgttacagCTTGATGACGTTATCGATCTTGTGATCCCAAGAGGAAGCAACAAGCTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttcttttgtatcttttgttaaactggaacccaccatttgcatttgtgttacagCTTGATGACGTTATCGATCTTGTGATCCCAAGAGGAAGCAACAAGCTTGTTACTCAGATAAAAAATACTACAAAAATCCCTGTGCTAGGTCATGCTG
          tatcttttgttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaacagatttacaagctaggagctgcaacagttcttttgtatcttttgttaaactggaacccaccatttgcatttgtgttacagCTTGATGACGTTATCGATCTTGTGATCCCAAGAGGAAGCAACAAGCTTGTTACTCAGATAAAAAATACTACAAAAATCCCTGTGCTAGGTCATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG