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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttaggaatccgtatttatattcacctgaaatagagtttgagattctgatagttatggatgtaacagtagtatttattgtaagatttttgtttccctgagataatatctgataagtagtaagtctaagtatatcaatttgacacagAATTCAAGGATGACCCAGAACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAG

Basic information

species Arabidopsis thaliana
transcript AT1G56340.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G28890.2 (Glycine max), 3'ss of exon 8
gtaatttaggaatccgtatttatattcacctgaaatagagtttgagattctgatagttatggatgtaacagtagtatttattgtaagatttttgtttccctgagataatatctgataagtagtaagtctaagtatatcaatttgacacagAATTCAAGGATGACCCAGAACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAG
                                       |||    ||    | | |  |  |      |||| ||||| || |||  | |||       | |||||| || |  | |  | |      ||  | ||   |      |||| |||||||||||||| || |||||||| |||||||| |||||||| || ||  |||| |||||||||
---------------------------------------gttcattat----acactcttctacaccgtagtaatattt-ttataaattattttgcattataagataa-atatattcaacatttg----aaaaacatttgt------cagATTTCAAGGATGACCCCGACCTCTATGTTTTCCCCAACTTGAAGTACGTGGGGATTGAATTGTGGCAG

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 8
gtaatttaggaatccgtatttatattcacctgaaatagagtttgagattctgatagttatggatgtaacagtagtatttattgtaagatttttgtttccctgagataatatctgataagtagtaagtctaagtatatcaatttgacacagAATTCAAGGATGACCCAGAACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAG
                                       |||    ||    |      |  |   |  |||| ||||||| ||||  | |||    |  | |||||| || |  | || | |      ||  | ||  ||      |||| |||||||||||||| || || ||||| |||||||| |||||||| || ||  |||| |||||||||
---------------------------------------gttcattat----acgcccttctacacagtagtaatatttat-gtaaattcttttgcactataagataa-atatattcagcatttg----aaaaacatttat------cagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 8
gtaatttaggaatccgtatttatattcacctgaaatagagtttgagattctgatagttatggatgtaacagtagtatttattgtaagatttttgtttccctgagataatatctgataagtagtaagtctaagtatatcaatttgacacagAATTCAAGGATGACCCAGAACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAG
                                                     |   |||  ||| | | |     | |||   |   || || |||    |   |  | ||  | |   ||  | |   |   | |  || |   ||||| ||||| |||||||||||  ||||||| |||||| | ||||||||||| ||  ||||  | ||||||
----------------------------------------------------gttcctatccatgcacctgcttcttctatgccatagttatttttt----ggtttggtctc-aacattcagacacttataaactgttcatattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG

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|125241870|gb|EL255955.1|EL255955
EST:     GAACCCCGCTTACAAGGGCAAGTGGAAGGCTCCAATGATCGACAACCCTG                         AATTCAAGGATGACCCAG
genomic: GAACCCCGCTTACAAGGGCAAGTGGAAGGCTCCAATGATCGACAACCCTGgtaatttagg ... tttgacacagAATTCAAGGATGACCCAG
EST: gi|125301959|gb|EL316044.1|EL316044
EST:     AGGGCAAGTGGAAGGCTCCAATGATCGACAACCCTG                         AATTCAAGGATGACCCAGAACTCTATGTCTTCCCCAAATTGAAGTATGTTG
genomic: AGGGCAAGTGGAAGGCTCCAATGATCGACAACCCTGgtaatttagg ... tttgacacagAATTCAAGGATGACCCAGAACTCTATGTCTTCCCCAAATTGAAGTATGTTG
EST: gi|125070099|gb|EL135638.1|EL135638
EST:     AAGGCTCCAATGATCGACAACCCTG                         AATTCAAGGATGACCCAGAACTCTATGTCTTCCC-AAATTGAAGTATGTTG
genomic: AAGGCTCCAATGATCGACAACCCTGgtaatttagg ... tttgacacagAATTCAAGGATGACCCAGAACTCTATGTCTTCCCCAAATTGAAGTATGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccctgagataatatctgataagtagtaagtctaagtatatcaatttgacacagAATTCAAGGATGACCCAGAACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAG
                                            atttgac  putative branch site (score: 4)
                                 taagtatatcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttaggaatccgtatttatattcacctgaaatagagtttgagattctgatagttatggatgtaacagtagtatttattgtaagatttttgtttccctgagataatatctgataagtagtaagtctaagtatatcaatttgacacagAATTCAAGGATGACCCAGAACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG