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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatataatttttaaatggttcattttgcttactggagttgttaatattttgatgcctttgataattaattctgacgttaattgtatgccaacctttttgtcactttttttttcccatttgatttgatatgatagCAAATTCAGAACTTTGGGGAACCCTTTTTCTTGGTCATACATGAAGGGGAGACTTTGGCTGAAATTAAAGTAAGAATACAGAAGAAACTTCAAGTCCCTG

Basic information

species Glycine max
transcript GLYMA02G43930.1
intron # 28
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 28
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 28
gtatataatttttaaatggttcattttgcttactggagttgttaatattttg--atgcctttgataattaattctgacgttaattgtatgccaacctttttgtcactttttttttcccatttgatttgatatgatagCAAATTCAGAACTTTGGGGAACCCTTTTTCTTGGTCATACATGAAGGGGAGACTTTGGCTGAAATTAAAGTAAGAATACAGAAGAAACTTCAAGTCCCTG
                |   | ||| |   ||| |   ||    |   ||||  ||    | ||   |   | |||||   || | | |||  |   | |   | |||| ||  ||  ||||  | |  | ||||||||||||||||| || ||||| || |||||||||||||| ||||| || || ||| |||||||| |||| ||  | ||||||||||| || |  || || |
---------------gtaactaattata--taccgagattaactagggtttgtcatatactcgaatttctgtactgaca--aactatttgctgaaactgtaaac-ctttcttgctcaaatttcctcttgtttgatagCAAATTCAGAATTTCGGGGAGCCTTTTTTCTTGGTCATCCATGAGGGTGAAACTCTGGCTGAAGTTAAGGTGCGGATACAGAAGAAGCTGCTGGTTCCAG
















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|208164063|gb|GD959363.1|GD959363
EST:     GTCTAATCCATGTGTATCATTTCACTAAAGACACAGCTCAGAACCAAATG                         CAAATTCAGAACTTTGGG-A-CCCTTTT-CTTGGTCATACATG
genomic: GTCTAATCCATGTGTATCATTTCACTAAAGACACAGCTCAGAACCAAATGgtatataatt ... gatatgatagCAAATTCAGAACTTTGGGGAACCCTTTTTCTTGGTCATACATG
EST: gi|10231860|gb|BE800748.1|BE800748
EST:     GTCTAATCCATGTGTATCATTTCACTAAAGACACAGCTCAGAACCAAATG                         CAAATTCAGAACTTTGGGGAACCCTTTTTCTTGGTCATACATGAAGGGGAG
genomic: GTCTAATCCATGTGTATCATTTCACTAAAGACACAGCTCAGAACCAAATGgtatataatt ... gatatgatagCAAATTCAGAACTTTGGGGAACCCTTTTTCTTGGTCATACATGAAGGGGAG
EST: gi|208183465|gb|GD982849.1|GD982849
EST:     GTCTAATCCATGTGTATCATTTCACTAAAGACACAGCTCAGAACCAAATG                         CAAATTCAGAACTTTGGGGAACCCTTTT-CTTGGTCATACATGAAGGGGAG
genomic: GTCTAATCCATGTGTATCATTTCACTAAAGACACAGCTCAGAACCAAATGgtatataatt ... gatatgatagCAAATTCAGAACTTTGGGGAACCCTTTTTCTTGGTCATACATGAAGGGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtatgccaacctttttgtcactttttttttcccatttgatttgatatgatagCAAATTCAGAACTTTGGGGAACCCTTTTTCTTGGTCATACATGAAGGGGAGACTTTGGCTGAAATTAAAGTAAGAATACAGAAGAAACTTCAAGTCCCTG
                                    atttgatttgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatataatttttaaatggttcattttgcttactggagttgttaatattttgatgcctttgataattaattctgacgttaattgtatgccaacctttttgtcactttttttttcccatttgatttgatatgatagCAAATTCAGAACTTTGGGGAACCCTTTTTCTTGGTCATACATGAAGGGGAGACTTTGGCTGAAATTAAAGTAAGAATACAGAAGAAACTTCAAGTCCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA