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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaattagttctaacgaaacaaaattatgaaactagattgaaccttctttttatgtgctaaaactgaagctaatgctattgaattgtctctttggaacagCCATTCAAGGACATGATCGAAGGGATGAGGATGGACCTGAGAAAGTCAAGATACGATAACTTTGATGAGCTCTACCTTTATTGCTACTATGTTGCTGGGA

Basic information

species Glycine max
transcript GLYMA02G45270.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G45270.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g43130.1 (Oryza sativa), 3'ss of exon 3
----------ctaattagttctaacgaaacaaaattatgaaactagattgaaccttctttttatgtgctaaaactgaagc-----------taatgctattgaattgt------ctctttgg--aacagCCATTCAAGGACATGATCGAAGGGATGAGGATGGACCTGAGAAAGTCAAGATACGATAACTTTGATGAGCTCTACCTTTATTGCTACTATGTTGCTGGGA
          | ||  || |      |||  |   ||||||      || ||  || ||  ||     ||||   |   |           | ||| |  || |  ||      ||||||     |||||||||||| |||||||| ||||| |||||| | |||||| | || ||||| ||    | |||||||||||||||||| || |||||||| |||||||| |
gtacagccaacaaaaaagctactgtaaaagcaggatatgaagtgcttttaaaagttattagtacacagtaaattggtgacacgcatttgtctgatgtttctgcaccgtcgggatctcttttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGGTATAGGAGCTTTGATGAGCTCTACCTCTACTGCTACTACGTTGCTGGCA

upper sequence: GLYMA02G45270.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0028g00960.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------------------------------------ctaattagttc-taacgaaacaaaattatgaaactagattgaaccttctttttatgtgctaaaactgaagctaatgc-tattga-attgtctctttggaacagCCATTCAAGGACATGATCGAAGGGATGAGGATGGACCTGAGAAAGTCAAGATACGATAACTTTGATGAGCTCTACCTTTATTGCTACTATGTTGCTGGGA
                                                                                      | || |||   ||    |     |    | |  ||   ||  ||||  | |    ||   | |   |  ||    | | || | | | |   |||    ||||| ||||| |||||||| ||||| |||||  ||||||||||||| ||||||||| | | ||||||||||||||| || || ||||| ||||||||||| |
gtacatttatatgggctcaaaactgattcacccatcttgcattttagctgctaatcaacctatgaacacgcacacatatgaacatttgatgagtaggtagtacattgtgacagagcacatattatgggcctttctgtatcatgaatatataaacacttccacatgttaataattttctttttatgcagCCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGAGAAAATCAAGATACAACAGCTTTGATGAGCTCTATCTGTACTGCTATTATGTTGCTGGAA
















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|207765619|gb|GD736424.1|GD736424
EST:     ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCAGTTGATATTCAG                         CCATTCAAGGACATGATCGAAGGGATGAGGA
genomic: ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCAGTTGATATTCAGgtactttaca ... tttggaacagCCATTCAAGGACATGATCGAAGGGATGAGGA
EST: gi|193636975|gb|FK579882.1|FK579882
EST:     ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCAGTTGATATTCAG                         CCATTCAAGGACATGATCGAAGGGATGAGGATGGACCTGAGAAAGTCAAGA
genomic: ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCAGTTGATATTCAGgtactttaca ... tttggaacagCCATTCAAGGACATGATCGAAGGGATGAGGATGGACCTGAGAAAGTCAAGA
EST: gi|193490445|gb|FK454142.1|FK454142
EST:     GTACCCAGTTGATATTCAG                         CCATTCAAGGACATGATCGGAAGGGATGAGGATGGACCTGAGAAAGTCAAG
genomic: GTACCCAGTTGATATTCAGgtactttaca ... tttggaacagCCATTCAAGGACATGATC-GAAGGGATGAGGATGGACCTGAGAAAGTCAAG
EST: gi|193666717|gb|FK608842.1|FK608842
EST:     ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCAGTTGATATTCAG                         CCATTCAAGGACATGATCGAAGGGATGAGGATGGACCTGAGAAAGTCAAGA
genomic: ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCAGTTGATATTCAGgtactttaca ... tttggaacagCCATTCAAGGACATGATCGAAGGGATGAGGATGGACCTGAGAAAGTCAAGA
EST: gi|193601589|gb|FK553484.1|FK553484
EST:     ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCAGTTGATATTCAG                         CCATTCAAGGACATGATCGAAGGGATGAGGATGGACCTGAGAAAGTCAAGA
genomic: ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCAGTTGATATTCAGgtactttaca ... tttggaacagCCATTCAAGGACATGATCGAAGGGATGAGGATGGACCTGAGAAAGTCAAGA
EST: gi|151405365|gb|EV275179.1|EV275179
EST:     ATGATGCTGCCCTCTCACATACTGTC--AAAGTACCCAGTTGATATTCAG                         CCATTCAAGGACATGATCGAAAGGATGAGGATGGACCTGAGAAAGTCAAGA
genomic: ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCAGTTGATATTCAGgtactttaca ... tttggaacagCCATTCAAGGACATGATCGAAGGGATGAGGATGGACCTGAGAAAGTCAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttttatgtgctaaaactgaagctaatgctattgaattgtctctttggaacagCCATTCAAGGACATGATCGAAGGGATGAGGATGGACCTGAGAAAGTCAAGATACGATAACTTTGATGAGCTCTACCTTTATTGCTACTATGTTGCTGGGA
                                      ttgtctcttt  CT-rich tract
                               tattgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaattagttctaacgaaacaaaattatgaaactagattgaaccttctttttatgtgctaaaactgaagctaatgctattgaattgtctctttggaacagCCATTCAAGGACATGATCGAAGGGATGAGGATGGACCTGAGAAAGTCAAGATACGATAACTTTGATGAGCTCTACCTTTATTGCTACTATGTTGCTGGGA

- - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctattg