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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACTCCTCAGAAGTAAAGAAGACCGAGGTTCTCATGGAAAATTTTAGACGGGCCATTGGTCTGCGTATTAAGGAAAACAAGGAAGTATATGAAGGAGAGgtgagtttgtgctattctcttgtcaaaactcggatgtgattgtgccttgtacatattgtagtttatgttttgctggtcttgtttaag

Basic information

species Glycine max
transcript GLYMA07G02170.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G02170.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 3
TTACTCCTCAGAAGTAAAGAAGACCGAGGTTCTCATGGAAAATTTTAGACGGGCCATTGGTCTGCGTATTAAGGAAAACAAGGAAGTATATGAAGGAGAGgtgag---tttgtg-ctattctcttgtcaaaactcggatgtgattgtgccttgtacatattgtagtttatgttttgctggtcttgtttaag-----------
 ||||||||||| || ||||| || ||||| || |||||||||||  |  | || || ||| ||||||| ||||||||||| || || |||||||||||||| ||   |   ||  ||||     |  |||||    |   | || ||       | | ||    ||||    |||        ||| ||            
GTACTCCTCAGAGGTCAAGAAAACTGAGGTGCTGATGGAAAATTTCCGTAGAGCTATAGGTTTGCGTATAAAGGAAAACAAAGAGGTTTATGAAGGAGAGgtaagcaatgcatggttattaaagcggtaaaacgttaaaacg-ttatgaaccac-ctttttaacatttaaacgttgaaacgaacgttgaaacgtcttttcag

upper sequence: GLYMA07G02170.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G018697_T02 (Zea mays), 5'ss of exon 3
TTACTCCTCAGAAGTAAAGAAGACCGAGGTTCTCATGGAAAATTTTAGACGGGCCATTGGTCTGCGTATTAAGGAAAACAAGGAAGTATATGAAGGAGAGgtgagt--ttgtgctattctcttgtcaaaact---cggatgt--gattgtgcct-tgtacatattgtagtttatgttttgctggtcttgtttaag-------------------------------------------------------------------------------------------
 |||||||| || || ||||| || ||||| || |||||||||||  |  | || || ||| ||||||| ||||||||||| || || |||||||||||||| ||   | |   ||| | | |||| ||  |   || ||    |  | |   |   |   |  | |  ||||| | |   |||| ||  |||                                                                                             
GTACTCCTCGGAGGTCAAGAAAACTGAGGTGCTGATGGAAAATTTCCGTAGAGCTATAGGTTTGCGTATAAAGGAAAACAAAGAGGTTTATGAAGGAGAGgtaagcaatggatatatgcccatgtccaagttaaacgaatactaggctataattgcattagtgatttcctttatttatcaatggttttcattatcgctttgatagctgatgttccacttcgtgcttctataataaatttaccattgttagtctataataaatttaccagtgttgctctgttcctag

upper sequence: GLYMA07G02170.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 3
TTACTCCTCAGAAGTAAAGAAGACCGAGGTTCTCATGGAAAATTTTAGACGGGCCATTGGTCTGCGTATTAAGGAAAACAAGGAAGTATATGAAGGAGAGgtgagtt----tgtgctattctcttgtcaaaactcggatgtgattgtgccttgtacatattgtagtttatgttttgctggtcttgt--ttaag
|||||| ||||| || ||||| || |||||||||||||| ||||||||||| ||||||||||| ||||| ||||||| ||| ||||| |||||||| |||||| |||    | |||  ||   ||  |     ||  |||  || |    |    |  ||||  |||| ||   || ||  |||||  |  ||
TTACTCATCAGAGGTTAAGAAAACAGAGGTTCTCATGGAGAATTTTAGACGTGCCATTGGTCTACGTATCAAGGAAACCAAAGAAGTCTATGAAGGGGAGgtgtgttgctatttgcggtttcttttgctgtgttcttatgcaatagcatgtctcgctaattg--gtttttgacatgttgtccttgtgttctag

upper sequence: GLYMA07G02170.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 5'ss of exon 3
TTACTCCTCAGAAGTAAAGAAGACCGAGGTTCTCATGGAAAATTTTAGACGGGCCATTGGTCTGCGTATTAAGGAAAACAAGGAAGTATATGAAGGAGAGgtgagtttgtgcta---------ttctcttgtcaaaactcggatgtg---attgtgccttgtacatattgtagt-ttatgtttt------------gctggtcttgtttaag------
    || ||||| |||||||| || ||| || | |||||||||||  ||||||| |||||||| ||||| |||||||| |||||||| |||||||||||||  ||||    ||          || | |||| || | |  ||  ||    |  |  | ||  | | |||| || ||||  | |            |||  |||| |||| |      
----TCATCAGAGGTAAAGAAAACTGAGATTTTAATGGAAAATTTCCGACGGGCTATTGGTCTACGTATCAAGGAAAATAAGGAAGTGTATGAAGGAGAGGCAAgttatcactgattatgagttttttttgttaatagtttgacttgccagtaatatcatgatctttttgttgtattatcatctttaaatcaagtagcttctcttttttaggtgacag

upper sequence: GLYMA07G02170.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ33466 (Selaginella moellendorffii), 5'ss of exon 3
TTACTCCTCAGAAGTAAAGAAGACCGAGGTTCTCATGGAAAATTTTAGACGGGCCATTGGTCTGCGTATTAAGGAAAACAAGGAAGTATATGAAGGAGAGgtgagttt--gtgctattctcttgtcaaaactcggatgtgattgtgccttgtacatattgtagtttatgttttgctggtcttgtttaag
|| ||| || ||||| ||||||||||| |||||||||||||| ||| | ||  | || || |||||||| ||||| |  |||||||| || |||||||| ||  ||||   | |||   |    || || | |   |||   |  || || |   | ||  ||                          
TTTCTCTTCCGAAGTTAAGAAGACCGAAGTTCTCATGGAAAACTTTCGTCGCTCGATCGGCCTGCGTATAAAGGAGACGAAGGAAGTTTACGAAGGAGAAgtatgttttcattctaacattcattctaagcactt-tgtttcttcgctttttcttttttaaag--------------------------

upper sequence: GLYMA07G02170.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ27201 (Selaginella moellendorffii), 5'ss of exon 3
TTACTCCTCAGAAGTAAAGAAGACCGAGGTTCTCATGGAAAATTTTAGACGGGCCATTGGTCTGCGTATTAAGGAAAACAAGGAAGTATATGAAGGAGAGgtgagtttgtgctattctcttgtcaaaactcggatgtgattgtgccttgtacatattgtagtttatgttttgctggtcttgtttaag
|| ||| || ||||| ||||||||||| |||||||||||||| ||| | ||  | || || |||||||| ||||| |  |||||||| || |||||||| ||  ||||   | |||||    |  |  ||  |   |  ||||  |||   | | || |  ||||                      
TTTCTCTTCCGAAGTTAAGAAGACCGAAGTTCTCATGGAAAACTTTCGTCGCTCGATCGGCCTGCGTATAAAGGAGACGAAGGAAGTTTACGAAGGAGAAgtatgttt---ccattctaacattcattctaagcatt--ttgtttctt-cgctttttcttttttaaag-------------------

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|193705357|gb|FK644455.1|FK644455
EST:     GGGCCATTGGTCTGCGTATTAAGGAAAACAAGGAAGTATATGAAGGAGAG                         GTCACCGAGCTCTCTCCGGAAGAAACTGAGAGTGTTACAGGTGGTTATGGT
genomic: GGGCCATTGGTCTGCGTATTAAGGAAAACAAGGAAGTATATGAAGGAGAGgtgagtttgt ... cttgtttaagGTCACCGAGCTCTCTCCGGAAGAAACTGAGAGTGTTACAGGTGGTTATGGT
EST: gi|208079183|gb|GD874923.1|GD874923
EST:     GGGCCATTGGTCTGCGTATTAAGGAAAACAAGGAAGTATATGAAGGAGAG                         GTCACCGAGCTCTCTCCGGAAGAAACTGAGAGTGTTACAGGTGGTTATGGT
genomic: GGGCCATTGGTCTGCGTATTAAGGAAAACAAGGAAGTATATGAAGGAGAGgtgagtttgt ... cttgtttaagGTCACCGAGCTCTCTCCGGAAGAAACTGAGAGTGTTACAGGTGGTTATGGT
EST: gi|193646003|gb|FK588360.1|FK588360
EST:     GGGCCATTGGTCTGCGTATTAAGGAAAACAAGGAAGTATATGAAGGAGAG                         GTCACCGAGCTCTCTCCGGAAGAAACTGAGAGTGTTACAGGTGGTTATGGT
genomic: GGGCCATTGGTCTGCGTATTAAGGAAAACAAGGAAGTATATGAAGGAGAGgtgagtttgt ... cttgtttaagGTCACCGAGCTCTCTCCGGAAGAAACTGAGAGTGTTACAGGTGGTTATGGT
EST: gi|151398565|gb|EV268436.1|EV268436
EST:     AAGGAAAACAAGGAAGTATATGAAGGAGAG                         GTCACCGAGCTCTCTCCGGAAGAAACTGAGAGTGTTACAGGTGGTTATGGT
genomic: AAGGAAAACAAGGAAGTATATGAAGGAGAGgtgagtttgt ... cttgtttaagGTCACCGAGCTCTCTCCGGAAGAAACTGAGAGTGTTACAGGTGGTTATGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACTCCTCAGAAGTAAAGAAGACCGAGGTTCTCATGGAAAATTTTAGACGGGCCATTGGTCTGCGTATTAAGGAAAACAAGGAAGTATATGAAGGAGAGgtgagtttgtgctattctcttgtcaaaactcggatgtgattgtgccttgtacatattgtagtttatgttttgctggtcttgtttaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA