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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCCATAAGCAGGAGCCTTTGACAACAGTCTTACGCCTTCTAATCCTATTTTCGATTACTAATTCTGGGTTGCCAAAGAAGCATTTTGACTACTTCAGgcaagctttcatgcttcattgatactttgtcctattcctttttttcattttgttacttttgtagatccttggaaattactaacctaaaatattattccctttctgccttttgtacaatatactagcaaatgttattttggagtacttagtgtattcttatatatttgtgacttccaatttatag

Basic information

species Glycine max
transcript GLYMA10G35210.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35210.2 (Glycine max), 5'ss of exon 15
lower sequence: LOC_Os04g14654.3 (Oryza sativa), 5'ss of exon 16
TGATCCATAAGCAGGAGCCTTTGACAACAGTCTTACGCCTTCTAATCCTATTTTCGATTACTAATTCTGGGTTGCCAAAGAAGCATTTTGACTACTTCAGgcaagctttcatgcttcattgatactttgtcctattcctttttttcattttgttacttttgtagatccttggaaattactaacctaaaatattattccctttctgccttttgtacaatatactagcaaatgttattttggagtacttagtgtattcttatatatttgtgacttccaatttatag
|||| ||||||||||||||| |   ||  ||  | ||||||||| |  || ||||  |||| ||| ||||||||||||||||| ||||||||||||| ||| | | ||   |   |  ||| |   |||   | |   | | ||  ||||| | ||  || |   | | |   | ||    | |||  |   |||        |                                                                                
TGATACATAAGCAGGAGCCTATTGAAAATGTTCTTCGCCTTCTAGTGTTACTTTCACTTACAAATGCTGGGTTGCCAAAGAAGAATTTTGACTACTTGAGgtatgtttatgttactttttg-tgtattgcttt-tgtttgtattaaattttatgaccattatcagttcat---atttttgcatctaggaggatatagtagcctta-------------------------------------------------------------------------------

upper sequence: GLYMA10G35210.2 (Glycine max), 5'ss of exon 15
lower sequence: Vv13s0019g04720.t01 (Vitis vinifera), 5'ss of exon 15
TGATCCATAAGCAGGAGCCTTTGACAACAGTCTTACGCCTTCTAATCCTATTTTCGATTACTAATTCTGGGTTGCCAAAGAAGCATTTTGACTACTTCAGgcaagctttcatgcttcattgatactttgtcctattcctttttttcattttgttacttttgtagatccttggaaattactaacctaaaatattattccctttctgccttttgtacaatatactagcaaatgttattttggagtacttagtgtattcttatatatttgtgacttccaatttatag
|||||||||||||||||||| |    |  ||| | |||||||| ||  ||||||| ||||| ||||| ||||| |||||||   ||||||| || || |||||||  |  |     ||   ||  ||| ||  ||   ||   |     || ||  |   | ||    |||  |||| | |   || |  | | ||    |||||| | ||    ||| | ||   || | ||    |||  ||                                        
TGATCCATAAGCAGGAGCCTCTTGTCAACGTCCTGCGCCTTCTCATTTTATTTTCAATTACAAATTCAGGGTTACCAAAGAGAAATTTTGATTATTTGAGgcaaggatgtacatgcca--aatcatttttctaataatttagatgtcactttttgttacagcaggatattgagaattgc-attttagagaaattttttacttctgcatcttcctaaatcttcttttaattttttccatggtttag---------------------------------------
















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|298183650|gb|HO028863.1|HO028863
EST:     TTTTCGATTACTAATTCTGGGTTGCCAAAGAAGCATTTTGACTACTTCAG                         GAGAGAACTACTCCACAGCTATGGATTTGAGCACATAGCAATGCTAAACAA
genomic: TTTTCGATTACTAATTCTGGGTTGCCAAAGAAGCATTTTGACTACTTCAGgcaagctttc ... caatttatagGAGAGAACTACTCCACAGCTATGGATTTGAGCACATAGCAATGCTAAACAA
EST: gi|192334521|gb|FK024480.1|FK024480
EST:     TTTTCGATTACTAATTCTGGGTTGCCAAAGAAGTATTTTGACTACTTCAG                         GAGAGAACTACTCCACAGCTATGGATTTGAGCACATAGCAATGCTAAACAA
genomic: TTTTCGATTACTAATTCTGGGTTGCCAAAGAAGCATTTTGACTACTTCAGgcaagctttc ... caatttatagGAGAGAACTACTCCACAGCTATGGATTTGAGCACATAGCAATGCTAAACAA
EST: gi|208058024|gb|GD859357.1|GD859357
EST:     TTTTCGATTACTAATTCTGGGTTGCCAAAGAAGCATTTTGACTACTTCAG                         GAGAGAACTACTCCACAGCTATGGATTTGAGCA
genomic: TTTTCGATTACTAATTCTGGGTTGCCAAAGAAGCATTTTGACTACTTCAGgcaagctttc ... caatttatagGAGAGAACTACTCCACAGCTATGGATTTGAGCA
EST: gi|120493752|gb|EH221919.1|EH221919
EST:     TTTTCGATTACTAATTCTGGGTTGCCAAAGAAGCATTTTGACTACTTCAG                         GAGAGAACTACTCCACAGCTATGGATTTGAGCACATAGCAATGCTAAACAA
genomic: TTTTCGATTACTAATTCTGGGTTGCCAAAGAAGCATTTTGACTACTTCAGgcaagctttc ... caatttatagGAGAGAACTACTCCACAGCTATGGATTTGAGCACATAGCAATGCTAAACAA
EST: gi|193384975|gb|FK351485.1|FK351485
EST:     GATTACTAATTCTGGGTTGCCAAAGAAGCATTTTGACTACTTCAG                         GAGAGAACTACTCCACAGCTATGGATTTGAGCACATAGCAATGCTAAACAA
genomic: GATTACTAATTCTGGGTTGCCAAAGAAGCATTTTGACTACTTCAGgcaagctttc ... caatttatagGAGAGAACTACTCCACAGCTATGGATTTGAGCACATAGCAATGCTAAACAA
EST: gi|193646811|gb|FK591366.1|FK591366
EST:     TTTTCGATTACTAATTCTGGGTTGCCAAAGAAGCATTTTGACTACTTCAG                         GAGAGAACTACTCCACAGCTATGGATTTGAGCACATAGCAATGCTAAACAA
genomic: TTTTCGATTACTAATTCTGGGTTGCCAAAGAAGCATTTTGACTACTTCAGgcaagctttc ... caatttatagGAGAGAACTACTCCACAGCTATGGATTTGAGCACATAGCAATGCTAAACAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATCCATAAGCAGGAGCCTTTGACAACAGTCTTACGCCTTCTAATCCTATTTTCGATTACTAATTCTGGGTTGCCAAAGAAGCATTTTGACTACTTCAGgcaagctttcatgcttcattgatactttgtcctattcctttttttcattttgttacttttgtagatccttggaaattactaacctaaaatattattccctttctgccttttgtacaatatactagcaaatgttattttggagtacttagtgtattcttatatatttgtgacttccaatttatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC