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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTTGAGTATGTTCCTGAGACTGTCCACCGAGTTATCAGACATTACAACAAAATGAATCAAAGAATGCCTTTGATATATGTGAAACTCTATTTTTACCAGgtactatattaaaatttattttcttctttcttgtaagttttactattaaggcaattgtctatatcactttgttggttctcatttcttctatttcttattttttag

Basic information

species Glycine max
transcript GLYMA10G01280.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G01280.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os05g04340.2 (Oryza sativa), 5'ss of exon 5
ACTTGAGTATGTTCCTGAGACTGTCCACCGAGTTATCAGACATTACAACAAAATGAATCAAAGAATGCCTTTGATATATGTGAAACTCTATTTTTACCAGgtactatattaaaattt-attttcttctttcttgtaagttttactattaaggcaattgtctatatcactttgttggttctcatttcttctatttcttattttttag
 ||||||||||| || |||||||  ||||| || || | |||||||||||| ||||| ||| | ||||| ||||||||||  ||||| ||  | || ||||||   |   | |  |  || ||||  | | |  ||      || |||| |   ||||  |||| || |        | | ||   |   |               
GCTTGAGTATGTGCCAGAGACTGCTCACCGTGTAATTAAACATTACAACAAGATGAACCAACGCATGCCATTGATATATGCAAAACTATACATGTATCAGgtaacgttacacacctagatcttctaatctatcctag----cacaattatgc--attgagtataaca-tggaaaacctattataattgacag--------------

upper sequence: GLYMA10G01280.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv07s0005g02100.t01 (Vitis vinifera), 5'ss of exon 5
ACTTGAGTATGTTCCTGAGACTGTCCACCGAGTTATCAGACATTACAACAAAATGAATCAAAGAATGCCTTTGATATATGTGAAACTCTATTTTTACCAGgtactatattaaa-atttattttcttctttcttgtaagttttactattaaggcaattgtctatatcactttgttggttctcatttcttctatttcttattttttag
 ||||||||||| ||||||||||| || || || |||| ||| ||||| || ||||| || || |||||  |||||||||||||||| ||   |||||||||  | ||||| | || ||| |  |    | || | |  ||| || ||       ||   |  |  |   |||||  | | || |||| ||| |   | | ||   
GCTTGAGTATGTCCCTGAGACTGTTCATCGGGTGATCAAACACTACAATAAGATGAACCAGAGGATGCCAATGATATATGTGAAACTTTACACTTACCAGgt-ttgtattatatatatatatagtctgattttattaactttgctgttttttatttttattccacaatcctgttgaattt-atatctt-tatatggcactatt---
















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|208064176|gb|GD862050.1|GD862050
EST:     AAATGAATCAAAGAATGCCTTTGATATATGTGAAACTCTATTTTTACCAG                         ATATGTAGAGCTCTAGCTTATATTCA
genomic: AAATGAATCAAAGAATGCCTTTGATATATGTGAAACTCTATTTTTACCAGgtactatatt ... tattttttagATATGTAGAGCTCTAGCTTATATTCA
EST: gi|193717136|gb|FK652146.1|FK652146
EST:     AAATGAATCAAAGAATGCCTTTGATATATGTGAAACCCTATTTTTACCAG                         ATATGTAGAGCTCTAGCTTATATTCACAACTGTATTGGAGTGTCTCACAGG
genomic: AAATGAATCAAAGAATGCCTTTGATATATGTGAAACTCTATTTTTACCAGgtactatatt ... tattttttagATATGTAGAGCTCTAGCTTATATTCACAACTGTATTGGAGTGTCTCACAGG
EST: gi|207704815|gb|GD684636.1|GD684636
EST:     AAATGAATCAAAGAATGCCTTTGATATATGTGAAACTCTATTTTTACCAG                         ATATGTAGAGCTCTAGCTTATATTCACAACTGTATTGGAGTGTCTCACAGG
genomic: AAATGAATCAAAGAATGCCTTTGATATATGTGAAACTCTATTTTTACCAGgtactatatt ... tattttttagATATGTAGAGCTCTAGCTTATATTCACAACTGTATTGGAGTGTCTCACAGG
EST: gi|208333681|gb|GE129554.1|GE129554
EST:     AAATGAATCAAAGAATGCCTTTGATATATGTGAAACTCTATTTTTACCAG                         ATATGTAGAGCTCTAGCTTATATTCACAACTGTATTGGAGTGTCTCACAGG
genomic: AAATGAATCAAAGAATGCCTTTGATATATGTGAAACTCTATTTTTACCAGgtactatatt ... tattttttagATATGTAGAGCTCTAGCTTATATTCACAACTGTATTGGAGTGTCTCACAGG
EST: gi|24205503|gb|BU964756.1|BU964756
EST:     AAATGAATCAAAGAATGCCTTTGATATATGTGAAACTCTATTTTTACCAG                         ATATGTAGAGCTCTAGCTTATATTCACAACTGTATTGGAGTGTCTCACAGG
genomic: AAATGAATCAAAGAATGCCTTTGATATATGTGAAACTCTATTTTTACCAGgtactatatt ... tattttttagATATGTAGAGCTCTAGCTTATATTCACAACTGTATTGGAGTGTCTCACAGG
EST: gi|208090264|gb|GD885285.1|GD885285
EST:     ATGAATCAAAGAATGCCTTTTGTATATATGTGAAACTCTATTTTTACCAG                         ATATGTAGAGCTCTAGCTTATATTCACAACTGTATTGGAGTGTCTCACAGG
genomic: ATGAATCAAAGAATGCC-TTTG-ATATATGTGAAACTCTATTTTTACCAGgtactatatt ... tattttttagATATGTAGAGCTCTAGCTTATATTCACAACTGTATTGGAGTGTCTCACAGG
EST: gi|151399753|gb|EV269624.1|EV269624
EST:     AAATGAATCAAAGAATGCCTTTGATATATGTGAAACTCTATTTTTACCAG                         ATATGTAGAGCTCTGGCTTATATTCACAACTGTATTGGAGTGTCTCACAGG
genomic: AAATGAATCAAAGAATGCCTTTGATATATGTGAAACTCTATTTTTACCAGgtactatatt ... tattttttagATATGTAGAGCTCTAGCTTATATTCACAACTGTATTGGAGTGTCTCACAGG
EST: gi|193317982|gb|FK284636.1|FK284636
EST:     AATC-AAGAATGCCTTTGATATATGTGAAACTCTATTTTTTACCAG                         ATATGTAGAGCTCTAGCTTATATTCACAACTGTATTGGAGTGTCTCACAGG
genomic: AATCAAAGAATGCCTTTGATATATGTGAAACTCTA-TTTTTACCAGgtactatatt ... tattttttagATATGTAGAGCTCTAGCTTATATTCACAACTGTATTGGAGTGTCTCACAGG
EST: gi|19453652|gb|BM955062.1|BM955062
EST:     AAATGAATCAAAGAATGCCTTTGATATACGTGAAACTCTATTTTTACCAG                         ATATGTAGAGCACTAGCTTATATTCACAACTGCATTGGAGTGTCTCACAGG
genomic: AAATGAATCAAAGAATGCCTTTGATATATGTGAAACTCTATTTTTACCAGgtactatatt ... tattttttagATATGTAGAGCTCTAGCTTATATTCACAACTGTATTGGAGTGTCTCACAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTGAGTATGTTCCTGAGACTGTCCACCGAGTTATCAGACATTACAACAAAATGAATCAAAGAATGCCTTTGATATATGTGAAACTCTATTTTTACCAGgtactatattaaaatttattttcttctttcttgtaagttttactattaaggcaattgtctatatcactttgttggttctcatttcttctatttcttattttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA