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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGAGCAAGGCATTCAAGAAATACAACAGCAAATTGGTGAAGTTAATGAGATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttattccatttccttttgttcttcctgattacttgcatctttattttactgaatgaatttatttttctgtacctgttcacgctatctaatgccactaaatttcattttgtag

Basic information

species Glycine max
transcript GLYMA16G08200.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G08200.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os01g15110.1 (Oryza sativa), 5'ss of exon 5
AGGGAGCAAGGCATTCAAGAAATACAACAGCAAATTGGTGAAGTTAATGAGATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttattccatttccttttgttcttcctgattacttgcatctt--tattttactgaatgaatttatttttctgtacctgttcacgctatctaatgcc--actaaatttcattttgtag
||||| || || || |||||||| || || ||||||  |||||| ||||| |||||||||||||||||||| || ||||| || ||||||   ||||||||||  |  | || ||     |  |   |   |||||  |||   ||  ||  ||   | | ||   |  |  | | | |  ||      ||||| ||     |     |   ||  || ||
AGGGATCAGGGAATACAAGAAATTCAGCACCAAATTACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTTCTAGTCCACGATCAAGGACAAATGATTGgtatgtggtaccgttggggatgatagatgg-gattatgtgctatttgatacgttgaagcacgaggctgctcatatat-ctggtatgttatatctgattgtgtatctcctcctatactgcag

upper sequence: GLYMA16G08200.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G120115_T01 (Zea mays), 5'ss of exon 5
AGGGAGCAAGGCATTCAAGAAATACAACAGCAAATTGGTGAAGTTAATGAGATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttattccatttccttttgttcttcctgattacttgcatctttattttactgaatgaatttatttttctgtacctgttcacgctatctaatgccactaaatttcattttgtag-----
||||| || || || ||||| || ||||| |||||   |||||| ||||| ||||||||||||||||||||||| |||||||| |||||||| ||||| ||||                | ||  ||||||    | ||| || |  |||| |     |  |   ||   ||||  |||  |  | | |||||||     |   | || ||||||       
AGGGATCAGGGAATACAAGAGATTCAACACCAAATCACTGAAGTAAATGAAATCTTCAAAGATCTTGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgta----------------tgtgaccttccttgcaaattggatatacatttcaacacgttcaagcataaatctg--cctacttcc-ccatctaattgtgtt---tctccttttgtgaaccag

upper sequence: GLYMA16G08200.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G017329_T01 (Zea mays), 5'ss of exon 5
AGGGAGCAAGGCATTCAAGAAATACAACAGCAAATTGGTGAAGTTAATGAGATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttattccatttccttttgttcttcctgattacttgcatctttattttactgaatgaatttatttttctgtacctgttcacgctatctaatgccactaaatttcattttgtag
||||| || || || ||||| || || || |||||   |||||| ||||| |||||||||||||| |||||||| |||||||| |||||||| ||||| |||   |    || ||        ||    ||    | ||  |  |||  |   |   ||| |||  |||| | | || || |         |         |||||| |        
AGGGATCAGGGAATACAAGAGATTCAGCACCAAATCACTGAAGTAAATGAAATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtgg--cctttctgaaaaattggatcta--cattttgaaatttcctacgccacatggattatttttacggcacatgattgga-----tgggattggaaaatttta--------

upper sequence: GLYMA16G08200.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G108087_T01 (Zea mays), 5'ss of exon 5
AGGGAGCAAGGCATTCAAGAAATACAACAGCAAATTGGTGAAGTTAATGAGATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttattccatttccttttgttcttcctgattacttgcatctt-tattttactgaatgaatttatttttctgtacctgttcacgctatctaatgccactaaatttcattttgtag
|||||||||| ||||||||| || |||||||| |||||||||||  ||||  | |||||||||||||||   ||||| |||   ||||||  ||| || || || |  || ||||   || ||    | |||  | || |  | |    | |||   || |  |  | |   |||| || |                                     
AGGGAGCAAGCCATTCAAGATATCCAACAGCAGATTGGTGAAGTACATGAAGTGTTCAAAGATCTTGCTACCCTTGTGCATTCCCAAGGAATCATAATCGgcaagtctttacattgtattgtgcatatgctg--tcctagtttttagcttcttagctaacgtgtacactgccctgttccag-------------------------------------

upper sequence: GLYMA16G08200.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G015509_T01 (Zea mays), 5'ss of exon 4
AGGGAGCAAGGCATTCAAGAAATACAACAGCAAATTGGTGAAGTTAATGAGATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttattccatttccttttgttcttcctgattacttgcatctttattttactgaatgaatttatttttctgtacctgttcacgctatctaatgccactaaatttcattttgtag--
||||| || || || ||||| || || || ||||||  |||||| || || || |||||||||||||||||||| || ||||  |||||||| ||||||||||  | |    |            | |    | |   ||||  || ||     |||    | ||  |||| | ||  |  |||   ||||||||   | |   | |  ||| ||    
AGGGATCAGGGAATACAAGAGATTCAGCACCAAATTACTGAAGTAAACGAAATTTTCAAAGATCTTGCTGTGCTAGTTCATGGTCAAGGAGCAATGATTGgtatgtgacctga------------cgtatgaaatttctgcagtttgatgggtttgagc--acttgattttgt-tatttcatcaatttatctaattatatttcttcttgtttggttcag

upper sequence: GLYMA16G08200.1 (Glycine max), 5'ss of exon 5
lower sequence: AT5G46860.1 (Arabidopsis thaliana), 5'ss of exon 5
AGGGAGCAAGGCATTCAAGAAATACAACAGCAAATTGGTGAAGTTAATGAGATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttattccatttccttttgttcttcctgattacttgcatctttattt-tactgaatgaatttatttttctgtacctgttcacgctatctaatgccactaaatttcattttgtag
|| |||||||| || |||||||| || |||||||||||||| ||||| ||||| |||||||||||||| || || ||  | || ||||||| |||||| |||||   |  | ||   || ||   |||  | |  || |||   |  |  |  | | |  ||| | | |||| | |  || | ||                                 
AGAGAGCAAGGAATACAAGAAATCCATCAGCAAATTGGTGAGGTTAACGAGATATTCAAAGATCTTGCGGTTCTGGTTAACGATCAAGGAGTCATGATAGgtaa---agacaat---ctattaaacttaattagaacatgcccttgaagctgcagttagagaactcacttttttctttct-tgcag--------------------------------

upper sequence: GLYMA16G08200.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv02s0012g01850.t01 (Vitis vinifera), 5'ss of exon 5
AGGGAGCAAGGCATTCAAGAAATACAACAGCAAATTGGTGAAGTTAATGAGATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttattccatttccttttgttcttcctgattacttgcatctttattttactgaatgaattt-atttttctgtacctgttcacgctatctaatgccactaaatttcattttgtag
|||||||| || || |||||||| || || |||||||| || || |||||||| |||||||||||||||||||| ||||||||||||||||  ||||||||||| | ||   | |  ||| |  |     |   || |  | |  | |||        ||| | | ||||   | |  || ||||                                 
AGGGAGCAGGGAATACAAGAAATCCAGCACCAAATTGGCGAGGTGAATGAGATTTTCAAAGATCTTGCTGTGCTGGTCCATGAGCAAGGAGTTATGATTGgtaactcatctgactctcttgt-ctagagttcgctattccctttctgattcaggctgctgactctcatttcaatttctcttttcag--------------------------------

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|6666502|gb|AW277896.1|AW277896
EST:     GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTG                         ATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
genomic: GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttatt ... cattttgtagATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
EST: gi|9564950|gb|BE474459.1|BE474459
EST:     GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTG                         ATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
genomic: GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttatt ... cattttgtagATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
EST: gi|207816978|gb|GD786713.1|GD786713
EST:     GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTG                         ATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
genomic: GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttatt ... cattttgtagATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
EST: gi|15000694|gb|BI321508.1|BI321508
EST:     GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTG                         ATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
genomic: GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttatt ... cattttgtagATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
EST: gi|21888894|gb|BQ742107.1|BQ742107
EST:     GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTG                         ATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
genomic: GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttatt ... cattttgtagATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
EST: gi|151398998|gb|EV268869.1|EV268869
EST:     GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTG                         ATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
genomic: GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttatt ... cattttgtagATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
EST: gi|27809121|gb|CB063543.1|CB063543
EST:     GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTG                         ATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
genomic: GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttatt ... cattttgtagATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
EST: gi|7232940|gb|AW568291.1|AW568291
EST:     GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTG                         ATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
genomic: GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttatt ... cattttgtagATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
EST: gi|192296912|gb|FG990258.1|FG990258
EST:     GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTG                         ATGATATTGGCTCCAACA
genomic: GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttatt ... cattttgtagATGATATTGGCTCCAACA
EST: gi|9819749|gb|BE555262.1|BE555262
EST:     GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTG                         ATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
genomic: GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttatt ... cattttgtagATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
EST: gi|192315290|gb|FK009610.1|FK009610
EST:     GATCTTCAAAGATCTTGCTGTGCTTGCCCATGAGCAAGGAGCCATGATTG                         ATGTTATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
genomic: GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttatt ... cattttgtagATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
EST: gi|42722596|gb|CK768495.1|CK768495
EST:     GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTG                         ATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
genomic: GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttatt ... cattttgtagATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
EST: gi|10254732|gb|BE822498.1|BE822498
EST:     GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTG                         ATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
genomic: GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttatt ... cattttgtagATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
EST: gi|21255947|gb|BQ452835.1|BQ452835
EST:     GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTG                         ATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
genomic: GATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttatt ... cattttgtagATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAACTGCACAAGCAA
EST: gi|9565390|gb|BE474899.1|BE474899
EST:     ATCTTCANAGATCTTGCTGTGCTTGTCCATGAGCCAGG-GACCATGATTG                         ATGATATTGGCTCGAACATTGAGAACTCCCATGCAGCCACCTGCCCA-GC
genomic: ATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAG-CCATGATTGgtaatttatt ... cattttgtagATGATATTGGCTCCAACATTGAGAACTCCCATGCAGCAAC-TGCACAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGAGCAAGGCATTCAAGAAATACAACAGCAAATTGGTGAAGTTAATGAGATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttattccatttccttttgttcttcctgattacttgcatctttattttactgaatgaatttatttttctgtacctgttcacgctatctaatgccactaaatttcattttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG