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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatttgtttattttggataaaaaatgggtacctatcagttgatatacaaattcacgaggttctgtctgctgacttttggaacaacacctcccccctccagtgcatatgttttccagtccttttacggtgatacatttactaactgtgaactatttctatag

Basic information

species Glycine max
transcript GLYMA11G10770.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G10770.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os09g10600.1 (Oryza sativa), 5'ss of exon 3
TTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatttgtttattttggataaaaaatgggtacctatcagttgatatacaaattcacgaggttctgtctgctgacttttggaacaacacctcccccctccagtgcatatgttttccagtccttttacggtgatacatttactaactgtgaactatttctatag
 ||||||||||| ||||||||||| ||||| ||||| |||||||| |||||| ||||||||||||| || || || ||||||||||| |||||||||||||||||||        || |     |  || ||  |   |||   |          |  |||    ||||   | || |  ||  |                                                                                  
ATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTACATGGGTACCTgtaagttg-------atctcattcacgaagtgtatcattatagatgttctggtggaaacacttaattctcatt-ctcatcttcag----------------------------------------------------------------------------------

upper sequence: GLYMA11G10770.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os08g23810.2 (Oryza sativa), 5'ss of exon 3
TTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatttgtttattttggataaaaaatgggtacctatcagttgatatacaaattcacgaggttctgtctgctgacttttggaacaacacctcccccctccagtgcatatgttttccagtccttttacggtgatacatttactaactgtgaactatttctatag
 || |||||||| ||||||||||||||||| ||||| ||||||||||||||  |||||||||| || || ||||||||||||||||| |||||||| |||||||||   |       ||    |    ||| || | |  |   ||  | | |   ||    |    ||   ||  || || |      |||                                                                           
GTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggatccaactcttgcagtgttcaatagggatcattttttt--ttttcctctttgtcattcacttaatggagagttctacctgcacag--------------------------------------------------------------------------

upper sequence: GLYMA11G10770.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G079256_T01 (Zea mays), 5'ss of exon 3
TTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatttgtttattttggataaaaaatgggtacctatcagttgatatacaaattcacgaggttctgtctgctgacttttggaacaacacctcccccctccagtgcatatgttttccagtccttttacggtgatacatttactaactgtgaactatttctatag
 ||||| ||||| ||||||||||| ||||| ||||| ||||||||||| ||  |||||||||| || || ||||| ||||||||||| |||||||| ||||||||||     | |  ||||  |||   || |      ||    ||   || || |   |  |     ||   |  | ||||| |                                                                                 
ATTTATAGCTGGAGTTGCTGATGATAATGGTTATGGTTGGGCAATTGCTAAGGCTCTTGCTGCTGCTGGTGCTGAGATTCTTGTTGGTACATGGGTGCCTgtaagttg---atctcatttgtgtaatttatcgtactggatgttctggcgtaaaattattctgga----gttatcaaaattttgtag--------------------------------------------------------------------------------

upper sequence: GLYMA11G10770.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G125052_T01 (Zea mays), 5'ss of exon 1
TTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatttgtttattttggataaaaaatgggtacctatcagttgatatacaaattcacgaggttctgtc-tgctgacttttggaacaacacctcccccctccagtgcatatgttttccagtccttttacggtgatacatttactaactgtgaactatttctatag
 || |||||||| ||||||||||| ||||| ||||||||||||||||||||  | |||||||| || || |||||||| |||||||| |||||||| || ||| |||  |     | |||  |  |    |  | |    ||| ||    | |  || ||     || |||  |  |    ||||  |                                                                                
ATTCATTGCTGGAGTTGCTGATGATAATGGCTATGGATGGGCAATTGCAAAGGCACTTGCTGCGGCTGGTGCTGAAATGCTTGTTGGTACATGGGTGCCGgtatgttgatcag--acttttaaagatttctttgcattggtcacttt---tgctgatccattgtcttatgtagtattctactttgacag-------------------------------------------------------------------------------

upper sequence: GLYMA11G10770.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G070422_T03 (Zea mays), 5'ss of exon 3
TTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagtt-atttgtttattttggataa----aaaatgggtacctatcagttgatatacaaattcacgaggttctgtctgctgacttttggaacaacacctcccccctccagtgcatatgttttccagtccttttacggtgatacatttactaactgtgaactatttctatag
 || |||||||| ||||||||||| ||||| ||||||||||||||||| ||  | |||||||| || || |||||||||||||| || |||||||| || ||| ||| ||  |  | ||   |||        | ||   || | |  | ||||  |     | | |  ||  | |    ||||                                                                                        
ATTCATTGCTGGAGTTGCTGATGATAATGGCTATGGATGGGCAATTGCGAAGGCACTTGCTGCGGCTGGTGCTGAAATTCTTGTGGGTACATGGGTGCCGgtatgttgatcagactcttacagatttctttgcattgaacactttt--gctgatcgattgtcttatgtagtattcttctttgacag--------------------------------------------------------------------------------------

upper sequence: GLYMA11G10770.1 (Glycine max), 5'ss of exon 3
lower sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 3
TTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatttgtttattttggataaaaaatgggtacctatcagttga--tatacaaattcacgag-gttctgtctgctgacttttggaacaacacctcccccctccagtgcatatgttttccagtccttttacggtgatacatttactaactgtgaactatttctatag
||| ||||||||| | |||||||| ||||| ||||| ||||| || ||||||||||||||||| || |||||||||||  | ||||| || ||||| ||||||||| ||||  ||  ||  | |       |  | | |    | | |  ||||| ||   | ||  |    |||| ||                                                                                           
TTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGACTTGGGTTCCTgtaagtcattt--ttggttcagctgcttttagtttccttcattgctaaattatactaacctatgaatggatggtctactag-----------------------------------------------------------------------------------------

upper sequence: GLYMA11G10770.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv06s0004g01310.t01 (Vitis vinifera), 5'ss of exon 3
TTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatttgtttattttggataaaaaa-tgggtacctatcagttgatatacaaattcacgaggttctgtctgctgacttttggaacaacacctcccccctccagtgcatatgttttccagtccttttacggtgatacatttactaactgtgaactatttctatag
 ||||||||||||||||||||||||||||||||||| |||||||| || ||||||||||| || || || |||||||||||||||||||||||||| ||||||||| | ||  | ||     |||  |   |  |     ||||     ||  |  |  || |    ||   |   ||  ||    |     |    ||   |  ||                                                             
CTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCACATGGGTTCCTgtaagtaaattaatgatcacatatatcattctctgctttaatcacagagtaatctgagccatg----tcaaaccattggattactaactgggaagctccttgtgtag-------------------------------------------------------------

upper sequence: GLYMA11G10770.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S29_256V6.1 (Physcomitrella patens), 5'ss of exon 2
TTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatttgtttattttggataaaaaatgggtacctatcagttgatatacaaattcacgaggttctgtctgctgactt--ttggaacaacacctcccccctccagtgcatatgttttccagtccttttacggtgatacatttactaactgtgaactatttctatag
 |||||||| ||||| || |||||| | || | ||| ||||| ||||| ||| |||| || ||||| ||||||||||||||||| || || ||||| || ||||| |||||     || | || |    ||   |    | || ||||  | | | |     ||||| |     |    ||  || || | |  |          || ||||                                                         
GTTTATTGCCGGTGTGGCGGATGACCAAGGTTTTGGCTGGGCCATTGCCAAAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctattttaaccttgttga-atttgattattcatcaccacttgaattgccactct--taggttattatgacaagtttaatttgatcgagcctctttttggacaatgcag--------------------------------------------------------

upper sequence: GLYMA11G10770.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ25882 (Selaginella moellendorffii), 5'ss of exon 2
TTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatttgtttattttggataaaaaatgggtacctatcagttgatatacaaattcacgaggttctgtctgctgacttttggaacaacacctcccccctccagtgcatatgttttccagtccttttacggtgatacatttactaactgtgaactatttctatag
 ||||| ||||| || || |||||  | |||||||||||||| ||||| ||| | |||||| | ||||| ||||||||||| || || || ||||| || |||| | || |||||| | |   | ||   | ||    |   |  |  | ||    || |                                                                                                           
ATTTATCGCTGGAGTGGCCGATGATCAAGGATATGGATGGGCGATTGCCAAAACGCTTGCTTCTGCCGGGGCTGAAATTCTCGTGGGAACCTGGGTTCCGgtaattcatgtgtttagtctctttcaactgttgg---gtgctaacttttctattcttttag----------------------------------------------------------------------------------------------------------

upper sequence: GLYMA11G10770.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ10940 (Selaginella moellendorffii), 5'ss of exon 2
TTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatttgtttattttggataaaaaatgggtacctatcagttgatatacaaattcacgaggttctgtctgctgacttttggaacaacacctcccccctccagtgcatatgttttccagtccttttacggtgatacatttactaactgtgaactatttctatag
 ||||| ||||| || || |||||  | |||||||||||||| ||||| ||| | |||||| | ||||| |||||||||||  | || || ||||| || |||| | ||   ||  | ||   |    |          | | ||||      || ||  | |  |||| |  |                                                                                             
ATTTATCGCTGGAGTGGCCGATGATCAAGGATATGGATGGGCGATTGCCAAAACGCTTGCTTCTGCCGGGGCTGAAATTCTCTTGGGAACCTGGGTTCCGgtaattcatgacttcgtgtttcttgtttagctctctttcaactgttgggtgctaacttttcta--ttcttttag---------------------------------------------------------------------------------------------

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|298166168|gb|HO009139.1|HO009139
EST:     AATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCT                         GCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCA
genomic: AATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatt ... atttctatagGCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCA
EST: gi|7796132|gb|AW781529.1|AW781529
EST:     AATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCT                         GCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGA
genomic: AATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatt ... atttctatagGCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGA
EST: gi|192307619|gb|FG999658.1|FG999658
EST:     AATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCT                         GCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCA
genomic: AATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatt ... atttctatagGCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCA
EST: gi|9986202|gb|BE660310.1|BE660310
EST:     AATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCT                         GCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCA
genomic: AATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatt ... atttctatagGCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCA
EST: gi|7796512|gb|AW781909.1|AW781909
EST:     AATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCT                         GCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCA
genomic: AATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatt ... atttctatagGCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCA
EST: gi|7041859|gb|AW471753.1|AW471753
EST:     AATCTCTTGCTGCAGCCGGAGCTGANATTCTTGTTGGCACATGGGTACCT                         GCTCTGAATATTTNTGAGTCCAGCCTACGG
genomic: AATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatt ... atttctatagGCTCTGAATATTTTTGAGTCCAGCCTACGG
EST: gi|298168738|gb|HO009668.1|HO009668
EST:     AATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCT                         GCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCA
genomic: AATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatt ... atttctatagGCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCA
EST: gi|192306220|gb|FG995056.1|FG995056
EST:     AATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCT                         GCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCA
genomic: AATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatt ... atttctatagGCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCA
EST: gi|15204411|gb|BI427179.1|BI427179
EST:     AATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCT                         GCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCA
genomic: AATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatt ... atttctatagGCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCA
EST: gi|9899327|gb|BE608295.1|BE608295
EST:     GGCACATGGGTACCT                         GCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCA
genomic: GGCACATGGGTACCTgtaagttatt ... atttctatagGCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCA
EST: gi|19053059|gb|BM731726.1|BM731726
EST:     TACCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCT                         GCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCA
genomic: AATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatt ... atttctatagGCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatttgtttattttggataaaaaatgggtacctatcagttgatatacaaattcacgaggttctgtctgctgacttttggaacaacacctcccccctccagtgcatatgttttccagtccttttacggtgatacatttactaactgtgaactatttctatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA