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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACGAGGACATGCTAAAGAAGCTTGGCGACCTTATGAACGAAAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgacttacagtactcttaaaatgtatgcattgtcaattgtttggttctgtctggaaggattattttataaggcatgatttgtcatgtgagcttttccaaccttaaaaatagcagaatgaagcatacttccttgtaaaatgtagtttcctttgtatgcactattgatattctttattaatggaatcag

Basic information

species Glycine max
transcript GLYMA07G36610.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G36610.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os03g61710.1 (Oryza sativa), 5'ss of exon 11
CGACGAGGACATGCTAAAGAAGCTTGGCGACCTTATGAACGAAAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgacttacagtactcttaaaatgtatgcattgtcaattgtttggttctgtctggaaggattattttataaggcatgatttgtcatgtgagcttttccaaccttaaaaatagcagaatgaagcatacttccttgtaaaatgtagtttcctttgtatgcactattgatattctttattaatggaatcag
 |  || || |||||  | || || ||||| |||||||| ||||||||  |||||||||| || |||||||||||||||||   | ||  |||| | | |   |   | |  ||   || |||     |||    ||   |||  |   |||  |  |  ||| ||  |  | | |      | | |||| ||            | ||  |||  | ||   |  ||       ||    || ||| ||  |  |||           
TGCGGAAGATATGCTTCAAAAACTGGGCGATCTTATGAATGAAAGTCACTATAGCTGCAGTGTGTTATATGAATGCAGgtacc-atttttagtagtgt-actttaactacgatgggtatcgttc----ctgagcagacacattgatacttaaaactcgtattgacacttcggatgt------catgaaaacag------------tcctctctttcagaaaaaaagtt-------atagcatactgacatattccattgcccag-----

upper sequence: GLYMA07G36610.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G458549_T01 (Zea mays), 5'ss of exon 11
CGACGAGGACATGCTAAAGAAGCTTGGCGACCTTATGAACGAAAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgacttacagtactcttaaaatgtatgcattgtcaattgtttggttctgtctggaaggattattttataaggcatgatttgtcatgtgagcttttccaaccttaaaaatagcagaatgaagcatacttccttgtaaaatgtagtttcctttgtatgcactattgatattctttattaatggaatcag
 || || | || ||| ||||| ||||| || ||||||||||| || ||| | |||||||||||  |||| |||||||||||       |  ||||| || |  |      |||  |         || ||||    |    ||  |||| ||  | |       ||      |   |  |       | ||| |||                                                                         
TGAGGAAGGCAAGCTTAAGAAACTTGGTGATCTTATGAACGAGAGCCATTACAGCTGCAGCGTGCTATACGAATGCAGgtacctttgcagtgtactgttcagcttctgaaattagc---------gtgctgtaaacagatgttgctttacaaaacttagg--aacacactgacgcatatatttcactatataccag-------------------------------------------------------------------------

upper sequence: GLYMA07G36610.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv05s0077g00690.t01 (Vitis vinifera), 5'ss of exon 11
CGACGAGGACATGCTAAAGAAGCTTGGCGACCTTATGAACGAAAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgacttacagtactcttaaaatgtatgcattgtcaattgtttggttctgtctggaaggattattttataaggcatgatttgtcatgtgagcttttccaaccttaaaaatagcagaatgaagcatacttccttgtaaaatgtagtttcctttgtatgcactattgatattctttattaatggaatcag
 || || ||||||||||||||||| || |||||||||||| | || ||  | |||||||| |||||||| || ||||||||   |  | || | ||| | ||    |    |||  ||           | |       | ||||  |   || |    |||||| |  |||| |    ||   ||  ||                                                                               
TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgta---aaattcaatcctcctgaatgcaacaacttggtaaccaacacaactttt-------gcttatactgctag-ctctttttgtccttagagcct----aagtataggaactt----------------------------------------------------------------------------

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|22931426|gb|BU548565.1|BU548565
EST:     CGAAAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG                         CTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
genomic: CGAAAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgactt ... atggaatcagCTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
EST: gi|151396691|gb|EV266564.1|EV266564
EST:     GACCTTATGAACGAAAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG                         CTGTCCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTC
genomic: GACCTTATGAACGAAAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgactt ... atggaatcagCTGTCC-GGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTC
EST: gi|12774697|gb|BG239624.1|BG239624
EST:     GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG                         CTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
genomic: GACCTTATGAACGAAAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgactt ... atggaatcagCTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
EST: gi|151408720|gb|EV278528.1|EV278528
EST:     GACCTTATGAACGAAAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG                         CTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
genomic: GACCTTATGAACGAAAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgactt ... atggaatcagCTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
EST: gi|31467576|gb|CD409604.1|CD409604
EST:     GACCTTATGAACGAAAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG                         CTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
genomic: GACCTTATGAACGAAAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgactt ... atggaatcagCTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
EST: gi|213607524|gb|DB978447.1|DB978447
EST:     TAGCTGCAGCGTTTTATATGTATGCAG                         CTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGATGCTCT
genomic: TAGCTGCAGCGTTTTATATGAATGCAGgtattgactt ... atggaatcagCTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
EST: gi|13482134|gb|BG511477.1|BG511477
EST:     CGAAAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG                         CTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
genomic: CGAAAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgactt ... atggaatcagCTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGACGAGGACATGCTAAAGAAGCTTGGCGACCTTATGAACGAAAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgacttacagtactcttaaaatgtatgcattgtcaattgtttggttctgtctggaaggattattttataaggcatgatttgtcatgtgagcttttccaaccttaaaaatagcagaatgaagcatacttccttgtaaaatgtagtttcctttgtatgcactattgatattctttattaatggaatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG