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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACGAGGACATGCTAAAGAAGCTTGGTGACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgacttacagacaacagtactcttaaattgtatgcatagtcaatcgtttggttccctctagaaggattgttttataaggcatgatttgtcatgtgagctttttcaaccttgaaaatagcagaatgaagaatacttgtaaaatttagtttccttgttcagcacttaaaattgatatattctttattcatggaatcag

Basic information

species Glycine max
transcript GLYMA17G03990.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G03990.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os03g61710.1 (Oryza sativa), 5'ss of exon 11
TGACGAGGACATGCTAAAGAAGCTTGGTGACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgacttacagacaacagtactcttaaattgtatgcatagtcaatcgtttggttccctctagaaggattgttttataaggcatgatttgtcatgtgagctttttcaaccttgaaaatagcagaatgaagaatacttgtaaaatttagtttccttgttcagcacttaaaattgatatattctttattcatggaatcag
||  || || |||||  | || || || || |||||||| || |||||  |||||||||| || |||||||||||||||||     ||      |  |||   ||| || |      || |  |     | | | |     |||   |||| |   |||  |  |  ||| ||  |  | | |    |         |  |     ||| || | || ||  ||  | |  | |  | ||   |  |                               
TGCGGAAGATATGCTTCAAAAACTGGGCGATCTTATGAATGAAAGTCACTATAGCTGCAGTGTGTTATATGAATGCAGgtaccatttt-----tagtagtgtactttaactacg---atgggta-----tcgttcctgagcagacacattgatacttaaaactcgtattgacacttcggatgtcatgaaaacagtcctctctttcagaaaaaaagttatagcat--actgacatattccattgcccag------------------------------

upper sequence: GLYMA17G03990.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G458549_T01 (Zea mays), 5'ss of exon 11
TGACGAGGACATGCTAAAGAAGCTTGGTGACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgacttacagacaacagtactcttaaattgtatgcatagtcaatcgtttggttccctctagaaggattgttttataaggcatgatttgtcatgtgagctttttcaaccttgaaaatagcagaatgaagaatacttgtaaaatttagtttccttgttcagcacttaaaattgatatattctttattcatggaatcag
||| || | || ||| ||||| |||||||| |||||||||||||| ||| | |||||||||||  |||| |||||||||||     || |||      ||||| || |  |   |    | | |        || |  |  | |    ||| |||| ||  | |       ||      |   |  |       | ||| |||                                                                           
TGAGGAAGGCAAGCTTAAGAAACTTGGTGATCTTATGAACGAGAGCCATTACAGCTGCAGCGTGCTATACGAATGCAGgtacc--tttgcagt-----gtactgttcagct---tctgaaattagc------gtgctgtaaacagatgttgctttacaaaacttagg--aacacactgacgcatatatttcactatataccag---------------------------------------------------------------------------

upper sequence: GLYMA17G03990.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv05s0077g00690.t01 (Vitis vinifera), 5'ss of exon 11
TGACGAGGACATGCTAAAGAAGCTTGGTGACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgacttacagacaacagtactcttaaattgtatgcatagtcaatcgtttggttccctctagaaggattgttttataaggcatgatttgtcatgtgagctttttcaaccttgaaaatagcagaatgaagaatacttgtaaaatttagtttccttgttcagcacttaaaattgatatattctttattcatggaatcag
||| || ||||||||||||||||| ||||||||||||||| |||| ||  | |||||||| |||||||| || ||||||||   | ||        || | ||| | |||            |||    |||||  ||   | ||   ||| || |||  || |   |  |  |||       ||  | | | |  |||| |   |                                                                        
TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgta--aaatt--------caatcctcctgaat-----------gcaacaacttggtaaccaacacaacttttgctt-atactgc-tagctctttttgt-----ccttagagcctaagtataggaactt------------------------------------------------------------------------

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|213606347|gb|DB976508.1|DB976508
EST:     ACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG                         CTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
genomic: ACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgactt ... atggaatcagCTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
EST: gi|7926145|gb|AW832171.1|AW832171
EST:     GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG                         CTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
genomic: GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgactt ... atggaatcagCTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
EST: gi|14205721|gb|BG839399.1|BG839399
EST:     GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG                         CTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
genomic: GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgactt ... atggaatcagCTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
EST: gi|41145398|gb|CK605609.1|CK605609
EST:     GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG                         CTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
genomic: GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgactt ... atggaatcagCTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
EST: gi|14205748|gb|BG839426.1|BG839426
EST:     GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG                         CTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
genomic: GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgactt ... atggaatcagCTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
EST: gi|58019629|gb|CX706371.1|CX706371
EST:     GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG                         CTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
genomic: GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgactt ... atggaatcagCTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
EST: gi|21601505|gb|BQ611836.1|BQ611836
EST:     GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG                         CTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
genomic: GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgactt ... atggaatcagCTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
EST: gi|26048836|gb|CA785289.1|CA785289
EST:     GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG                         CTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
genomic: GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgactt ... atggaatcagCTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
EST: gi|209712398|gb|BW671250.1|BW671250
EST:     CTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG                         CTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
genomic: CTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgactt ... atggaatcagCTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
EST: gi|207698661|gb|GD679290.1|GD679290
EST:     GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG                         CTGTCCGGAGTTGGAAG
genomic: GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgactt ... atggaatcagCTGTCCGGAGTTGGAAG
EST: gi|58019308|gb|CX706050.1|CX706050
EST:     GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG                         CTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
genomic: GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgactt ... atggaatcagCTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
EST: gi|209699971|gb|BW661200.1|BW661200
EST:     GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG                         CTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCT
genomic: GACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgactt ... 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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACGAGGACATGCTAAAGAAGCTTGGTGACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgacttacagacaacagtactcttaaattgtatgcatagtcaatcgtttggttccctctagaaggattgttttataaggcatgatttgtcatgtgagctttttcaaccttgaaaatagcagaatgaagaatacttgtaaaatttagtttccttgttcagcacttaaaattgatatattctttattcatggaatcag

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