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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTATGATTGAGTTAAGTCGCACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTGgtatgtttctgcatgatttaatagcaaaattctagatgtttttattatattatatactgaatggaggatcagatcttagttgatttgttgggcagcctattctctttttacaattttcaatatcttgtatttttgggtgcag

Basic information

species Glycine max
transcript GLYMA09G28650.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G28650.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os02g14929.1 (Oryza sativa), 5'ss of exon 5
TCTATGATTGAGTTAAGTCGCACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTGgtatgtttctgcatgatttaatagcaaaattctagatgtttttattatattatatactgaatggaggatcagatcttagttgatttgttgggcagcctattctctttttacaattttcaatatcttgtatttttgggtgcag
|||||||||||| |||| ||||| || ||||||||||| |||||||| ||||||||||| ||  |||||||||||    |   || |    ||     ||| ||   |     | |   ||| ||| |||| |       |||| |    |     |  |||  |   ||   |||                                    
TCTATGATTGAGCTAAGCCGCACACAGGATGAAGAAGTAGGAGATGGCACGACATCTGTTATTGTTCTTGgtatgccgtttt-tggtcccttatgcttattttaagagacc--agttggtta-atattgaacgcgcag--agatgtagcctagagggggggggggtgaataggctt------------------------------------

upper sequence: GLYMA09G28650.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 5'ss of exon 5
TCTATGATTGAGTTAAGTCGCACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTGgtatgtttctgcatgatttaatagcaaaattctagatgtttttattatattatatactgaatggaggatcagatcttagttgatttgttgggcagcctattctctttttacaattttcaatatcttgtatttttgggtgcag
|||||||||||| |||| || || || ||||||||||| || ||||| || |||||||||||  || | ||||||| |   | ||||| | |     | ||  |     |||||||    || ||     |||      ||   ||  | |   | ||  | || |   ||||  |   || |                             
TCTATGATTGAGCTAAGCCGTACACAGGATGAAGAAGTTGGTGATGGCACAACATCTGTCATTGTTTTAGgtatgtgttccc-tgattcattc----agtttcattcagttttatt----taaatgtcatatgagatcgcaacactaggata--tcgt--gacatctctttctggtcgaacta-----------------------------

upper sequence: GLYMA09G28650.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G175510_T02 (Zea mays), 5'ss of exon 5
TCTATGATTGAGTTAAGTCGCACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTGgtatgtttctgcatgatttaatagcaaaattctagatgtttttattatattatatactgaatggaggatcagatcttagttgatttgttgggcagcctattctctttttacaattttcaatatcttgtatttttgggtgcag
|||||||||||  ||||||| || |||||||||||||| || ||||| || |||||||||||  |||| ||||||  | |      |||  |  ||    | | |     || || |   |         |   |  |    ||   | || |||||     ||  |||      ||                                   
TCTATGATTGAACTAAGTCGTACACAAGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgcatatt-----ttttgtgacatttgttttgggaagttgatgactatgagcctatgacaaacaacagcattgcaatttatttgc--atcaaactaaaacagtt-----------------------------------

upper sequence: GLYMA09G28650.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv17s0000g08170.t01 (Vitis vinifera), 5'ss of exon 5
TCTATGATTGAGTTAAGTCGCACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTGgtatgtttctgcatgatttaatagcaaaattctagatgtttttattatattatatactgaatggaggatcagatcttagttgatttgttgggcagcctattctctttttacaattttcaatatcttgtatttttgggtgcag
|| |||||||| ||||| ||||| |||||||||||||| || |||||||| || || |||||  |||||||||  | |||   | |  |  ||| | |||| |   | |||  | || |  ||  | |  ||      ||   | | |  || |||| ||||  || |||    ||  |   |                             
TCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTGgtacatctct---taaacttgtag-ataattat---tctttcgaata-acaatgaattatattat---tcttgtttca--tgttttgatggggtgcatatatcattaatgtga-----------------------------

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|208048655|gb|GD847558.1|GD847558
EST:     CTGTCATCATTCTTG                         CTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCTA
genomic: CTGTCATCATTCTTGgtatgtttct ... ttgggtgcagCTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCTA
EST: gi|209725416|gb|BW658278.1|BW658278
EST:     CACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTG                         CTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCTA
genomic: CACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTGgtatgtttct ... ttgggtgcagCTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCTA
EST: gi|208122378|gb|GD920843.1|GD920843
EST:     CACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTG                         CTGGTGAGATGCTTCATGTCGCCG
genomic: CACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTGgtatgtttct ... ttgggtgcagCTGGTGAGATGCTTCATGTCGCCG
EST: gi|209711120|gb|BW676339.1|BW676339
EST:     CACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTG                         CTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCTA
genomic: CACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTGgtatgtttct ... ttgggtgcagCTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCTA
EST: gi|208324562|gb|GE118849.1|GE118849
EST:     CACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTG                         CTGGTGAGATGCTTCATGTCG
genomic: CACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTGgtatgtttct ... ttgggtgcagCTGGTGAGATGCTTCATGTCG
EST: gi|209700495|gb|BW660895.1|BW660895
EST:     CACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTG                         CTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCTA
genomic: CACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTGgtatgtttct ... ttgggtgcagCTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCTA
EST: gi|193333955|gb|FK301343.1|FK301343
EST:     CACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTG                         CTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCTA
genomic: CACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTGgtatgtttct ... ttgggtgcagCTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCTA
EST: gi|193426285|gb|FK389060.1|FK389060
EST:     CACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTG                         CTGGTGAGATGCTTCATGTCGCCGATGCGTTCATTGACAAAATTCACCCT
genomic: CACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTGgtatgtttct ... ttgggtgcagCTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCT
EST: gi|193408879|gb|FK371133.1|FK371133
EST:     CACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTG                         CTGGTGAGATGCTTCATGTCGCCGATGCGTTCTATTTGACAAAATTCACCC
genomic: CACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTGgtatgtttct ... ttgggtgcagCTGGTGAGATGCTTCATGTCGCCGATGCATTC-ATT-GACAAAATTCACCC
EST: gi|213618229|gb|DB972999.1|DB972999
EST:     CACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTG                         CTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCTA
genomic: CACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTGgtatgtttct ... ttgggtgcagCTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTATGATTGAGTTAAGTCGCACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTGgtatgtttctgcatgatttaatagcaaaattctagatgtttttattatattatatactgaatggaggatcagatcttagttgatttgttgggcagcctattctctttttacaattttcaatatcttgtatttttgggtgcag

- - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - GATGGA