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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttgatgttttcttccttacagttattagattataaaattaatcatgacattttgtatttggcaagaatgagaatgtacgaacaatggaaaatag...

Basic information

species Glycine max
transcript GLYMA10G35230.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35230.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 7
GATGGCACT-GACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttgatgttttcttccttacagttattagattataaaattaatcatgacattttgtatttggcaagaatgagaatgtacgaacaatggaaaatag--------
    ||||  || |||||||||||||||  |||| ||||||| |||||||| ||||||||||| |||||||||||  || | |||||||||||     |    | |       || |||| | ||  |  ||    || ||       ||  |  |||||  ||  |||       | |  ||| ||         
-GAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCAGCAAAGACAGCTGATAATATAAACCAAGTATTTGAGgtatgccccctagcatat-----gaagctatttgctttcacgat-gtccaagaagcaggatagctaacaaga--gaacatgctattttatttcaaattaatcaagctg

upper sequence: GLYMA10G35230.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 8
GATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttgatgttttcttccttacagttattagattataaaattaatcatgacattttgtatttggcaagaatgagaatgtacgaacaatggaaaatag--
||||     ||||| |||||||||||   |||||||||||| ||||| || || |||||||| |||||||||||  |||||||||||||||| ||   ||        |    ||| ||| || | |      |  |  |    || ||  ||  |    | |   | | | | |  | ||||| |   
GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttgagtgcatgaaatgtttgtt-ttacataacatgcaagaggagaagcaattctagctgcaactgttaatgttattcta-ctttagaaaagatca

upper sequence: GLYMA10G35230.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM5G863105_T01 (Zea mays), 5'ss of exon 3
GATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttgatgttttcttccttacagttat---tagattataaaattaatcatgacattttgtatttggcaagaatgagaatgtacgaacaatggaaaatag
||||     |||||||||||||||||    ||||||||||| ||||| || || |||||||| |||||||||||  |||||||||||||||| ||    |       ||    ||| |   ||   | ||| || |   |  | || | |       ||  ||||  | | |  |   ||   | |  ||
GATGCACAGGACTATGCAGAGAAGAACAAAATGTTTTTCATTGAGACGTCAGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttgaatacataaactgtttgttttacataacatgtaagatgagaaacaa-atctagctgcaaccattaatgctattct-tgtttaa-aaagaccag

upper sequence: GLYMA10G35230.1 (Glycine max), 5'ss of exon 7
lower sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 7
GATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttgatgttttcttccttacagttattagattataaaattaatcatgacattttgtatttggcaagaatgagaatgtacgaacaatggaaaatag--
||||| |  ||   |||||||||||| || ||||| ||||| ||||| || || |||||||| ||||| |||||| ||||||||||||| ||     |  |||||| | |    ||  |     ||    ||   |    |||||  |        |  ||  |  | |   |    |    ||| |  
GATGGAATGGAGCTTGCAGAGAAGAACGGCATGTTCTTCATTGAGACGTCAGCCAAGACAGCCGATAACATAAATCAACTGTTTGAGgtgtgcac--ttctttcttgcctctgatttatgatcgattttcttgtcctctgcatttattgagatcttattatccgtttctttcattgctttggaattgga

upper sequence: GLYMA10G35230.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 7
GATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtt-tgatgttttcttccttacagttattagattataaaattaatcatgacatt-ttgtatttggcaagaatgagaatgtacgaacaatgga-aaatag-
||||| | ||| ||||||||||||||||||||||| || || || ||||||||||||||||| ||||| |||||  | ||||||||||||  |  |||  |||  ||  | |  || |  |  || ||   ||  | | ||||||  |  | ||      ||   |    ||  | |  | ||  || |  
GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctgaaatttattttttaatggtaaccattttcta---tttgt-aggacattgctaaaattaatggcaagctgtgaataatagctctagatgaacaaa

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|7587998|gb|AW703803.1|AW703803
EST:     TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAAATTGCCAAAAGACTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGACTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
EST: gi|193684956|gb|FK626914.1|FK626914
EST:     TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAAATTGCCAAAAGACTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGACTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
EST: gi|151394915|gb|EV264786.1|EV264786
EST:     TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAA-TTGCCAAAAGACTGCCTCGCCCATCAGTTAGTTGATGTAGCCTGATA
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGACTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
EST: gi|9900885|gb|BE609853.1|BE609853
EST:     TCATACAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTGTGAG                         GAAATTGCCAAAAGACTGCCTCGCCCATCAGTTAGT
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGACTGCCTCGCCCATCAGTTAGT
EST: gi|151411846|gb|EV281657.1|EV281657
EST:     TCATGGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAAATTGCCAAAAGACTGCCTCGCCCATCAGTTAGTTGAT
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGACTGCCTCGCCCATCAGTTAGTTGAT
EST: gi|207709348|gb|GD691040.1|GD691040
EST:     TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAAATTGCCAAAAGACTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGACTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
EST: gi|208190741|gb|GD991389.1|GD991389
EST:     TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG                         GAAATTGCCAAAAGACTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA
genomic: TCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttga ... cttttcacagGAAATTGCCAAAAGACTGCCTCGCCCATCAGTTAGTTGATGTAGCCAGATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttgatgttttcttccttacagttattagattataaaattaatcatgacattttgtatttggcaagaatgagaatgtacgaacaatggaaaatag

- - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT