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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGAAGAACGGATGACATTGTGCAACATGGTTGTTGAAGCTGGTGGAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAGgtttgtgcaactgagtagatgcactgaaattgatattttgcctctaaagttatatgttgtcattggtaaagatttcataatatcttgattgtatcctaga...

Basic information

species Glycine max
transcript GLYMA14G40570.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 8
ATGGAAGAACGGATGACATTGTGCAACATGGTTGTTGAAGCTGGTGGAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAGgt--ttgtgcaactgagtagatgc-----actgaaat---tgatattttgcctctaaagttatatgttgtcattggtaaagatttcataatatcttgattgtatcctaga----------------------------------------------------------------
|||||||| || |||||| |||||||||||||| ||||||||||||| |||||||||||||| ||||| ||    ||||||||||| |||||||||||  ||      |     | ||||     | | ||||    ||||||||    | ||    | |      |||   |||   |   |||| |     | | | | | |||                                                                
ATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAGgtactttaatggcctttaaaatgcttggtaataaaatgagcgatatttttatgcaaataaaacaacccaacatccttaagcttcgaataagaag--aaatatttacaagaacaaatttctaacttttacataatgataattatgactccatatcggtcatcctggtaactgcag

upper sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G370852_T01 (Zea mays), 5'ss of exon 8
ATGGAAGAACGGATGACATTGTGCAACATGGTTGTTGAAGCTGGTGGAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAGgt-------ttgtgcaactgagtagatgcactgaaattga--tattttgcctctaaagttatatgttgtcattggtaaagatttcataatatcttgattgtatcctaga--------------------------------------------------------------------
||||||||||| |||||| | |||||||||||||||||||||||||||||||| ||||| || ||||||||    |||||||||||||| ||||||||       | || |   | | |      |   || |||    | | ||| | |        |  ||   ||  ||      |  | | |     ||     |   |||                                                                    
ATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaactagtccccttaaatgctcataacaaagttgggccaatatgcttttctttcataacattccaataagtttgagatagagagtgctcagaacaatttgcagaagtgagcttctaccatttagtttgtaggatagttctgacatcaatattgttgtgctggtatactgcag

upper sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G133988_T01 (Zea mays), 5'ss of exon 3
ATGGAAGAACGGATGACATTGTGCAACATGGTTGTTGAAGCTGGTGGAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAGgtttgtgca-actgagtagatgcactgaaattgatattttgcctctaaagttatatgttgtcat-tggtaaagatttcataatatct--tgattgtatcctaga---------------------------------------------------------------------------------
|||||||| || |||||| | |||||||||||| ||||||||||||||||||| |||||||| ||||||||    |||||||||||||| ||||||||        | |   | ||    || | | | |  ||  |||  |    || | | |  | |  |   ||  | ||    |||     || |  | | |||                                                                                   
ATGGAAGAGCGTATGACACTATGCAACATGGTTATTGAAGCTGGTGGAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaagtagtcccttgaaatgctcataataaagttgggccaatgtgcttttctttcataacgttccaataactttgagatagagagtgctcttgtactaagaccaatttgcaaaaatgagcttctactatttagtttgtacgataattctgacgtcattgccgttgtgttggtatactgcag

upper sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G010044_T02 (Zea mays), 5'ss of exon 8
ATGGAAGAACGGATGACATTGTGCAACATGGTTGTTGAAGCTGGTGGAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAGgtttgtg-caactgagtagatgcactgaaattgatattttgcctctaaagttatatgttgtcat-tggtaaagatttcataatatct--tgattgtatcctaga---------------------------------------------------------------------------------
|||||||| || |||||| | |||||||||||| ||||||||||||||||||| |||||||| ||||||||    |||||||||||||| ||||||||      | | |   | ||    || | | | |  ||  |||  |    || | | |  | |  |   ||  | ||    |||     || |  | | ||| |                                                                                 
ATGGAAGAGCGTATGACACTATGCAACATGGTTATTGAAGCTGGTGGAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAGgtacaaaactagtcccttgaaatgctcataataaagttgggccaatgtgcttttctttcataacgttccaataactttgagatagagagtgttcttgtactaaaactaatttgcaaaaatgagcttctactatttagtttgtaggacaattctgacatcatcgctgttgtgttggtatactgcag

upper sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 9
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 9
ATGGAAGAACGGATGACATTGTGCAACATGGTTGTTGAAGCTGGTGGAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAGgtttgtgcaactgagtagatgcactgaaattgatattttgcctctaaagttat-atgttgtcat-tggtaaagatttcataatatcttgattgtatcctaga
||||||||| | ||||||||||||||||||||||| |||||||| ||||||||||||||  | ||| ||||    || ||||| || ||| ||||||  |||  | |||  | | |    || || | |||| || | || |   | || || |||   | ||    |    | ||  ||| |    || |       
ATGGAAGAAAGAATGACATTGTGCAACATGGTTGTGGAAGCTGGGGGAAAGAATGGTGTCATCCCTCCTGATGCGACGACATTAAATTATGTTGAGgcatgtata-ctgtcttgttttcttgtaaatcatatgtttcttcaaggatcattatattgatgtatgtcttactcctgatcttatatcttctgcag------

upper sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 5'ss of exon 9
ATGGAAGAACGGATGACATTGTGCAACATGGTTGTTGAAGCTGGTGGAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAGgtttgtgcaactgagtagatgcactgaaattgatattttgcctctaaagttatatgttgtcatt---ggtaaagatttcataatatcttgattgtatcctaga-------------------------------------
||||||||| |||||||||| ||||||||||||||||||||||| |||||||||||||||||||||||||| || ||||||  ||| || ||||||||  |   || | |||   | | ||     | ||||||     |||  | || | |     |     || | | | ||  |  | | |||    |||| |  |                                     
ATGGAAGAAAGGATGACATTATGCAACATGGTTGTTGAAGCTGGAGGAAAGAATGGTGTTGTTCCTGCTGATAGTACTACACATAAGTACCTTGAGgtcggaataaatcagt---ttctctttctctaatatttgtgtgctattgataaacgaaaaaaaaaaaggaacaaaatttgttct-ttttgtgcttatcatgcaactattttgtttggcttaagtcagtttctttgcacag

upper sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 5'ss of exon 9
ATGGAAGAACGGATGACATTGTGCAACATGGTTGTTGAAGCTGGTGGAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAGgtttgtgcaactgagtagatgcactgaaattgatatt-------ttgcctctaaagttatatgttgtca-ttggtaaagatttcataatatcttgattgtatcctaga------------------
||||||||| | |||||||| |||||||||||| |||||||||| ||||||||||||||||| |||||||| || ||||||  ||| || ||||||||| |   || | | |     | ||     |   ||        |||||   |  || || | || ||  ||  |    |||    ||  ||||  || |  |  ||                   
ATGGAAGAAAGAATGACATTATGCAACATGGTTATTGAAGCTGGGGGAAAGAATGGTGTTGTCCCTGCTGATAGTACTACACATAAGTACCTTGAGgttagaagaaatcattcatctctctctctctctcatgcttgctattgccaaaagggtgattttttttctctttatgcttattgtgcaac-tctttcttctggctaagtcattgtttctttgcacag

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|193487468|gb|FK449649.1|FK449649
EST:     GAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAG                         GGCAAGACATCTCTGCCATATGAACCTGTTTATAGTGACGATCAAGCAAG
genomic: GAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAGgtttgtgcaa ... tcttttgcagGGCAAGACATCTCTGCCATATGAACCTGTTTATAGTGACGATCAAGCAAG
EST: gi|193466002|gb|FK429757.1|FK429757
EST:     GAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAG                         GGCAAGACATCTCTGCCATATGAACCTGTTTATAGTGACGATCAAGCAAG
genomic: GAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAGgtttgtgcaa ... tcttttgcagGGCAAGACATCTCTGCCATATGAACCTGTTTATAGTGACGATCAAGCAAG
EST: gi|193664006|gb|FK608698.1|FK608698
EST:     GAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAG                         GGCAAGACATCTCTGCCATATGAACCTGTTTATAGTGACGATCAAGCAAG
genomic: GAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAGgtttgtgcaa ... tcttttgcagGGCAAGACATCTCTGCCATATGAACCTGTTTATAGTGACGATCAAGCAAG
EST: gi|15286391|gb|BI470282.1|BI470282
EST:     GAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAG                         GGCAAGACATCTCTGCCATATGAACCTGTTTATAGTGACGATCAAGCAAG
genomic: GAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAGgtttgtgcaa ... tcttttgcagGGCAAGACATCTCTGCCATATGAACCTGTTTATAGTGACGATCAAGCAAG
EST: gi|23733371|gb|BU764882.1|BU764882
EST:     GAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAG                         GGCAAGACATCTCTGCCATATGAACCTGTTTATAGTGACGATCAAGCAAG
genomic: GAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAGgtttgtgcaa ... tcttttgcagGGCAAGACATCTCTGCCATATGAACCTGTTTATAGTGACGATCAAGCAAG
EST: gi|308222649|gb|HO760564.1|HO760564
EST:     GAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAG                         GGCAAGACATCTCTGCCATATGAACCTGTTTATAGTGACGATCAAGCAAG
genomic: GAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAGgtttgtgcaa ... tcttttgcagGGCAAGACATCTCTGCCATATGAACCTGTTTATAGTGACGATCAAGCAAG
EST: gi|7684899|gb|AW755547.1|AW755547
EST:     GAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAGATATCTTGAC                         GGCAAGACATCTCTGCCATATGAACCTGTTTATAGTGACGATCAAGCAAG
genomic: GAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAGgtttgtgcaa ... tcttttgcagGGCAAGACATCTCTGCCATATGAACCTGTTTATAGTGACGATCAAGCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGAAGAACGGATGACATTGTGCAACATGGTTGTTGAAGCTGGTGGAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAGgtttgtgcaactgagtagatgcactgaaattgatattttgcctctaaagttatatgttgtcattggtaaagatttcataatatcttgattgtatcctaga

- - - - - - - - - - - - - - - - - - - - - - -  AAAGAA