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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgttctcctttgacaataattgaaccatgtttcatacactcgataacaatctaacaagcattcaaattgcaacctgattgttctactag

Basic information

species Glycine max
transcript GLYMA13G36230.2
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G36230.2 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G114861_T01 (Zea mays), 5'ss of exon 13
ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgttctcctttgacaataattgaaccatgtttcat--acactcgataacaatctaacaagcattcaaattg-caac--ctgattgttctactag-------------------------------------------------------------
 |||||||| || ||||||||||||||||| || || ||||||||||||||||||||  |    |||| |||    || ||||||   | |  |   ||  | ||| ||   |||| | |  |   | |     |     |    | | | |||| | || | ||      || ||  || |                                                              
GTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAGgtagaatggaacattttc-ataattatcataccaagatctaccaaaatatagtggtccttatgctatctttcagactgacgacgatccctttttagacaaatattttgcatgctaataacgtatcctgagagagcatcgctttcattttttcttttttgcag

upper sequence: GLYMA13G36230.2 (Glycine max), 5'ss of exon 14
lower sequence: Vv19s0014g05070.t01 (Vitis vinifera), 5'ss of exon 13
ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgttctcctttgacaataattgaaccatgtttcatacactcgataacaatctaacaa-gcattcaaattgcaacctgattgttct-actag
 |||||||| ||||| ||||||||||| ||||| || |||||||||||||| |||||||| || |||| |||||| ||||||||||      |      || |     |      |  ||  || | || ||| |   | ||||   |  |||   |||        || |  | || ||
GTCTGTGGGCAAAACACAGATGAATGAGCAATCATCCAGAAGTCATTTTGTGTTCACTCTGCGGATATCTGGTGTTAATGAGgtataaagtcttcatggtgccctctgtgctgatacattg-atgctcttgattatgttttaactctgttttctctttgtttttcacttatattgaccag
















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|208139518|gb|GD937276.1|GD937276
EST:     CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAG                         AGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGATCTTGCTGGG
genomic: CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgt ... gttctactagAGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGATCTTGCTGGG
EST: gi|208088757|gb|GD891199.1|GD891199
EST:     CTTCTAGAAGTCATTTTG-ATTCACTCTTCGAATATATGGTGTAAATGAG                         AGCACTGACCAACAAGTACAAGGTATTCTAAA
genomic: CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgt ... gttctactagAGCACTGACCAACAAGTACAAGGTATTCTAAA
EST: gi|208278560|gb|GE075805.1|GE075805
EST:     CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAG                         AGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGATCTTGCTGGG
genomic: CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgt ... gttctactagAGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGATCTTGCTGGG
EST: gi|208325770|gb|GE124506.1|GE124506
EST:     CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAG                         AGCACTGACCAACAAGTACAAGGTATTCTAAA
genomic: CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgt ... gttctactagAGCACTGACCAACAAGTACAAGGTATTCTAAA
EST: gi|208270354|gb|GE067344.1|GE067344
EST:     CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAG                         AGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGATCTTGCTGGG
genomic: CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgt ... gttctactagAGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGATCTTGCTGGG
EST: gi|193508563|gb|FK465426.1|FK465426
EST:     CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAG                         AGCACTGACCAACAAGTACAAGGTATT
genomic: CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgt ... gttctactagAGCACTGACCAACAAGTACAAGGTATT
EST: gi|208112030|gb|GD912422.1|GD912422
EST:     CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAG                         AGCACTGACCAACAAGTACAAGGTATTCTAAA
genomic: CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgt ... gttctactagAGCACTGACCAACAAGTACAAGGTATTCTAAA
EST: gi|208218829|gb|GE016147.1|GE016147
EST:     TTTGTATTCACTCTTCGAATATATGGTGTAAATGAG                         AGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGATCTTGCTGGG
genomic: TTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgt ... gttctactagAGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGATCTTGCTGGG
EST: gi|208223822|gb|GE020951.1|GE020951
EST:     CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAG                         AGCACTGACCAACAAGTAC
genomic: CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgt ... gttctactagAGCACTGACCAACAAGTAC
EST: gi|193542299|gb|FK497517.1|FK497517
EST:     AGTCA-TTTGTATTCACTCTTCGAATATATGGTGTAAATGAG                         AGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGATCTTGCTGGG
genomic: AGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgt ... gttctactagAGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGATCTTGCTGGG
EST: gi|208232837|gb|GE035362.1|GE035362
EST:     CTTCTAGAAGTCATTTTGTATTCACTCTTCGATTATATGGTGTAAATGAG                         AGCACTGACCAACAAGCACAAGGTATTCTAAATCTCATTGATCT
genomic: CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgt ... gttctactagAGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGATCT
EST: gi|208034047|gb|GD831479.1|GD831479
EST:     CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAG                         AGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGATCTTGC
genomic: CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgt ... gttctactagAGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGATCTTGC
EST: gi|207687107|gb|GD669795.1|GD669795
EST:     CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAG                         AGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGATCTTGCTGGG
genomic: CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgt ... gttctactagAGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGATCTTGCTGGG
EST: gi|193306454|gb|FK273379.1|FK273379
EST:     CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAG                         AGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGATCTTGCTGGG
genomic: CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgt ... gttctactagAGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGATCTTGCTGGG
EST: gi|207733080|gb|GD710932.1|GD710932
EST:     CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAG                         AGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGAT
genomic: CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgt ... gttctactagAGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGAT
EST: gi|207685304|gb|GD668650.1|GD668650
EST:     CTTCTAGAAGTCATTT-GTATTCACTCTTCGAATATATGGTGTAAATGAG                         AGCACTGACCAACAAGTACAAGGTATTCTAAAT
genomic: CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgt ... gttctactagAGCACTGACCAACAAGTACAAGGTATTCTAAAT
EST: gi|208117539|gb|GD917781.1|GD917781
EST:     CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAG                         AGCACTGATCAACAAGTACA
genomic: CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgt ... gttctactagAGCACTGACCAACAAGTACA
EST: gi|208045340|gb|GD841134.1|GD841134
EST:     CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATACGGTGTAAATGAG                         AGCACTGACCAACAAGTACAAGGTATTCTAAAT
genomic: CTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgt ... gttctactagAGCACTGACCAACAAGTACAAGGTATTCTAAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAGgtatggttgttctcctttgacaataattgaaccatgtttcatacactcgataacaatctaacaagcattcaaattgcaacctgattgttctactag

- - - - - - - - - - - - - - - - - -  AGAAGT