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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGTGGAAATGGTTTTCAGAGTATAGTGATATCACTGAAAGACACCTTTTATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGGgtaaatttcttgatatcattaattgatttaaatagtatgtttatggcactagctcagtgtattgacctggtttacttggaatttgcag

Basic information

species Glycine max
transcript GLYMA13G18470.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G18470.1 (Glycine max), 5'ss of exon 18
lower sequence: GRMZM2G416069_T02 (Zea mays), 5'ss of exon 9
ATGGTGGAAATGGTTTTCAGAGTATAGTGATATCACTGAAAGACACCTTTTATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGGgtaaatttcttgatat-cattaattgatttaaatagtatgtttatggcactagctcagtgtattgacctggtttacttggaatttgcag
|||| |  | |||||||||||| ||||| ||||| ||||| ||||  || |||||||| ||||| ||| | ||||| ||||| || ||||| ||| || ||||  |     | ||| ||||| |  |  |   |  ||| |     || |  ||| |    | |||   | | | |             
ATGGCGAGAGTGGTTTTCAGAGCATAGTTATATCTCTGAAGGACAGTTTCTATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcg---ggtatgcattactgcacctgtct--tatttcctgtgcgcatgcttaacacagtgattggatgtgcag-----------

upper sequence: GLYMA13G18470.1 (Glycine max), 5'ss of exon 18
lower sequence: Vv07s0005g03440.t01 (Vitis vinifera), 5'ss of exon 12
ATGGTGGAAATGGTTTTCAGAGTATAGTGATATCACTGAAAGACACCTTTTATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGGgtaaatttcttgatatcatta-attgatttaaatagtatgt-ttatggcactagct--------------cagtgtattgacctggtttacttggaatttgcag-----------------------------
| || || | ||||||||||||||| |||||||||||||| || | |||||||||||| || |||||  | |||||||||||||| |||||||| || |||||| |||||| ||   |||| ||| | ||||   || |   || |||  |||  |              |||| | |  |||   || || ||  |     ||                             
AGGGAGGCAGTGGTTTTCAGAGTATCGTGATATCACTGAAGGATAGCTTTTATGACAAGGCTGAAGCTCTGGTTGGGGTTTACAGGGACTCTGATAGGGGgtaagtttcttcatgatattatatttagttaatgcgttttcattttggtgctactttctgggttgttttccagtatgtccaccaaattaacctgctaagcagagacaatgctaatacctatatttaattgcag
















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|9565678|gb|BE475187.1|BE475187
EST:     TATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGG                         CTGTTCGAGAACTCTCACATTTGATTTGACTAAATACCGAGAGTTCTAAAA
genomic: TATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGGgtaaatttct ... gaatttgcagCTGTTCGAGAACTCTCACATTTGATTTGACTAAATACCGAGAGTTCTAAAA
EST: gi|193545264|gb|FK499487.1|FK499487
EST:     TATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGG                         CTGTTCGAGAACTCTCACATTTGATTTGACTAAATACCGAGAGTT
genomic: TATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGGgtaaatttct ... gaatttgcagCTGTTCGAGAACTCTCACATTTGATTTGACTAAATACCGAGAGTT
EST: gi|10231191|gb|BE800007.1|BE800007
EST:     TATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGG                         CTGTTCGAGAACTCTCACATTTGATTTGACTAAATACCGAGAGTTCTAAAA
genomic: TATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGGgtaaatttct ... gaatttgcagCTGTTCGAGAACTCTCACATTTGATTTGACTAAATACCGAGAGTTCTAAAA
EST: gi|6726074|gb|AW310473.1|AW310473
EST:     TATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGG                         CTGTTCGAGAACTCTCACATTTGATTTGACTAAATACCGAGAGTTCTAAAA
genomic: TATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGGgtaaatttct ... gaatttgcagCTGTTCGAGAACTCTCACATTTGATTTGACTAAATACCGAGAGTTCTAAAA
EST: gi|10237487|gb|BE806375.1|BE806375
EST:     ATGACAAAGCCGAAGCATTTAGTTGGG-TTTACAGAGACTCTGAAAGAGG                         CTGT-CGAGAACTCTCA
genomic: ATGACAAAGCCGAAGCATT-AGTTGGGGTTTACAGAGACTCTGAAAGAGGgtaaatttct ... gaatttgcagCTGTTCGAGAACTCTCA
EST: gi|6502274|gb|AW203647.1|AW203647
EST:     TATGACAAAGCCGAAGCATTAGTTGGGGTNTACAGAGACTCTGAAAGAAG                         CTGGTCGAGAACTCTCACATTTG
genomic: TATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGGgtaaatttct ... gaatttgcagCTGTTCGAGAACTCTCACATTTG
EST: gi|16343490|gb|BI969085.1|BI969085
EST:     TATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGG                         CTGTTCGAGAACTCTCACATTTGATTTGACTAAATACCGAGAGTTCTAAAA
genomic: TATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGGgtaaatttct ... gaatttgcagCTGTTCGAGAACTCTCACATTTGATTTGACTAAATACCGAGAGTTCTAAAA
EST: gi|31471677|gb|CD413705.1|CD413705
EST:     TATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGG                         CTGTTCGAGAACTCTCACATTTGATTTGACTAAATACCGAGAGTTCTAAAA
genomic: TATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGGgtaaatttct ... gaatttgcagCTGTTCGAGAACTCTCACATTTGATTTGACTAAATACCGAGAGTTCTAAAA
EST: gi|13562462|gb|BG550682.1|BG550682
EST:     TATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGG                         CTGTTCGAGAACTCTCACATTTGATTTGACTAAATACCGAGAGTTCTAAAA
genomic: TATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGGgtaaatttct ... gaatttgcagCTGTTCGAGAACTCTCACATTTGATTTGACTAAATACCGAGAGTTCTAAAA
EST: gi|31311145|gb|CD396348.1|CD396348
EST:     TATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGG                         CTGTTCGAGAACTCTCACATTTGATTTGACTAAATACCGAGAGTTCTAAAA
genomic: TATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGGgtaaatttct ... gaatttgcagCTGTTCGAGAACTCTCACATTTGATTTGACTAAATACCGAGAGTTCTAAAA
EST: gi|13252606|gb|BG363509.1|BG363509
EST:     TATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGG                         CTGTTCGAGAACTCTCACATTTGATTTGACTAAATACCGAGAGTTCTAAAA
genomic: TATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGGgtaaatttct ... gaatttgcagCTGTTCGAGAACTCTCACATTTGATTTGACTAAATACCGAGAGTTCTAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGTGGAAATGGTTTTCAGAGTATAGTGATATCACTGAAAGACACCTTTTATGACAAAGCCGAAGCATTAGTTGGGGTTTACAGAGACTCTGAAAGAGGgtaaatttcttgatatcattaattgatttaaatagtatgtttatggcactagctcagtgtattgacctggtttacttggaatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG