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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAACAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTGgtagtttccaattcaatctctctctctctctctctctcttgttatgttatggtgctcaacaagtgatgctttatttgaattgtatttggcag

Basic information

species Glycine max
transcript GLYMA09G01270.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G01270.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os02g10310.1 (Oryza sativa), 5'ss of exon 7
GCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAACAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTGgtagtttccaattcaatctctctctctctctctctctcttgttatgttatggtgctcaacaagtgatgctttatttgaattgtatttggcag
||  | ||||||||||| || |||||||||||||||||| | ||||||||  ||||| |||| || |||||||| ||  |  | |||||||| ||||||||||| |     ||  |  | ||  ||        |   |  ||  ||||   ||         | ||  |  |                   
GCAGCCATTGTTGGACCAGGGAATGAATTGGGAAAACCTATCGATATTAATGATGCTGAAGAACATATCTTTGGCCTAATGATAATGAATGATTGGAGTGgtaggtattcttttcagttttcgttcagatcagttgcatactttggttaaactgagttttgtataatattgcag------------------

upper sequence: GLYMA09G01270.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv00s0187g00340.t01 (Vitis vinifera), 5'ss of exon 7
GCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAACAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTGgtagtttccaattcaatctctctctctctctctctctcttgttatgttatggtgctcaacaagtgatgctttatttgaa-ttgtatttggcag
||| |||| ||||| ||||| |||||||| ||||| ||||||||| ||||  | |||  |||||| ||||||||||||||  | |||||||||||||||||||     ||  | | |   |   ||  |  |    | |  ||  ||| |  |      ||  |    ||| |   ||| |||| |||| |||
GCTGCTATAGTTGGTCCTGGTAATGAATTAGGAAAGCCTGTGGATGTTAATGAGGCTGCAGATCATATCTTTGGACTTGTGATCATGAATGACTGGAGTGgta---cacatgttatttgttgattcatttccaagttttcattgggtt-taatat----cagttctatcttgacaagaagttgtttttgacag

upper sequence: GLYMA09G01270.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv00s0187g00300.t01 (Vitis vinifera), 5'ss of exon 4
GCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAACAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTGgtagtttccaattcaatctctctctctctctctctctcttgttatgttatggtgctcaacaagtgatgctttatttgaa-ttgtatttggcag
||| |||| ||||| ||||| |||||||| ||||| ||||||||| ||||  | |||  |||||||||||||||||||||  | |||||||||||||||||||   | ||  | | |   |   ||  |  |    | |  ||  ||| |  |      ||  |    ||| |   ||| |||| |||| |||
GCTGCTATAGTTGGTCCTGGTAATGAATTAGGAAAGCCTGTGGATGTTAATGAGGCTGCAGATCACATCTTTGGACTTGTGATCATGAATGACTGGAGTGgta---tacatgttatttgttgattcatttccaagttttcattgggtt-taatat----cagttctatcttgacaagaagttgtttttgacag

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|298195581|gb|HO043972.1|HO043972
EST:     CAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTG                         CTCGAGATATTCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCA
genomic: CAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTGgtagtttcca ... tatttggcagCTCGAGATATTCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCA
EST: gi|208298210|gb|GE095847.1|GE095847
EST:     CAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTG                         CTCGAGATATTCAGGCATGGGAATATATTCCTCT
genomic: CAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTGgtagtttcca ... tatttggcagCTCGAGATATTCAGGCATGGGAATATATTCCTCT
EST: gi|151405820|gb|EV275635.1|EV275635
EST:     CAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTG                         CTCGAGATATTCAGGCATGGGAATATATTCCTCTTGGTCCATTTTCTTGGC
genomic: CAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTGgtagtttcca ... tatttggcagCTCGAGATATTCAGGCATGGGAATATATTCCTCTTGGTCCATTT-CTTGGC
EST: gi|193724130|gb|FK656410.1|FK656410
EST:     GGACTTGTTCTGATGAATGTACTTGGAGTG                         CTCGAGATATTCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGC
genomic: GGACTTGTTCTGATGAATG-AC-TGGAGTGgtagtttcca ... tatttggcagCTCGAGATATTCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGC
EST: gi|6567242|gb|AW234853.1|AW234853
EST:     CAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTG                         CTCGAGATATTCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCA
genomic: CAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTGgtagtttcca ... tatttggcagCTCGAGATATTCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCA
EST: gi|213601975|gb|DB976222.1|DB976222
EST:     CAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTG                         CTCGAGATATTCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCA
genomic: CAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTGgtagtttcca ... tatttggcagCTCGAGATATTCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCA
EST: gi|151410471|gb|EV280286.1|EV280286
EST:     CAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGA-TGACTGGAGTG                         CTCGAGATAT-CAG-CATGGGA
genomic: CAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTGgtagtttcca ... tatttggcagCTCGAGATATTCAGGCATGGGA
EST: gi|10847964|gb|BF071656.1|BF071656
EST:     CAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTG                         CTCGAGATATTCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCA
genomic: CAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTGgtagtttcca ... tatttggcagCTCGAGATATTCAGGCATGGGAATATATTCCTCTTGGTCCATTTCTTGGCA
EST: gi|208203370|gb|GD998810.1|GD998810
EST:     CAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTG                         CTCGAGATATTCAGGCATGGGAATATATTCCTCT
genomic: CAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTGgtagtttcca ... tatttggcagCTCGAGATATTCAGGCATGGGAATATATTCCTCT
EST: gi|192327116|gb|FK015508.1|FK015508
EST:     CA-TGCTAAAGATCACATCTTTGGACTTGTTCTGATGA-TGACTG-A-TG                         CTCGAGATAT-CAG-CATGG-A-TATATTC
genomic: CAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTGgtagtttcca ... tatttggcagCTCGAGATATTCAGGCATGGGAATATATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAACAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTGgtagtttccaattcaatctctctctctctctctctctcttgttatgttatggtgctcaacaagtgatgctttatttgaattgtatttggcag

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