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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccccctgtaatagagattttctccatgagtttgatcttagtttaatcttaataccggctcttatcagtattgttattgaattgccatacttgtttaacagGAACAAAGTTATCAGAAGATAGCAGGAAATATGGTGCAGATAATACATGTACCAGTGGTAGTACTTTATCAAGAGCTGCGCTAAATTATGCACGTGCCCG

Basic information

species Glycine max
transcript GLYMA06G01120.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 3
lower sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 3
------------ccccctgtaatagagattttctccatgagtttgatcttagtttaatcttaataccggctcttatcagtattgttattgaattgccatac-ttgtttaacagGAACAAAGTTATCAGAAGATAGCAGGAAATATGGTGCAGATAATACATGTACCAGTGGTAGTACTTTATCAAGAGCTGCGCTAAATTATGCACGTGCCCG
             ||| |  | |    | ||  |  ||   |||     |  | ||  ||| | |  |||||    |||   |||  || | ||  ||  | || || | |||| || || || || || |||||||||||||||||| |||| ||||||||||| | |||||     ||| || | ||||| || || ||||  ||||| ||
gtgatttttttgaccctttgagttttaacttattgtatttttttatgtctgttatagacttga-attggctca---caggcctgtctttcattttgcactcatttttcatcagGTACGAAATTGTCTGAGGATAGCAGGAAATATGGTTCAGAGAATACATGTACGAATGGTAACGTATTAACACGGGCTGCACTGAACTATGGGCGTGCTCG

upper sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g13530.t01 (Vitis vinifera), 3'ss of exon 3
ccccctgtaatagagattttctccatgagtttgatcttagtttaatcttaataccggctcttatcagtattgttattgaattgccatacttgtttaacagGAACAAAGTTATCAGAAGATAGCAGGAAATATGGTGCAGATAATACATGTACCAGTGGTAGTACTTTATCAAGAGCTGCGCTAAATTATGCACGTGCCCG
            | ||  | ||      ||||   |||  ||     || ||  |   |  |     |    |||   | |||| ||  || |  |||||| || ||||| |||||||| ||||| ||||||||||  || || || ||||||||||| ||||| ||||| | ||||||  |||  | |||  | || ||
------------gtgagctgctgagactgtttttcctttattggtatttcatttca--tgctgctttttcatttacgtacttgcaatctttat--aacagGTACCAAGTTGTCAGAAGACAGCAGAAAATATGGTGTTGAAAACACTTGTACCAGTGGCAGTACCTTATCTAAAGCTGCATTAAGCTTTGCTAGAGCTCG

upper sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 3
ccccctgtaatagagattttctccatga-gtttgatcttagtttaatcttaat-------accggctcttatcagtattgttattgaattgccatacttgtttaacagGAACAAAGTTATCAGAAGATAGCAGGAAATATGGTGCAGATAATACATGTACCAGTGGTAGTACTTTATCAAGAGCTGCGCTAAATTATGCACGTGCCCG
     |||  | | ||   | |  ||   ||||  |  || | ||||   |||       |  | ||    |  || ||||| | | | || || ||||||||  |||||||||| || ||||||||| |||||||||||||||  || ||||| ||||||||||||| ||| ||||| | ||||||  | ||||||| ||| || ||
----gtgtgttggtgaaacttttgattttgttttttactattataattcaaatgaatgcaaaggacttgactttgttttgttgt-gtactgtca-acttgtttttcagGAACAAAATTGTCAGAAGATTGCAGGAAATATGGTGTTGAAAATACTTGTACCAGTGGTAATACGTTATCGAAAGCTGCATTGAATTATGGACGAGCTCG

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|298181208|gb|HO022647.1|HO022647
EST:     CCGCGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATGG                         GAACAAAGTTATCAGAAGATAGCAGGAAATATGGTGCAGATAATACATGTA
genomic: CCGCGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAGgtcagtaatt ... tgtttaacagGAACAAAGTTATCAGAAGATAGCAGGAAATATGGTGCAGATAATACATGTA
EST: gi|9987696|gb|BE661804.1|BE661804
EST:     CCGCGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAG                         GAACAAAGTTATCAGAAGATAGCAGGAAATATGGTGCAGATAATACATGTA
genomic: CCGCGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAGgtcagtaatt ... tgtttaacagGAACAAAGTTATCAGAAGATAGCAGGAAATATGGTGCAGATAATACATGTA
EST: gi|193633792|gb|FK582426.1|FK582426
EST:     CCGTGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAG                         GAACAAAGTTATCAGAAGATAACAGGAAATATGGTGCAGATAATACGTGTA
genomic: CCGCGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAGgtcagtaatt ... tgtttaacagGAACAAAGTTATCAGAAGATAGCAGGAAATATGGTGCAGATAATACATGTA
EST: gi|151395558|gb|EV265435.1|EV265435
EST:     CCGCGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAG                         GAACAAAGTTATCAGAAGATAGCAGGAAATATGGTGCAGATAATACATGTA
genomic: CCGCGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAGgtcagtaatt ... tgtttaacagGAACAAAGTTATCAGAAGATAGCAGGAAATATGGTGCAGATAATACATGTA
EST: gi|18040044|gb|BM308338.1|BM308338
EST:     CCGTGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAG                         GAACAAAGTTATCAGAAGATAACAGGAAATATGGTGCAGATAATACGTGTA
genomic: CCGCGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAGgtcagtaatt ... tgtttaacagGAACAAAGTTATCAGAAGATAGCAGGAAATATGGTGCAGATAATACATGTA
EST: gi|11688247|gb|BF595923.1|BF595923
EST:     CCGTGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAT                         GAACAAAGTTATCAGAAGATAACAGGAAATATGGTGCAGATAATACGTGTA
genomic: CCGCGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAGgtcagtaatt ... tgtttaacagGAACAAAGTTATCAGAAGATAGCAGGAAATATGGTGCAGATAATACATGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttaataccggctcttatcagtattgttattgaattgccatacttgtttaacagGAACAAAGTTATCAGAAGATAGCAGGAAATATGGTGCAGATAATACATGTACCAGTGGTAGTACTTTATCAAGAGCTGCGCTAAATTATGCACGTGCCCG
                                           cttgttt  CT-rich tract
                      tattgttattgaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccccctgtaatagagattttctccatgagtttgatcttagtttaatcttaataccggctcttatcagtattgttattgaattgccatacttgtttaacagGAACAAAGTTATCAGAAGATAGCAGGAAATATGGTGCAGATAATACATGTACCAGTGGTAGTACTTTATCAAGAGCTGCGCTAAATTATGCACGTGCCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
ccccctg
- - - - - - - - - ttctcca
- - - - - - - - - - - - - gagtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatact