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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaaatggacaaaaaattaaagtaaaacacatgatgtagacttactgacataaatggtccaagttggctcaatgtatttgaatttcaattattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACGTATACGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA

Basic information

species Glycine max
transcript GLYMA08G39340.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G39340.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g50260.1 (Oryza sativa), 3'ss of exon 3
-------tgcaaatggacaaaaaattaaagtaaaacacatgatgtagacttactgacataaatggtccaagttggctcaatgtatttgaatttcaattattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACGTATACGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA
         ||  || | |||     |   |  |  || | | | | |  ||   |||    | || |||||      | |    ||   | ||  | ||   ||||| ||||| ||| |||| || || || || |||    || || || |||| ||||| |||||||||||||||||||| |||||||||||  ||||||||| 
ttcagtgctcacttgtagaaaccgacaggattcaggac-taagggaaagctaaaaacac---tagtacaagtatctgaagtaatatttgctctctgtgat---gcagGCGATGATTGTGTTTCCATCCAGACAGGCTGCAGTGACATAAACATACATAATGTGAACTGTGGACCAGGGCATGGGATCAGCATTGGTGGTCTAGGAAG

upper sequence: GLYMA08G39340.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g45060.1 (Oryza sativa), 3'ss of exon 5
tgcaaatggacaaaaaattaaagta-aaacacatgatgtagacttact-gacataaatggtccaagttggctca-atgtatttgaatttcaattattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACGTATACGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA
   |||     | |  | | || ||  ||   ||  | |  | |||||  ||| ||   |   ||  | | | | ||||| ||     || | |||  |||||| ||||||||  | || || ||||| ||||||   ||  || |  |||||||||| || |||||||| || |||||||||||||||||| | |||||   
---aaacttcaagagtactgaactatgaagctatcttttgcagttactcaacaaaagcagaaaaacatagttaacatgtaatttttggtcgaatatgatgcagGTGATGACTGCGTCTCCATTCAAACAGGATGCAGCAATATAAATATACACAATGTGAATTGTGGACCTGGCCATGGAATCAGCATTGGAGGCCTAGGCCG

upper sequence: GLYMA08G39340.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g44970.1 (Oryza sativa), 3'ss of exon 5
tgcaaatggacaaaaaattaaagta-aaacacatgatgtagacttact-gacataaatggtccaagttggctca-atgtatttgaatttcaattattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACGTATACGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA
   |||     | |  | | || ||  ||   ||  | |  | |||||  ||| ||   |   ||  | | | | ||||||||     ||   |||  |||||| ||||||||  | || || ||||| ||||||   ||  || |  |||||||||| || |||||||| || |||||||||||||||||| | |||||   
---aaacttcaagagtactgaactatgaagctatcttttgcagttactcaacaaaagcagaaaaacatagttaacatgtattttttggtcgtatatgatgcagGTGATGACTGCGTCTCCATTCAAACAGGATGCAGCAATATAAATATACACAATGTGAATTGTGGACCTGGCCATGGAATCAGCATTGGAGGCCTAGGCCG

upper sequence: GLYMA08G39340.2 (Glycine max), 3'ss of exon 4
lower sequence: AT1G60590.1 (Arabidopsis thaliana), 3'ss of exon 5
tgcaaatggacaaaaaattaaagtaaaacacatgatgtagacttactgacataaatggtccaagttggctcaatgtatttgaatttcaattattttgc-agGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACGTATACGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA
     | | || ||   | |  | ||||  | | ||  | |||      | |||||    |  ||   || ||| |  |||| || |   | |||| | |||||| || ||||||||||| ||||| || ||||| || || || || |||||||| || ||||||||||||||||||||||||||||| || || || ||
---gtacgaactaattgtaatcgaaaaaatcgttata-aaact------cgtaaata--tcgggt---cttaatatcgttgatttccctctgtttttccagGAGACGATTGTATTTCGATTCAAACCGGTTGCTCCAATGTGTATGTTCACAATGTGAATTGTGGACCAGGGCATGGAATCAGCATTGGTAGCCTTGGTAA

upper sequence: GLYMA08G39340.2 (Glycine max), 3'ss of exon 4
lower sequence: AT1G10640.1 (Arabidopsis thaliana), 3'ss of exon 5
tgcaaatggacaaaaaattaaagtaaaacacatgatgtagacttactgacataaatggtccaagttggctcaatgtatttgaatttcaattattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACGTATACGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA
                  |||  | |    ||   |  |  | |       ||||   ||  | ||  || ||  | |   ||  |  |  ||| |||||||||||||||||| ||||| ||||| || ||||||||||| |  || |||||||| ||||||||||| || || || ||||||||||| ||||| || ||
-----------------gtaatatgatctccaatcttaaatcctgaatctttaaaaaatctcaatt--cttaa-atctagaaaccttga--attatgcagGAGATGACTGTATCTCGATCCAAACGGGTTGCTCGAACGTGTTTGTGCACAATGTGAACTGTGGACCGGGTCACGGGATCAGCATTGGTAGTCTCGGCAA

upper sequence: GLYMA08G39340.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0127g00400.t01 (Vitis vinifera), 3'ss of exon 6
tgcaaatggacaaaaaattaaagtaaaacacatgatgtagactta-ctgacataaatg-gtccaagttggctcaatgtatttgaatttcaattatt-ttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACGTATACGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA
    ||   | ||  |     | ||   || |  ||  | |  || | | |  | |||     |  ||     |  |  | | ||| | |||  |   |||||||||||||||| |||| ||||||||||||||||| || |||||| |||||||||| |||||||| ||||| ||||| ||||| || ||| | || |||| 
---taacacataagcatagctaatagcccagacaattaacatctaacaggcccatatgtagatatattctaatacgggctctaaatcttaatgctcactgcagGAGATGACTGTGTTTCTATACAAACTGGATGCTCAAATGTATACATACACAATGTGAACTGTGGGCCAGGACATGGGATCAGTATAGGAGGACTTGGAAG

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|208230231|gb|GE031146.1|GE031146
EST:     CCTTCAGAACTCCAAAGATGTGTTAATATACGGCAGCACCATGGCCTGCG                         GAGATGACTGTATTTCGATACAAACTGGATGCTCGAACGTATACGTACACA
genomic: CCTTCAGAACTCCAAAGATGTGTTAATATACGGCAGCACCATGGCCTGCGgtaatatttc ... tattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACGTATACGTACACA
EST: gi|193562329|gb|FK517348.1|FK517348
EST:     CCTTNAGAACTCCAAAGATGTGTTAATATACGGCAGCACCATGGCCTGCG                         GAGATGACTGTATTTCGATACAAACTGGATGCTCGAACGTNTACGTACAC
genomic: CCTTCAGAACTCCAAAGATGTGTTAATATACGGCAGCACCATGGCCTGCGgtaatatttc ... tattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACGTATACGTACAC
EST: gi|193426830|gb|FK397459.1|FK397459
EST:     GTTAATATACGGCAGCACCATGGCCTGCG                         GAGATGACTGTATTTCGATACAAACTGGATGCTCGAACGTATACGTACACA
genomic: GTTAATATACGGCAGCACCATGGCCTGCGgtaatatttc ... tattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACGTATACGTACACA
EST: gi|208299132|gb|GE100507.1|GE100507
EST:     AAAGATGTGTTAATATACGGCAGCACCATGGCCTGCG                         GAGATGACTGTATTTCGATACAAACTGGATGCTCGAACGTATACGTACACA
genomic: AAAGATGTGTTAATATACGGCAGCACCATGGCCTGCGgtaatatttc ... tattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACGTATACGTACACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgacataaatggtccaagttggctcaatgtatttgaatttcaattattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACGTATACGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA
                                            ttatttt  CT-rich tract
                        tcaatgtatttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcaaatggacaaaaaattaaagtaaaacacatgatgtagacttactgacataaatggtccaagttggctcaatgtatttgaatttcaattattttgcagGAGATGACTGTATTTCGATACAAACTGGATGCTCGAACGTATACGTACACAATGTCAACTGTGGACCAGGGCATGGAATCAGCATTGGAAGTCTAGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG