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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttacctgtaatatgaaaaagtgaattctgtaatgcatacactcctgaagtgacataaagttgacttcaaagaaaattttaagactgaaattgatctaataagcactcagttttttatctgtaaaccttataaactgtaatttgtggaatataactgtgcagATACATGGTATTTCGAGGAGCAAACAAGCAAAAGCATGTGTTCAAAAAGAATCCAAAGGCTCCTATCTGGGGTAAGCCTCCAAAAGTCATTGGTGGAAAG

Basic information

species Glycine max
transcript GLYMA13G21450.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G21450.2 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G473533_T05 (Zea mays), 3'ss of exon 9
gtaacttacctgtaatatgaaaaagtgaattctgtaatgcatacactcctgaagtgacataaagttgacttcaaagaaaattttaagactgaaattgatctaataagcactcagttttttatctgtaaacct------tataaactgtaatttgtggaatataactgtgcagATACATGGTATTTCGAGGAGCAAACAAGCAAAAGCATGTGTTCAAAAAGAATCCAAAGGCTCCTATCTGGGGTAAGCCTCCAAAAGTCATTGGTGGAAAG
                                                                      |     | ||| | ||  ||  |    || | |||   ||    || ||    |||||   |      || |  || ||   ||||| || |   |   ||| ||| | || || |||||||| ||||||||||| ||||||||||| ||| | || || |||||||| ||||| || ||||| |||||  | || ||||||
----------------------------------------------------------------------ttctccagaatatcaaagctatagc-aatttgatatatacctgtttcttgcattgtaactttgttgtctacatgctataccatgtggcatgtgg-tactcagCTACCTAGTGTTCCGAGGAGCTAACAAGCAAAAACATGTGTTCAAGAAGGACCCCAAAGCTCCTATATGGGGAAAACCTCCCAAAGTTGTCGGGGGAAAG

upper sequence: GLYMA13G21450.2 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G473533_T06 (Zea mays), 3'ss of exon 10
gtaacttacctgtaatatgaaaaagtgaattctgtaatgcatacactcctgaagtgacataaagttgacttcaaagaaaattttaagactgaaattgatctaataagcactcagttttttatctgtaaacct------tataaactgtaatttgtggaatataactgtgcagATACATGGTATTTCGAGGAGCAAACAAGCAAAAGCATGTGTTCAAAAAGAATCCAAAGGCTCCTATCTGGGGTAAGCCTCCAAAAGTCATTGGTGGAAAG
                                                     ||    |    ||  || || |    || | ||  ||  |    || | |||   ||    || ||    |||||   |      || |  || ||   ||||| || |   |   ||| ||| | || || |||||||| ||||||||||| ||||||||||| ||| | || || |||||||| ||||| || ||||| |||||  | || ||||||
-----------------------------------------------------gtactcttggtttttctccaga----atatcaaagctatagc-aatttgatatatacctgtttcttgcattgtaactttgttgtctacatgctataccatgtggcatgtgg-tactcagCTACCTAGTGTTCCGAGGAGCTAACAAGCAAAAACATGTGTTCAAGAAGGACCCCAAAGCTCCTATATGGGGAAAACCTCCCAAAGTTGTCGGGGGAAAG

upper sequence: GLYMA13G21450.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv08s0007g03930.t01 (Vitis vinifera), 3'ss of exon 10
gtaacttacctgtaatatgaaaaagtgaattctgtaatgcatacactcctgaagtgacataaagttgacttcaaagaaaattttaagactgaaattgatctaataagcactcagttttttatctgtaaaccttataaactgtaatttgtggaatataactgtgcagATACATGGTATTTCGAGGAGCAAACAAGCAAAAGCATGTGTTCAAAAAGAATCCAAAGGCTCCTATCTGGGGTAAGCCTCCAAAAGTCATTGGTGGAAAG
                                                               || |   || |   |    |||    ||  |||   |  |        ||  |||||  | |   ||||  |||| ||  | || |  | || ||  | |||| ||    || ||| |||| || ||||| |||||||| ||||| || |||||||| ||||| | ||| |||||||||||||||| ||| ||||| ||||||
---------------------------------------------------------------gtaggtctctatcga---cttatatttggcatttggcagactcat-tccaactttttcccagagcacctgctaaaatgacacttttata-taaaatggggcagGTATCAAGTGTTTAGAGGGGCTAACAAACAAAAGCACGTGTTTAAGAAGAATCCCAAGGCACTTATTTGGGGTAAGCCTCCAAGAGTTATTGGGGGAAAG

upper sequence: GLYMA13G21450.2 (Glycine max), 3'ss of exon 10
lower sequence: EFJ22157 (Selaginella moellendorffii), 3'ss of exon 9
gtaacttacctgtaatatgaaaaagtgaattctgtaatgcatacactcctgaagtgacataaagttgacttcaaagaaaattttaagactgaaattgatctaataagcactcagttttttatctgtaaaccttataaactgtaatttgtggaatataactgtgc-agATACATGGTATTTCGAGGAGCAAACAAGCAAAAGCATGTGTTCAAAAAGAATCCAAAGGCTCCTATCTGGGGTAAGCCTCCAAAAGTCATTGGTGGAAAG-
                                                                                                                  | || | |||  |    |||   | |    |    | |   | | ||| | || ||     ||||| |||| ||||||||||||||||| | |||||| ||||| ||||||||||| || ||||| || || ||     |||| || |||||  
------------------------------------------------------------------------------------------------------------------tattgtttctccag-ttttacttattacgct----gaagcttgattgttccaggTATGCAATATTTAGAGGTGCAAACAAGCAAAAGCACGAGTTCAAGAAGAACCCAAAGGCTCCAATATGGGGGAAACCACCTGTTCTCATCGGAGGAAAAC

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|192294028|gb|FG987197.1|FG987197
EST:     GAGTTAACACCAGCTGCCATTGTAGCTAATTGCTTTGTGTTCCTGATTGG                         ATACATGGTATTTCGAGGAGCAAACAAGCAAAAGCATGTGTTCAAAAAGAA
genomic: GAGTTAACACCAGCTGCCATTGTAGCTAATTGCTTTGTGTTCCTGATTGGgtaacttacc ... aactgtgcagATACATGGTATTTCGAGGAGCAAACAAGCAAAAGCATGTGTTCAAAAAGAA
EST: gi|193335814|gb|FK299744.1|FK299744
EST:     GAGTTAACACCAGCTGCCATTGTAGCTAATTGCTTTGTGTTCCTGATTGG                         ATACATGGTATTTCGAGGAGCAAACAAGCAAAAGCATGTGTTCAAAAAGAA
genomic: GAGTTAACACCAGCTGCCATTGTAGCTAATTGCTTTGTGTTCCTGATTGGgtaacttacc ... aactgtgcagATACATGGTATTTCGAGGAGCAAACAAGCAAAAGCATGTGTTCAAAAAGAA
EST: gi|192299546|gb|FG992574.1|FG992574
EST:     GAGTTAACACCAGCTGCCATTGTAGCTAATTGCTTTGTGTTCCTGATTGG                         ATACATGGTATTTCGAGGAGCAAACAAGCAAAAGCATGTGTTCAAAAAGAA
genomic: GAGTTAACACCAGCTGCCATTGTAGCTAATTGCTTTGTGTTCCTGATTGGgtaacttacc ... aactgtgcagATACATGGTATTTCGAGGAGCAAACAAGCAAAAGCATGTGTTCAAAAAGAA
EST: gi|254340702|gb|GR854430.1|GR854430
EST:     GAGTTAACACCAGCTGCCATTGTAGCTAATTGCTTTGTGTTCCTGATTGG                         ATACATGGTATTTCGAGGAGCAAACAAGCAAAAGCATGTGTTCAAAAAGAA
genomic: GAGTTAACACCAGCTGCCATTGTAGCTAATTGCTTTGTGTTCCTGATTGGgtaacttacc ... aactgtgcagATACATGGTATTTCGAGGAGCAAACAAGCAAAAGCATGTGTTCAAAAAGAA
EST: gi|254335603|gb|GR847131.1|GR847131
EST:     GAGTTAACACCAGCTGCCATTGTAGCTAATTGCTTTGTGTTCCTGATTGG                         ATACATGGTATTTCGAGGAGCAAACAAGCAAAAGCATGTGTTCAAAAAGAA
genomic: GAGTTAACACCAGCTGCCATTGTAGCTAATTGCTTTGTGTTCCTGATTGGgtaacttacc ... aactgtgcagATACATGGTATTTCGAGGAGCAAACAAGCAAAAGCATGTGTTCAAAAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttttttatctgtaaaccttataaactgtaatttgtggaatataactgtgcagATACATGGTATTTCGAGGAGCAAACAAGCAAAAGCATGTGTTCAAAAAGAATCCAAAGGCTCCTATCTGGGGTAAGCCTCCAAAAGTCATTGGTGGAAAG
                                         atataac  putative branch site (score: 3)
                    ttataaactgtaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttacctgtaatatgaaaaagtgaattctgtaatgcatacactcctgaagtgacataaagttgacttcaaagaaaattttaagactgaaattgatctaataagcactcagttttttatctgtaaaccttataaactgtaatttgtggaatataactgtgcagATACATGGTATTTCGAGGAGCAAACAAGCAAAAGCATGTGTTCAAAAAGAATCCAAAGGCTCCTATCTGGGGTAAGCCTCCAAAAGTCATTGGTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA