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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctactcttctcttatttttatttttattttccgatgattcatttttcatatccctcgtttatttttttttgttggcaatttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAGAAGAGCGGTGAAACAGCCACCGAAGAAGAGTAAAGTGCCACTCTCAAAT

Basic information

species Glycine max
transcript GLYMA17G03550.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G03550.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g28750.1 (Oryza sativa), 3'ss of exon 1
--------gtattctactcttctcttatttttatttttattt--tccgatgattcatttttcatatccctcgtttatttttttttgttggcaatttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAGAAGAGCGGTGAAACAGCCACCGAAGAAGAGTAAAGTGCCACTCTCAAAT
          |||| | | | |||    || | ||   |||   |||  |       ||| |   | | |   |   || |||  ||       |||| |||||||| |||||||| || ||||||||||||||| |||||||||| ||||||||||| |||||  | |   |||| ||  |                    
tcggaaatcaattcaaatgtcctcgctgttatgttgaaattgaatcctgttgccttgtttccgcgttcttacctgggttcttt--gtaaattgcttttatagATGGACCCAAAGTTCCTCAGGAACCAGAGGTACTCGAGGAAGCACAACAAGAAGAGTGGTGAGGCTGAATCCGAGGAGTAA-------------------

upper sequence: GLYMA17G03550.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g19840.1 (Oryza sativa), 3'ss of exon 2
---------gtattctactcttctcttatttttatttttattttccgatgattcatttttcatatccctcgtttatttttttttgttggcaatttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAGAAGAGCGGTGAAACAGCCACCGAAGA---AGAGTAAAGTGCCACTCTCAAAT
          |  | ||    ||  | | | || |    |  | |  |   ||    |    ||  | ||  | | |  | ||| ||  | || ||| |||||||| |||||||| |||||||||||||| ||  | |||||||||||||||||||| |||||  | |   |||| ||   |||   ||||    || ||    
ttatcttgaattgtttatcaatcaatcagtattgtgcacaaatccaaaatttttgcctcctttacacttctctcactgatcttt-ttcaccatgtttatagATGGACCCAAAGTTCCTGAGGAACCAGAGATATTCCAGGAAGCATAACAAGAAGAGTGGTGAGGCTGAATCCGAGGAGTAAGATGGAAGTTGTCCTTTCG---
















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|12772062|gb|BG236989.1|BG236989
EST:     AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
EST: gi|24205832|gb|BU965085.1|BU965085
EST:     AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
EST: gi|58014658|gb|CX701400.1|CX701400
EST:     AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
EST: gi|254343184|gb|GR859346.1|GR859346
EST:     AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
EST: gi|16280819|gb|BI944162.1|BI944162
EST:     AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
EST: gi|17963907|gb|BM270650.1|BM270650
EST:     AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
EST: gi|254341697|gb|GR852834.1|GR852834
EST:     AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
EST: gi|6951358|gb|AW423426.1|AW423426
EST:     AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
EST: gi|14990191|gb|BI315864.1|BI315864
EST:     AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
EST: gi|209701113|gb|BW652641.1|BW652641
EST:     AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
EST: gi|192319415|gb|FK005855.1|FK005855
EST:     AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
EST: gi|209701112|gb|BW652640.1|BW652640
EST:     AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
EST: gi|192319416|gb|FK005856.1|FK005856
EST:     AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
EST: gi|6667850|gb|AW279301.1|AW279301
EST:     AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
EST: gi|11274886|gb|BF325211.1|BF325211
EST:     AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
EST: gi|15815077|gb|BI787352.1|BI787352
EST:     AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
EST: gi|8285210|gb|BE022769.1|BE022769
EST:     AGAATGGCATCAAAAAGCCAAAGAGGC-TCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
EST: gi|12690103|gb|BG156439.1|BG156439
EST:     AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
EST: gi|192325585|gb|FK019441.1|FK019441
EST:     AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
EST: gi|21675358|gb|BQ627709.1|BQ627709
EST:     AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGG                         ATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG
genomic: AGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAAAGGGgtattctact ... atttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgattcatttttcatatccctcgtttatttttttttgttggcaatttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAGAAGAGCGGTGAAACAGCCACCGAAGAAGAGTAAAGTGCCACTCTCAAAT
                                              tttttgt  CT-rich tract
                         tttatttttttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattctactcttctcttatttttatttttattttccgatgattcatttttcatatccctcgtttatttttttttgttggcaatttttgtagATGGATCCAAAGTTTCTGAGGAACCAGAGGTACGCGAGGAAGCATAACAAGAAGAGCGGTGAAACAGCCACCGAAGAAGAGTAAAGTGCCACTCTCAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG