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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataagaacaccatttcatggtttatgggagcttacattagacttatgcaaacattcaatccattttggacaatatttgaagattttattttattcacagGTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAAAACAGTTTTTCAG

Basic information

species Glycine max
transcript GLYMA15G13380.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G13380.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g41170.1 (Oryza sativa), 3'ss of exon 4
----------------------------aataagaacaccatttcatggtttatgggagcttac---attagacttatgcaaacattcaatccattttg-gacaatatttgaagattttat-tttattcacagGTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAAAACAGTTTTTCAG
                            | | ||  ||   | | |   ||  |   ||| | |    ||  ||||    | | | |  ||| | ||   |||  | | | |  |   ||| | | |  | |||||||| ||||||||||| || |||||||| || ||||| |||||| |||||||||| ||||||
gtgagttactcaattgttcaactctactactgagctcatattatgaaaattcctcatagccttctaggttgaactttaatatataattcatcaacttcatgactttgtattaccaccatatgtatgtcgatagGTGGTGCCATGATATTGGCCGGGAACAAGCTGCCAATAAGCCTCTTCTAAAAACAGTATTTCAG

upper sequence: GLYMA15G13380.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G390374_T01 (Zea mays), 3'ss of exon 4
aataaga-acaccatttcatggtttatgggagcttacattagacttatgca---aacattcaatc----cattttggacaatatttgaagattttattt-tattcacagGTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAAAACAGTTTTTCAG
  | ||  || |  | | ||  | | |  ||| |  | ||||||||||      ||| || | |     || |    ||   |||| |    | | ||| | |  |||||||||| ||||||||||| || |||||||| || |||||||| ||| |||| || || ||||||
-gtgagtcaccctgtatgatattgt-tacgagttccccttagacttatttgttgaacctttagttatcacactacatacttaattttatctctatgtttatgtgtacagGTGGTGCCATGATATTGGCCGTGAACAAGCTGCCAATAAACCACTTCTAAAGACTGTATTTCAG

upper sequence: GLYMA15G13380.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0116g00810.t01 (Vitis vinifera), 3'ss of exon 3
aataagaacaccatttcatggtttatgggagcttacatta-gacttatgcaaacattcaatccattttggacaatatttgaa--gatttt--attttattcacagGTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAAAACAGTTTTTCAG
      | ||  |  ||| |  ||  |    | || ||   |  | ||||  |   |  ||   | | | || ||||  | |  || |||  || |   | |||||||||| ||||||||||||||||| || || || || ||||||||| | ||||||||||| |||
-----aatcatgagatcaagagtttcgcagacataaatggcgggtgatgctcagggtatattgttatagaactatatgagcattgaatttgaatatctattacagGTGGTGCCATGATATTGGTCGAGAGCATGCTGCGAACAAACCTCTTCTGAAAACAGTTTTCCAG

upper sequence: GLYMA15G13380.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ31796 (Selaginella moellendorffii), 3'ss of exon 5
aataagaacaccatttcatggtttatgggagcttacattagacttatgcaaacattcaatccattttggacaatatttgaagattttattttattcacagGTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAAAACAGTTTTTCAG
                                      ||   |  || |   | |   ||  |||      || || |    |  | |  ||     |||||||||||||||||||||||||| || ||||| || |||||| |  | || || || ||||||
-------------------------------------gtaagttgttgtag-tacttcgtctgttt------atgttcgtcagtactttcgta----aagGTGGTGTCATGATATTGGTCGAGAGCACGCAGCCAACAAACCTTTGCTGAAGACCGTCTTTCAG

upper sequence: GLYMA15G13380.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ38064 (Selaginella moellendorffii), 3'ss of exon 4
aataagaacaccatttcatggtttatgggagcttacattagacttatgcaaacattcaatccattttggacaatatttgaagattttattttattcacagGTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAAAACAGTTTTTCAG
                                         | || |   |  | |   ||  |||      || || |    |  | |  ||     |||||||||||||||||||||||||| || ||||| || |||||| |  | || || || ||||||
--------------------------------------gtaagttgtcgtagtacttcgtctgttt------atgttcgtcagtactttcgta----aagGTGGTGTCATGATATTGGTCGAGAGCACGCAGCCAACAAACCTTTGCTGAAGACCGTCTTTCAG

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|11689067|gb|BF596743.1|BF596743
EST:     CAGAGTGCTCTTTTTGCTTTGGCAATATCAGATATTGTTCTGATAAACAT                         GTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAA
genomic: CAGAGTGCTCTTTTTGCTTTGGCAATATCAGATATTGTTCTGATAAACATgtaagttttt ... ttattcacagGTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcaaacattcaatccattttggacaatatttgaagattttattttattcacagGTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAAAACAGTTTTTCAG
                                      ttttatttt  CT-rich tract
                        acaatatttgaagatt  TA-rich tract