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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatgccaaggtattattggtggtggtagcaattgtgaagcaggttaataataacaatgtacttttttaacagGTCTTGCTGTTAGCAACAGACATACTTACATGTTCTCTGCTGGTGACGATAAACAAGTTAAATGTTGGGATCTTGAACAGAATAAG

Basic information

species Glycine max
transcript GLYMA09G04910.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G04910.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 3'ss of exon 9
---------------------------------gtatgatgccaaggtattattggtggtggtagc-----aattgtgaagcaggttaataataacaatgtacttttttaacagGTCTTGCTGTTAGCAACAGACATACTTACATGTTCTCTGCTGGTGACGATAAACAAGTTAAATGTTGGGATCTTGAACAGAATAAG
                                 ||||     |     | |  |  | ||  ||       | || | |      ||| | |||| | |  |  |   |   ||| |||||||| ||| |  | || || ||  | || ||||||||||| || |||||||| || ||||||||||||||||| || |||
gtacgtttttcttggcattggttattaggatctgtatagcagccttccactgctacttgttttactctataagttataagttcatttactgataa-attcaatgtgcattgtagGGCTTGCTGTGAGCCAACGGCACACATATTTATTTTCTGCTGGTGATGACAAACAAGTAAAGTGTTGGGATCTTGAACAAAACAAG

upper sequence: GLYMA09G04910.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G017089_T02 (Zea mays), 3'ss of exon 7
---------------------------------gtatgatg-ccaaggtattattggtggtg-gtagcaattgtgaagcaggttaataataacaatgtacttttttaacagGTCTTGCTGTTAGCAACAGACATACTTACATGTTCTCTGCTGGTGACGATAAACAAGTTAAATGTTGGGATCTTGAACAGAATAAG
                                      |   ||| | ||  ||| |||       | ||   |  || |   | || |      || || ||  ||  ||| |||||||| ||| |  | || |||||  | || ||||||||||| || |||||||| |||||||||||||||||||| || |||
gtaagtttttctttgtttttgtgagcaggatctactcaacatccacgctaagatttgtgccccactgtaaaactttagtaa-ctgatgaatgttctgcacattacta-tagGACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAG

upper sequence: GLYMA09G04910.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S402_49V6.1 (Physcomitrella patens), 3'ss of exon 7
------------gtatgatgccaaggtattattggtggtggtagcaattg---tgaagcaggttaataataac--aatgtacttttttaacagGTCTTGCTGTTAGCAACAGACATACTTACATGTTCTCTGCTGGTGACGATAAACAAGTTAAATGTTGGGATCTTGAACAGAATAAG
            || ||     |    ||| ||     | ||  | ||||   ||   || ||| | |  ||   |||| |  |  |   |||| ||||| || |||  | | ||| ||||  | ||||| |||||||| || ||||| || |||||||||||||||||| | ||||||
gtttgttactgagtttggccaaatcccatttttacacttagtttctattgatgtggcacatgttgacagcaaatgaatggatgtgatcggcagGCCTTGCAGTGAGCGCCCGGCATCCTTATTTATTCTCAGCTGGTGATGACAAACAGGTCAAATGTTGGGATCTTGAATACAATAAG

upper sequence: GLYMA09G04910.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S169_73V6.2 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------------------------gtatgatgccaaggtattattggtggtggtagcaattgtgaagcag--gttaataataacaatgtacttttttaacagGTCTTGCTGTTAGCAACAGACATACTTACATGTTCTCTGCTGGTGACGATAAACAAGTTAAATGTTGGGATCTTGAACAGAATAAG
                                                            ||| | |     ||||  |        |    ||   || ||||  |||||   ||     ||   | || ||||||||| || || ||     ||||| |||||||||| || |||||||| ||||| ||||| ||||| |||||||||||  | || |||
gtacgtcaagtcattaggtcaattgcgctcgcttttgaatcgacgatgaaatcccatttaatggtacatgcttatttcttcactcttttctgatccagatgcagaggttaaaggtacatgagtggatgttgaacagGTCTCGCAGTGAGTGCTCGACATCCTTACATGTTTTCAGCTGGTGATGATAAGCAAGTCAAATGCTGGGATCTTGAGTACAACAAG

upper sequence: GLYMA09G04910.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ31158 (Selaginella moellendorffii), 3'ss of exon 9
gtatgatgccaaggtattattggtggtggtagcaattgtgaagcaggttaataataacaatgtacttttttaacagGTCTTGCTGTTAGCAACAGACATACTTACATGTTCTCTGCTGGTGACGATAAACAAGTTAAATGTTGGGATCTTGAACAGAATAAG
    | |  ||   ||   |||  | | | |   | | | ||  | |||  |  ||    | |   |||  || ||| || ||||||||     | ||| |||||||||| || ||||| ||||| || ||||| |||||||||||||| ||| | || |||
----gtttgcattctacatttgaagtttggatttagtcttaa--atgtttcttgta----tatttgtttgaaaaagGGCTGGCTGTTAGTCCACGCCATCCTTACATGTTTTCGGCTGGAGACGACAAGCAAGTGAAATGTTGGGATCTCGAATACAACAAG

upper sequence: GLYMA09G04910.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ17196 (Selaginella moellendorffii), 3'ss of exon 3
gtatgatgccaaggtattattggtggtggtagcaattgtgaagcaggtt--aataataacaatgtacttttttaacagGTCTTGCTGTTAGCAACAGACATACTTACATGTTCTCTGCTGGTGACGATAAACAAGTTAAATGTTGGGATCTTGAACAGAATAAG
            | |   |||        | | | ||  ||   ||  |  |||  |     | ||  |||  || ||| || ||||||||     | ||| |||||||||| || ||||| ||||| || ||||| |||||||||||||| ||| | || |||
------------gtttgcatt--ctacatttgaagtttggatttagtcttaaatgtttcttgtatatgtttgaaatagGGCTGGCTGTTAGTCCACGCCATCCTTACATGTTTTCGGCTGGAGACGACAAGCAAGTGAAATGTTGGGATCTCGAATACAACAAG

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|193543318|gb|FK502497.1|FK502497
EST:     AAGTGGAGTATTGAAGCTCACATTAACAGGCCACATTGAACAAGTTAGAG                         GTCTTGCTGCTAGCAACAGACATACTTACATGTTCTCTGCTGGTGATGATA
genomic: AAGTGGAGTATTGAAGCTCACATTAACAGGCCACATTGAACAAGTTAGAGgtatgatgcc ... tttttaacagGTCTTGCTGTTAGCAACAGACATACTTACATGTTCTCTGCTGGTGACGATA
EST: gi|254313963|gb|GR831592.1|GR831592
EST:     AAGTGGAGTATTGAAGCTCACATTAACAGGCCACATTGAACAAGTTAGAG                         GTCTTGCTGTTAGCAACAGACATACTTACATGTTCTCTGCTGGTGATGATA
genomic: AAGTGGAGTATTGAAGCTCACATTAACAGGCCACATTGAACAAGTTAGAGgtatgatgcc ... tttttaacagGTCTTGCTGTTAGCAACAGACATACTTACATGTTCTCTGCTGGTGACGATA
EST: gi|208049582|gb|GD849367.1|GD849367
EST:     AAGTGGAGTATTGAAGCTCACATTAACAGGCCACATTGAACAAGTTAGAG                         GTCTTGCTGTTAGCAACAGACATACTTACATGTTCTCTGCTGGTGACGATA
genomic: AAGTGGAGTATTGAAGCTCACATTAACAGGCCACATTGAACAAGTTAGAGgtatgatgcc ... tttttaacagGTCTTGCTGTTAGCAACAGACATACTTACATGTTCTCTGCTGGTGACGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtggtggtagcaattgtgaagcaggttaataataacaatgtacttttttaacagGTCTTGCTGTTAGCAACAGACATACTTACATGTTCTCTGCTGGTGACGATAAACAAGTTAAATGTTGGGATCTTGAACAGAATAAG
                              taataac  putative branch site (score: 1)
                                         tactttttt  putative PPT
                          ttaataataacaatgt  TA-rich tract