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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttaacttctgtgttctgtttcactctatatcctaagttggggcagtggctgatttttatgtttctggttttttttcagGGTGCACAAAATGAAAGTTTGCCGTATGTATATTATAACTATGGATATGCACAGTCTCCATACAATCCATATAATCCTTACATTCCTGGTGCTATGATTG

Basic information

species Glycine max
transcript GLYMA09G03590.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G03590.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G17330.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------gtaagtttaacttctgtgttctgtttc----actctatat--cctaag---ttggggcagtggct--gatttttatgtttctggttttttttcagGGTGCACAAAATGAAAGTTTGCCGTATGTATATTATA------ACTATGGATATGCACAGTCTCCATACAATCCATATAATCCTTACATTCCTGGTGCTATGATTG
                 | |  || |||| |   |  || ||       |  | ||  |||||     |||  |  |   |  | || | ||   |||| |   | |||||||||  |||||||||| |   || ||| | |  ||||        |||||||||||||||||||| ||||||||                                
gttgataggctggttcatgaaatttacttatcactcttgcttttgtggttgcaaattgcctaaaattctggaaccttttttcagGTTATGATTCATCTG-TGGGTCTTCAGGGTGGGCAAAATGAAAATGCTCCCTATATCTGCTATACACCAAGTTATGGATATGCACAGTCTCCCTACAATCC--------------------------------

upper sequence: GLYMA09G03590.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G17330.2 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------------gtaagtttaacttctgtgttctgtttc----actctatat--cctaag---ttggggcagtggct--gatttttatgtttctggttttttttcagGGTGCACAAAATGAAAGTTTGCCGTATGTATATTATA------ACTATGGATATGCACAGTCTCCATACAATCCATATAATCCTTACATTCCTGGTGCTATGATTG
                                 | |  || |||| |   |  || ||       |  | ||  |||||     |||  |  |   |  | || | ||   |||| |   | |||||||||  |||||||||| |   || ||| | |  ||||        |||||||||||||||||||| ||||||||                                
gcttattactcttcaggttgataggctggttcatgaaatttacttatcactcttgcttttgtggttgcaaattgcctaaaattctggaaccttttttcagGTTATGATTCATCTG-TGGGTCTTCAGGGTGGGCAAAATGAAAATGCTCCCTATATCTGCTATACACCAAGTTATGGATATGCACAGTCTCCCTACAATCC--------------------------------

upper sequence: GLYMA09G03590.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G48110.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------gtaagttta-acttctgtgttctgtttcactctatatcctaagttggggcagtggctgatttt-tatgtttctggttttttttcagGGTGCACAAAATGAAAGTTTGCCGTATGTATATTATA------ACTATGGATATGCACAGTCTCCATACAATCCATATAATCCTTACATTCCTGGTGCTATGATTG
           | |  |  | ||||||   |  |  || | |   | |  ||  ||  |  | | | |||  |  |||  || |  | ||| | |||||||  || ||||||| ||  || ||| |||  ||||        |||||||||||||||||||| || |||||||  ||||||||||| ||||| |||       
gtactaatctcggacataaagacttctcattaatcgttgatttgttcttatacattttg-tatttgttgacatgatatcctttttttgtttctccagGGTGGGCAGAATGAAAATTCTCCCTATATATGCTATACACCTAGTTATGGATATGCACAGTCTCCTTATAATCCATTCAATCCTTACATACCTGGCGCTT------

upper sequence: GLYMA09G03590.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------gtaagtttaacttctgtgttctgtttcactctatatcctaagttggggcagtggctgatttttatgtttctggttttttttcagGGTGCACAAAATGAAAGTTTGCCGTATGTATATTATA------ACTATGGATATGCACAGTCTCCATACAATCCATATAATCCTTACATTCCTGGTGCTATGATTG
                                    |   || ||     || |  ||||||  | ||  |  | | ||| |   ||   | || |  |  ||  |    ||  |||||||||| |||| ||| |||||||| |||||||||||||       |||||||||||||||||| |||||||| ||||| ||||||||||| |||||||| |      
gtaagttaaatatgtcatttattttcatttgctaactctcttaaatacaagtttgatgtttc-ttttagttgatcatttgtgattgttcgtaatgtccaccttctt---cttgcttcagGGTGCGCAAACTGATAGTTTGCCTTATGTATATTATACACCTAGCTATGGATATGCACAGTCACCATACAACCCATACAATCCTTACATACCTGGTGCCA------

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|11412481|gb|BF424492.1|BF424492
EST:     AGGACCACCATAGGATTTTTGGTGTAGATGGTCCCAATATTCAGTTCATG                         GGTGCACAAAATGAAAGTTTGCCGTATGTATATTATAACTATGGATATGCA
genomic: AGGACCACCATAGGATTTTTGGTGTAGATGGTCCCAATATTCAGTTCATGgtaagtttaa ... tttttttcagGGTGCACAAAATGAAAGTTTGCCGTATGTATATTATAACTATGGATATGCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatatcctaagttggggcagtggctgatttttatgtttctggttttttttcagGGTGCACAAAATGAAAGTTTGCCGTATGTATATTATAACTATGGATATGCACAGTCTCCATACAATCCATATAATCCTTACATTCCTGGTGCTATGATTG
                       ggctgat  putative branch site (score: 4)
                                     tttctggttttttttc  putative PPT
                          tgatttttatgttt  TA-rich tract