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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaatttttttttctaggtctagctccatcatccttctatgggtttctaaaaaaattgctataaatttacagATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCAGCATTTCGAACATCACCCTTGTTTCGATTTGATTGGTTTGTCAAATCTC

Basic information

species Glycine max
transcript GLYMA13G28720.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 22
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 22
----------gtacaatttttttttctaggtctagctccatcatccttctatgggtttctaaaaaaattgctataaatttacagATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCAGCATTTCGAACATCACCCTTGTTTCGATTTGATTGGTTTGTCAAATCTC
            |||||| ||  |      | ||   || |  | ||| | ||  |||   || |  |||     |  |||||| ||||||||||||||||||| || || || |||||||||||  | || ||||| ||||| |  || |||||||| ||||||||||||||||| || ||| 
gtatgctacaccacaattgttcctgaacaatttaagcccct--ttcttttttgcatttt--aacagcttgtgtcta--ttacagTTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCAGCCTTTCGCATGTCGCCCTTGTTCCGATTTGATTGGTTTGTGAAGTCTA

upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 14
gtacaatttttttttc----taggtctagctccat-catccttctatgggtttctaaaaaaattgctataaatttacagATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCAGCATTTCGAACATCACCCTTGTTTCGATTTGATTGGTTTGTCAAATCTC
|||   |||| |   |    || || ||  |   |   |   |  |||   |    |  ||  ||   | |  || ||| | |||||||||||||||||||| ||||| |||||||||||  | || || || || || |  || |||||||||||||||||||||||||| || ||  
gtatgtttttctcaccatgttatgtgtatttatgtatttgagtacatgacatggctactaagctggagttacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGTATGTCTCCCTTGTTTCGATTTGATTGGTTTGTGAAGTCCA

upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 22
lower sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 22
------------------gtacaatttttttttctaggtc--tagctccatcatccttctatgggtttctaaaaaaatt-gctataaatttacagATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCAGCATTTCGAACATCACCCTTGTTTCGATTTGATTGGTTTGTCAAATCTC
                     |  |||  | ||||   ||  ||  |  |||||     | | |  |  | |  || || | |    |   |||||| |||||| | ||||||||||| |||||||| ||||||||| |||||||||||||| | |||||  |  ||||  | ||||| |||||||| ||||| |
gtatgtctttttctcgtttccctttttgctgttctgtctcattaattatatcatgaagtttttgactgttgaggaactttggtggtgaaaaacagATCTGCATGATTCACAAACTTGGTTATGGGAATTGGGATGAGCTAAAGGCAGCATTTAGGACATCGTCTGTGTTCAGGTTTGACTGGTTTGTGAAATCCC

upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 22
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 22
---------------gtacaatttttttttctaggtctagctccatcatccttct---atgggtttctaaaaaaattgctataaattta-cagATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCAGCATTTCGAACATCACCCTTGTTTCGATTTGATTGGTTTGTCAAATCTC
                |  || | ||| ||     |  |     ||  |  |  |   ||  | |  | |    ||     |    ||| |||||||||||||| || |||||||| ||||| |||||||||||| |||||||||| ||||| ||||| ||||||||| | ||||| |||||||| ||||| |
gtatgacatctatttatcaaactctttgttgagatttcattgttattgttttattctaatatgatattgacccgatgaacttgtgattatcagATATGCATGGTCCATAAACTTGGGTATGGAAACTGGGATGAGCTAAAGGCAGCGTTTCGGACATCCCCCTTGTTTAGGTTTGACTGGTTTGTAAAATCCC

upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 22
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 22
-------------------gtacaatttttttt-tctaggtctagctccatcatccttctatgggt----ttctaaaaaaattg----ctataaattt---acagATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCAGCATTTCGAACATCACCCTTGTTTCGATTTGATTGGTTTGTCAAATCTC
                    |  | ||| |||  |  |  | | | |   |  |  ||  | |  |    |||  |    |||     ||  | | ||     ||||||||||||| ||||||||||| |||||||||||||||||| | |||||||||||||| || || ||||||||||| |||||||||||||| || ||||
gtgagaattgcaatcatctctctagtttgtttgatacaaatgttggtgtgtttttgtttgacgattgatcttccgagtgtattcatgcctccatacttcatgtagATATGCATGGTTCACAAACTTGGATATGGGAACTGGGATGAGCTGAAGGCAGCATTTCGCACTTCTCCCTTGTTTCGTTTTGATTGGTTTGTAAAGTCTC

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|24136997|gb|BU927507.1|BU927507
EST:     ATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATG                         ATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCA
genomic: ATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATGgtacaatttt ... aaatttacagATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCA
EST: gi|298166870|gb|HO010309.1|HO010309
EST:     ATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATG                         ATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCA
genomic: ATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATGgtacaatttt ... aaatttacagATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCA
EST: gi|37997763|gb|CF809352.1|CF809352
EST:     ATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATG                         ATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCA
genomic: ATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATGgtacaatttt ... aaatttacagATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctagctccatcatccttctatgggtttctaaaaaaattgctataaatttacagATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCAGCATTTCGAACATCACCCTTGTTTCGATTTGATTGGTTTGTCAAATCTC
                           ttctaaa  putative branch site (score: 2)
                          tttctaaaaaaattgc  TA-rich tract