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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctttttctcgtttccctttttgctgttctgtctcattaattatatcatgaagtttttgactgttgaggaactttggtggtgaaaaacagATCTGCATGATTCACAAACTTGGTTATGGGAATTGGGATGAGCTAAAGGCAGCATTTAGGACATCGTCTGTGTTCAGGTTTGACTGGTTTGTGAAATCCC

Basic information

species Arabidopsis thaliana
transcript AT3G06400.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 22
gtatgtctttttctcgtttccctttttgctgttctgtctca--ttaattatatcatgaagtttttgactgttgaggaactttggtggtgaaaaacagATCTGCATGATTCACAAACTTGGTTATGGGAATTGGGATGAGCTAAAGGCAGCATTTAGGACATCGTCTGTGTTCAGGTTTGACTGGTTTGTGAAATCCC
|||    ||||     ||||  |||||  | |||| |||     ||  |  |||||     | | |  |  | |  || || | |    |   |||||| |||||| | ||||||||||| |||||||| ||||||||| |||||||||||||| | |||||  |  ||||  | ||||| |||||||| ||||| |
gtacaaattttatgtctttcaatttttttt-ttctttctaggtctagctccatcatccttctatcggtttctaaaaaaatt-gctataaatttacagATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCAGCATTTCGAACATCACCCTTGTTTCGATTTGATTGGTTTGTCAAATCTC

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

upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 22
-----------------------------------------gtatgtctttttctcgtttccctttttgctgttctgtctcattaattatatcatgaagtttttgactgttgaggaactttggtggtgaaaaacagATCTGCATGATTCACAAACTTGGTTATGGGAATTGGGATGAGCTAAAGGCAGCATTTAGGACATCGTCTGTGTTCAGGTTTGACTGGTTTGTGAAATCCC
                                          ||| ||||||  |   |   |  ||   ||||  ||||  |   ||     |   | || |||  ||||     ||||   |    |    ||||| || ||||||||||||||||| ||||| |||||||||||||| |||||||| ||| | |  ||| |  ||||  | ||||| |||||||| || || |
gtgtgaaatttatttccttttgtttttatttttgcccaaatttatttcttttcgttcatgttcagttccttgtttagtctggtgttttccga-acagaattcttg--tgttttctgacttcacttaaaacttgcagATTTGTATGATTCACAAACTTGGCTATGGTAATTGGGATGAGCTGAAGGCAGCTTTTCGAATGTCGCCCTTGTTTCGATTTGATTGGTTTGTCAAGTCTC

upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 22
-----------------------------------------gtatgtctttttctcgtttccctttttgctgttctgtctcattaattatatcatgaagtttttgactgttgaggaactttggtggtgaaaaacagATCTGCATGATTCACAAACTTGGTTATGGGAATTGGGATGAGCTAAAGGCAGCATTTAGGACATCGTCTGTGTTCAGGTTTGACTGGTTTGTGAAATCCC
                                           || ||||||| |   |   |  ||   ||||  ||||  |   ||     |   | || |||  |||||    |||||  |    |    ||||| || ||||||||||||||||| ||||| |||||||||||| | |||||||| ||| | |  ||| |  ||||  | ||||| |||||||| || || |
gtgtgaattttatttccttttgtttttatttttgcccaaattcatttctttttgttcatgttcagttccttgtttagtctggtgttttccga-acagaattcttg--tgttgtctgactttacttaaaacttgcagATATGTATGATTCACAAACTTGGCTATGGTAATTGGGATGAGTTGAAGGCAGCTTTTCGAATGTCGCCCTTGTTTCGATTTGATTGGTTTGTCAAGTCTC

upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 22
---------gtatgtctttttctcgtttccct--ttttgctgttc-tgtctcattaattatatcatgaagtttttgactgttgaggaactttggtggtgaaaaacagATCTGCATGATTCACAAACTTGGTTATGGGAATTGGGATGAGCTAAAGGCAGCATTTAGGACATCGTCTGTGTTCAGGTTTGACTGGTTTGTGAAATCCC
         | |    | | ||| ||||   |  |     ||||  ||| |  ||  ||  |  ||  |  ||  || |||       | |   |  |  |    |||| |||||| ||||||||||||| |||||||| ||||||||||| |||||||||||| | || ||  |  ||||  | ||||| |||||||| || || |
gtgagaattgcaatcatctctctagtttgtttgatacaaatgttggtgtgtttttgtttg-acgattgatcttccgagtgtattcatgcctccatacttcatg-tagATATGCATGGTTCACAAACTTGGATATGGGAACTGGGATGAGCTGAAGGCAGCATTTCGCACTTCTCCCTTGTTTCGTTTTGATTGGTTTGTAAAGTCTC

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|116481379|gb|EG523971.1|EG523971
EST:     ATGGTCAGAACAAAGGCAAGCTGTACAATGAAGAGTGTGACCGTTTCATG                         ATCTGCATGATTCACAAACTTGGTTATGGGAATTGGGATGAGCTAAAGGCA
genomic: ATGGTCAGAACAAAGGCAAGCTGTACAATGAAGAGTGTGACCGTTTCATGgtatgtcttt ... tgaaaaacagATCTGCATGATTCACAAACTTGGTTATGGGAATTGGGATGAGCTAAAGGCA
EST: gi|116436611|gb|EG479203.1|EG479203
EST:     ATGGTCAGAACAAAGGCAAGCTGTACAATGAAGAGTGTGACCGTTTCATG                         ATTTGCATGATTCACAAACTTGGTTATGGGAATTGGGATGAGCTAAAGGCA
genomic: ATGGTCAGAACAAAGGCAAGCTGTACAATGAAGAGTGTGACCGTTTCATGgtatgtcttt ... tgaaaaacagATCTGCATGATTCACAAACTTGGTTATGGGAATTGGGATGAGCTAAAGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaattatatcatgaagtttttgactgttgaggaactttggtggtgaaaaacagATCTGCATGATTCACAAACTTGGTTATGGGAATTGGGATGAGCTAAAGGCAGCATTTAGGACATCGTCTGTGTTCAGGTTTGACTGGTTTGTGAAATCCC
                   ttttgac  putative branch site (score: 3)
     ttatatcat  TA-rich tract