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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactatatgtctgtttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtagGTATCATCCTGCGTGTGTTGGCATGACGATTGAAGAAGCAAAGAAGCTTGATCACTTTGTATGTGCTGAATGCAGTTCTGATGACGATGTCAAAAAATCG

Basic information

species Arabidopsis thaliana
transcript AT4G22140.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G22140.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 3
gtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactatatgtctgtttttaaacttacgtattc---ttttccaggaattattgataataagcattaattcgctgttgtagGTATCATCCTGCGTGTGTTGGCATGACGATTGAAGAAGCAAAGAAGCTTGATCACTTTGTATGTGCTGAATGCAGTTCTGATGACGATGTCAAAAAATCG
                                     |   |||||    || | ||  | |    |||   |||  | |  || ||   |   | ||  |   |  |   ||   || | ||       | ||||||||| |||||||| ||  | |||||||| ||||||||||||||||| || ||||| ||||||||| |||||||    |||||||| ||| | || ||| | 
----------------------------------acaatgagtgtt----caaagaatcgtcctattgtggatttccatatctatgtcaccatatattttatagaacacatatttcaatctttgtaggtttcttgtagGTACCATCCTGCTTGCATGGGCATGACTATTGAAGAAGCAAAGAAACTAGATCATTTTGTATGTTCTGAATGTTCATCTGATGATGATATGAAGAAACCC

upper sequence: AT4G22140.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G35680.1 (Glycine max), 3'ss of exon 3
gtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactatatgtctgttttta-aacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtagGTATCATCCTGCGTGTGTTGGCATGACGATTGAAGAAGCAAAGAAGCTTGATCACTTTGTATGTGCTGAATGCAGTTCTGATGACGATGTCAAAAAATCG
                       | |  |       ||||  |||||               | |  |||||||| ||  ||     |  | || |  | |||  | || | |  |    ||  |   | ||||||||| |||||||| || || |||||||| |||||||||||||||||  | || || ||||| ||| | |||||    |||||||| ||  | || ||| | 
-----------------------taaggagtagtgctactgctgttttttt-----------ttttcgtctgtttgtatgaccctattgattttatgaaagaaacactgttcaatattggtaggtt--ttttgtagGTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGACCATTTTGTTTGTTCAGAATGTTCATCTGATGATGACATGAAGAAACCC

upper sequence: AT4G22140.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G34740.1 (Glycine max), 3'ss of exon 3
gtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactatatgtctgtttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtagGTATCATCCTGCGTGTGTTGGCATGACGATTGAAGAAGCAAAGAAGCTTGATCACTTTGTATGTGCTGAATGCAGTTCTGATGACGATGTCAAAAAATCG
                   | | | |  |       ||||| | |||               | | | ||||||| | | | ||   ||| || |  | |||  | || | |       ||  |   | ||||||||| |||||||| || || |||||||| |||||||||||||||||  | || || ||||| ||| | |||||    |||||||| ||  | || ||| | 
------------------gtatctgagaagtagtgctacttttttttt--------------tttttttctgtttgtgaccctatagatt-ttatgaaagaaacactgttcaattttggtaggtt--ttttgtagGTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGAACATTTTGTTTGTTCAGAATGTTCATCTGATGATGACATGAAGAAACCC

upper sequence: AT4G22140.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G35680.2 (Glycine max), 3'ss of exon 3
gtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactatatgtctgttttta-aacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtagGTATCATCCTGCGTGTGTTGGCATGACGATTGAAGAAGCAAAGAAGCTTGATCACTTTGTATGTGCTGAATGCAGTTCTGATGACGATGTCAAAAAATCG
                      ||  | || ||    | | ||| | |  | |         | |  |||||||| ||  ||     |  | || |  | |||  | || | |  |    ||  |   | ||||||||| |||||||| || || |||||||| |||||||||||||||||  | || || ||||| ||| | |||||    |||||||| ||             
---------------------attgttaaatttaaggagtagtgctactgctgtttttt--tttttcgtctgtttgtatgaccctattgattttatgaaagaaacactgttcaatattggtagGTT--TTTTGTAGGTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGACCATTTTGTTTGTTCAGAATGTTCATCTGATGATGACA-----------

upper sequence: AT4G22140.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G34850.2 (Glycine max), 3'ss of exon 1
gtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactatatgtctgtttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtagGTATCATCCTGCGTGTGTTGGCATGACGATTGAAGAAGCAAAGAAGCTTGATCACTTTGTATGTGCTGAATGCAGTTCTGATGACGATGTCAAAAAATCG
                           | | |     |    |  | | |  |   |     |  || ||||||  |     ||  | || | |   || |   ||  ||   || | ||       | ||||||||| |||||||| ||  | |||||||| ||||||||||| ||||| || ||||| ||||||||| | |||||    |||||||| ||| | || ||| | 
---------------------------tgagtgttcaaagaatcgtcctattgtggat---ttccatatctgttgatgtcgctatatgttttat---agaacacat--atttcaatctttgtaggtttcttgtagGTACCATCCTGCTTGCATGGGCATGACTATTGAAGAAGCTAAGAAACTAGATCATTTTGTATGTTCCGAATGTTCATCTGATGATGATATGAAGAAACCC

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|164189621|gb|ES019576.1|ES019576
EST:     TGGTGCAGTGTGAAGGCTGCAAAGACTG                         GTATCATCCTGCGTGTGTTGGCATGACGATTGAAGAAGCAAAGAAGCTTGA
genomic: TGGTGCAGTGTGAAGGCTGCAAAGACTGgtaaatgttg ... gctgttgtagGTATCATCCTGCGTGTGTTGGCATGACGATTGAAGAAGCAAAGAAGCTTGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttacgtattcttttccaggaattattgataataagcattaattcgctgttgtagGTATCATCCTGCGTGTGTTGGCATGACGATTGAAGAAGCAAAGAAGCTTGATCACTTTGTATGTGCTGAATGCAGTTCTGATGACGATGTCAAAAAATCG
                    aattattgataataag  TA-rich tract