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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctctttagcttattctgtctaaaatccccttttcgggatcaaacactaataatatagacaactatatggttgggctatgcagACGTACCCGAGGGTTGTGTCATTTTAAGAGAGCATGTTCCCATAAGCAACCTCTTCACTTGTCTTTGGTTCAACGAAGTTGACCGATTCACTTCTAGAGA

Basic information

species Arabidopsis thaliana
transcript AT1G28240.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os05g45490.1 (Oryza sativa), 3'ss of exon 7
gtatgtctctttagcttattctgtctaaaatccccttttcgggatcaaacactaataatatagacaactatatggttgggctatgcagACGTACCCGAGGGTTGTGTCATTTTAAGAGAGCATGTTCCCATAAGCAACCTCTTCACTTGTCTTTGGTTCAACGAAGTTGACCGATTCACTTCTAGAGA
||  ||    | |    | | || | ||||    |  ||| |  | |    || | | | ||     |  | | |    | | |  ||| || || || |||||||||||  | ||||||||  ||||||| |  || |||||||| || ||||||||||| ||||||||||| ||||| || || ||
gtcagtgatctcattgaagtatggcgaaaa----cagttcag--ttactttctgagattttaactgtcctttttgcattggttt--agATGTCCCTGAAGGTTGTGTCATCATCAGAGAGCACATTCCCATCACGAATCTCTTCACATGCCTTTGGTTCAATGAAGTTGACCGTTTCACCTCCAGGGA

upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G24770.1 (Glycine max), 3'ss of exon 7
----gtatgtctctttagcttattctgtctaaaatccccttttcgggatcaaacactaataatatagacaactatatggttgggctatgcagACGTACCCGAGGGTTGTGTCATTTTAAGAGAGCATGTTCCCATAAGCAACCTCTTCACTTGTCTTTGGTTCAACGAAGTTGACCGATTCACTTCTAGAGA
    |||   ||   |  ||   | | ||||  ||    |   |  | |    || |  |  | || | |  | | |          |||||| || || || || ||||| ||  || ||||||||||||| || ||||||||||| ||||||||||||||||| |||||||||||||| ||||| || ||
gtaggtagaactgccttcctgtatttatctaggatgagttgcacctgttt---cattgtttttttaaaaacttgttt---caaatgctgcagATGTTCCTGAAGGATGTGTGATAGTACGAGAGCATGTTCCTATTAGCAACCTCTTTACTTGTCTTTGGTTCAATGAAGTTGACCGATTTACTTCAAGGGA

upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G08090.1 (Glycine max), 3'ss of exon 7
gtatgtctctttagcttattctgtctaaaatccccttttcgggatcaaacactaataatatagacaactatatggttgggctatgcagACGTACCCGAGGGTTGTGTCATTTTAAGAGAGCATGTTCCCATAAGCAACCTCTTCACTTGTCTTTGGTTCAACGAAGTTGACCGATTCACTTCTAGAGA
||| |      |      |||  | | | ||    |     | | |     ||  |  | |   ||||  |   |     || |||||| || || || || ||||| ||  || |||||||||||||||| ||||| || || || |||||||||||||| ||||||||||||||||||||||| ||
gtaagctaaactttgcgtttccttgttagatgagat-----gcaactggttctggttcttttctcaaccttgatggctaact-tgcagATGTTCCTGAAGGGTGTGTAATAGTACGAGAGCATGTTCCCATCAGCAATCTTTTTACATGTCTTTGGTTCAATGAAGTTGACCGATTCACTTCTAGGGA

upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G31680.1 (Glycine max), 3'ss of exon 7
----gtatgtctctttagcttattctgtctaaaatccccttttcgggatcaaacactaataatatagacaactatatggttgggctatgcagACGTACCCGAGGGTTGTGTCATTTTAAGAGAGCATGTTCCCATAAGCAACCTCTTCACTTGTCTTTGGTTCAACGAAGTTGACCGATTCACTTCTAGAGA
    |||   ||   |  ||     | ||||  ||    |   |  | |    || |  |  | || | |||  | |  |    |  | |||| || || || || ||||| ||  || ||||||||||||| || |||||||||||  |||||||||||||||| |||||||||||||| ||||| || ||
gtaggtaaaactgccttcctgtacttatctaggatgagttgcacctgttt---cattgtttttttaaa-aacatttt--tcaaacgctacagATGTTCCTGAAGGATGTGTGATAGTACGAGAGCATGTTCCTATTAGCAACCTCTTTGCTTGTCTTTGGTTCAATGAAGTTGACCGATTTACTTCAAGGGA

upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G31260.1 (Glycine max), 3'ss of exon 7
gtatgtct--ctttagcttattctgtctaaaatccccttttcgggatcaaacactaataatatagacaactatatggttgggctatgcagACGTACCCGAGGGTTGTGTCATTTTAAGAGAGCATGTTCCCATAAGCAACCTCTTCACTTGTCTTTGGTTCAACGAAGTTGACCGATTCACTTCTAGAGA
||| |     ||| |  ||    ||| |  |          | || ||     |   | || |    | ||  |||| |    | |||||| || || || || ||||| ||  || |||||||||||||||| ||  | || || || |||||||||||||| ||||||||||||||||||||||| ||
gtaagctaaacttcatgtttccttgt-tggatgagatgcaactggttctggttcatttcatttctcaaccttgatggctaa--tttgcagATGTTCCTGAAGGATGTGTAATAGTACGAGAGCATGTTCCCATTAGTGATCTTTTTACATGTCTTTGGTTCAATGAAGTTGACCGATTCACTTCTAGGGA

upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G18630.1 (Glycine max), 3'ss of exon 7
gtatgtctctttagcttattctgtctaaaatccccttttcgggatcaaacactaataatatagacaactatatggttgggctatgcagACGTACCCGAGGGTTGTGTCATTTTAAGAGAGCATGTTCCCATAAGCAACCTCTTCACTTGTCTTTGGTTCAACGAAGTTGACCGATTCACTTCTAGAGA------------------------
                                                 || |   | |    | | || ||||| |    | |||||| || || || || ||||| ||  || |||| ||||||||||| ||| | || || || |||||||||||||| ||||||| | ||||||||||||| ||                        
----------------------------------------------gttcattttcatttctca-acctttatggctaa--tttgcagatgttcctgaaggatgtgtaatagTATGAGACCATGTTCCCATTAGCGATCTTTTTACATGTCTTTGGTTCAATGAAGTTGGCTGATTCACTTCTAGGGACCAGATTAGTTTCTCAACTGTCAG

upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv00s0265g00120.t01 (Vitis vinifera), 3'ss of exon 7
gtatgtct----ctttagcttattctgtctaaaatccccttttcgggatcaaacactaataatatagacaactatatggttgggctatgcagACGTACCCGAGGGTTGTGTCATTTTAAGAGAGCATGTTCCCATAAGCAACCTCTTCACTTGTCTTTGGTTCAACGAAGTTGACCGATTCACTTCTAGAGA
||| |||        |   |   | ||| |  | ||   |||    | || | |  | ||    |   |   | |   | |||| | |||||| || || || || || || ||| |||| || ||  |||| || |||||||| || ||||| ||||||||||||||||||||||| || ||||| || ||
gtaggtccaagatcattcttctctttgtttttattcggttttatctgttccatctttcattcagttttctggtttcatgctgggtt-tgcagATGTGCCTGAAGGGTGCGTGATTGTAAGGGAACACATTCCTATTAGCAACCTATTTACTTGCCTTTGGTTCAACGAAGTTGACCGTTTTACTTCCAGGGA

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|116429469|gb|EG472061.1|EG472061
EST:     GAACGAAGGGTTAACCCCTTATTCTGTCGCAAAGCTCCCAATCACAAGCG                         ACGTACCCGAGGGTTGTGTCATTTTAAGAGAGCATGTTCCCATAAGCAACC
genomic: GAACGAAGGGTTAACCCCTTATTCTGTCGCAAAGCTCCCAATCACAAGCGgtatgtctct ... ggctatgcagACGTACCCGAGGGTTGTGTCATTTTAAGAGAGCATGTTCCCATAAGCAACC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttttcgggatcaaacactaataatatagacaactatatggttgggctatgcagACGTACCCGAGGGTTGTGTCATTTTAAGAGAGCATGTTCCCATAAGCAACCTCTTCACTTGTCTTTGGTTCAACGAAGTTGACCGATTCACTTCTAGAGA
                cactaat  putative branch site (score: 2)
                   taataatatagacaac  TA-rich tract