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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattctccatatatcaatactgtctcagctatcttctattgcctgtgtattttttgttttcttgtagcaaggggctttttgttttgcttgtctttccgagatttaataattgatggatctcttttattatataagGTTGTTTTCATTGGAGGACGTACTCAAACTGGTTCAGTGAAATCTGATGAAGGGGAACGCCACCCTTACTCTATAATCGACTGTGAACCAAAGCGTGAAG

Basic information

species Arabidopsis thaliana
transcript AT1G65220.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G65220.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G47780.1 (Glycine max), 3'ss of exon 4
gtaaattctccatatatcaatactgtctcagctatcttctattgcctgtgtattttttgttttcttgtagcaaggggctttttgttttgcttgtctttccgagatttaataattgatggatctcttttattatataagGTTGTTTTCATTGGAGGACGTACTCAAACTGGTTCAGTGAAATCTGATGAAGGGGAACGCCACCCTTACTCTATAATCGACTGTGAACCAAAGCGTGAAG
                                    |  |  ||| |    | | | || ||| |  |     |  | ||  ||| |  |||  |  |     | | |  | ||  |    || ||  ||||  | |||||| ||||| ||| || ||||| ||| ||||  |    ||  ||||||| ||||| |||||||| ||||||||||| || ||||| || ||||||||| 
----------------------------------gttcttgatgcattctgaatctctggtttttactgttttgttgattagtgtctgacttaccaatgtcctactgaccagttact---ccttttgcattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAGGGGGACCGCCACCCATACTCTATAATAGAGTGTGAGCCTAAGCGTGAA-

upper sequence: AT1G65220.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 5
gtaaattctccatatatcaatactgtctcagctatcttctattgcctgtgtattttt-tgttttcttgtagcaaggggctttttgttttgcttgtctttccgagatttaataattgatggatctcttttattatataagGTTGTTTTCATTGGAGGACGTACTCAAACTGGTTCAGTGAAATCTGATGAAGGGGAACGCCACCCTTACTCTATAATCGACTGTGAACCAAAGCGTGAAG
                           |  | | | | | |||   | | ||||||  |||  | |  | |  |       ||| || |     |   |  | |||||||| |||            ||||||    ||||||| ||||  ||||| || || ||| ||||  ||   || |||||||| ||||| ||||| |||||||||||||| || |||||||| || |||| ||
---------------------------tgggttttgtacaattctatttttattttcctgtcatttgctggtgaaataacatttattatatactttgatttgggatttaattatt------------ttattactgcagGTTGTCTTCACCGGAGGTCGCACACAACCTGGCACAACAAAGTCTGATGAGGGGGAGCGCCATCCTTACTCTATAATTGATTGTGAACCTAATCGTGTAG
















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|125237162|gb|EL251247.1|EL251247
EST:     TAGAGTCATCTGATCTTAATTTCTCAAGATACGGTGATATTTTCTTTGAG                         GTTGTTTTCATTGGAGGACGTACTCAAACTGGTTCAGTGAAATCT
genomic: TAGAGTCATCTGATCTTAATTTCTCAAGATACGGTGATATTTTCTTTGAGgtaaattctc ... attatataagGTTGTTTTCATTGGAGGACGTACTCAAACTGGTTCAGTGAAATCT
EST: gi|301502270|gb|HO207810.1|HO207810
EST:     TAGAGTCATCTGATCTTAATTTCTCAAGATACGGTGATATTTTCTTTGAG                         GTTGTTTTCATTGGAGGACGTACTCAAACTGGTTCAGTGAAATCTGATGAA
genomic: TAGAGTCATCTGATCTTAATTTCTCAAGATACGGTGATATTTTCTTTGAGgtaaattctc ... attatataagGTTGTTTTCATTGGAGGACGTACTCAAACTGGTTCAGTGAAATCTGATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgcttgtctttccgagatttaataattgatggatctcttttattatataagGTTGTTTTCATTGGAGGACGTACTCAAACTGGTTCAGTGAAATCTGATGAAGGGGAACGCCACCCTTACTCTATAATCGACTGTGAACCAAAGCGTGAAG
                           aattgat  putative branch site (score: 4)
                                     tctcttttatt  putative PPT
                    atttaataattgatgg  TA-rich tract