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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatttatctacttgattagcttaatctctgttttgttggattctgaagcaataatgtcggcgtcatatgtttcaatactttatttctcttgttagaaaggagcccaaactaggttgttcttaatggttgagtatttcctaagagtttctctcaatgtctggggctctttgcagGAAGCACAAAACGCTAAGGAAAAGTCTCATGGCTACAAGTTGGACAAGTCTCACATCTTTGCTGTAAACATGTTCGATGATTTTGACAGGTTGATGAATG

Basic information

species Arabidopsis thaliana
transcript AT5G27640.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os10g41960.1 (Oryza sativa), 3'ss of exon 2
gttatttatctacttgattagcttaatctctgttttgttggattctgaagcaataatgtcggcgtcatatgtttcaatactttatttctcttgttagaaaggagcccaaactaggttgttcttaatggttgagtatttcctaagagtttctctcaatgtctggggctctttgcagGAAGCACAAAACGCTAAGGAAAAGTCTCATGGCTACAAGTTGGACAAGTCTCACATCTTTGCTGTAAACATGTTCGATGATTTTGACAGGTTGATGAATG
                                                                        |   | | |  |   |||| ||  ||   |   |     || |||  | || |  ||  ||||     ||||  | | |  |  ||| ||    | | | ||||||||  |    |||| ||||||| |  |||| |||||| | |||||||||||||||||||| || |||||||| ||||| ||||||| ||  ||||| |
----------------------------------------------------------------------aataggaaattgaacgactct-gtcggat--gtttcgtttttatgttcattttta-agtctagtagggtttaagtttgtattactttgtttgacattatgt-cagGAAGCTGAGCTTGCTAGGGAAAAGACAAATGGGTACAAGCTCGACAAGTCTCACATCTTTGCAGTTAACATGTTTGATGACTTTGACAAGTACATGAAAG

upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0008g07070.t01 (Vitis vinifera), 3'ss of exon 2
gttatttatctacttgattagcttaatctctgttttgttggattctgaagcaataatgtcggcgtcatatgtttcaatactttatttctcttgttagaaaggagcccaaactaggttgttcttaatggttgagtatttcctaagagtttctctcaatgtctggggctctttgcagGAAGCACAAAACGCTAAGGAAAAGTCTCATGGCTACAAGTTGGACAAGTCTCACATCTTTGCTGTAAACATGTTCGATGATTTTGACAGGTTGATGAATG
                                                                           |||  |  | |  |   || |     |  |   | |  |||  |  || ||  |   | ||||  | |  |  |||   |||   |||   |  |||||||||||  |    |||  ||| ||| |  |||| ||||||||||||| | | || || ||||||||||| ||||| ||||| ||||||||||| ||||| |
--------------------------------------------------------------------------taatcatcaactattggagtcaattgtgctcttcatcatggtgctgattgata-taatgcattttgtcattgcatctgaaaattattggtcgttgttgcagGAAGCCGAGCTTGCTCGGGAGAAGACCAATGGGTACAAGTTGGACAGGGCGCATATATTTGCTGTAAATATGTTTGATGACTTTGACAGGTTCATGAAAG
















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|125280040|gb|EL294125.1|EL294125
EST:     CTGTTTTATTGAGTTCAACACTCCTCAG                         GAAGCACAAAACGCTAAGGAAAAGTCTCATGGCTACAAGTTGGACAAGTCT
genomic: CTGTTTTATTGAGTTCAACACTCCTCAGgttatttatc ... ctctttgcagGAAGCACAAAACGCTAAGGAAAAGTCTCATGGCTACAAGTTGGACAAGTCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaatggttgagtatttcctaagagtttctctcaatgtctggggctctttgcagGAAGCACAAAACGCTAAGGAAAAGTCTCATGGCTACAAGTTGGACAAGTCTCACATCTTTGCTGTAAACATGTTCGATGATTTTGACAGGTTGATGAATG
 tcttaat  putative branch site (score: 3)
                                             ctctttgc  putative PPT
           agtattt  TA-rich tract