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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gctagttgatgactctcctgtttcatgtttccttagtttttagtatctctggtacaatatttgatgttggtgactctcctgtttttgtaattaaacagATACAAGAACTTGTTGAAGCCATTGTGTTGCCAATGACTCATAAAGAGCAGTTCGAAAAGTTGGGTATCCGTCCACCAAAAGGTGTACTCTTGTATGGTC

Basic information

species Arabidopsis thaliana
transcript AT1G09100.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 4
gctagttgatgactctcctgtttca-tgtttccttagtttttagtatctctg-gtacaatatttgatgttggtgactctcctgtttt-tgtaattaaac--agATACAAGAACTTGTTGAAGCCATTGTGTTGCCAATGACTCATAAAGAGCAGTTCGAAAAGTTGGGTATCCGTCCACCAAAAGGTGTACTCTTGTATGGTC
    |  | |  || |  |   ||| | ||   | ||   | | ||   | | ||     || || |    ||  || |    |||| ||| ||| ||   |||| ||||| ||||| || || |||||  |||| ||||| |||||||| | |||| | ||||||||||| ||||| |||||||| || || ||||| || |
---gggaggtccctttgttccatcagtcttatataagaaatgaataatgccgtgttgctcatctgttacatgtatcttttgaattttatgtcattgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGGTTCCAGAAGTTGGGTATTCGTCCTCCAAAAGGGGTTCTTTTGTACGGAC

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 4
gctagttgatgactctcctgtttcatgtttccttagtttttagtatctctggtacaatatttgatgttggtgactctcctgtttttgtaattaaacagATACAAGAACTTGTTGAAGCCATTGTGTTGCCAATGACTCATAAAGAGCAGTTCGAAAAGTTGGGTATCCGTCCACCAAAAGGTGTACTCTTGTATGGTC
         |||   |  || ||| ||      |   ||  || |  |    |      || | |  | |   |||||  ||  ||  ||| || ||||| |||||| | |||||||||||||| ||||| ||||| || || |||| |||| ||||||| ||  | ||||| || || || || || |||||||| |
--------gtgagctt--tggttcttgccataatttattgaagcactttcttttgggggttaggtaattg-atctctcaggtcatttcaatcaa-cagATTCAAGAATTAGTTGAAGCCATTGTTTTGCCCATGACCCACAAGGAGCGGTTCCAAAAGTTAGGAGTTCGTCCTCCCAAGGGAGTGCTGTTGTATGGAC
















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|125136795|gb|EL176825.1|EL176825
EST:     ACGAAAAACCTACTGAAGACTACAATGATATAGGGGGACTAGAAAAACAG                         ATACAAGAACTTGTTGAAGCCATTGTGTTGCCAATGACTCATAAAGAGCAG
genomic: ACGAAAAACCTACTGAAGACTACAATGATATAGGGGGACTAGAAAAACAGgctagttgat ... aattaaacagATACAAGAACTTGTTGAAGCCATTGTGTTGCCAATGACTCATAAAGAGCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctctggtacaatatttgatgttggtgactctcctgtttttgtaattaaacagATACAAGAACTTGTTGAAGCCATTGTGTTGCCAATGACTCATAAAGAGCAGTTCGAAAAGTTGGGTATCCGTCCACCAAAAGGTGTACTCTTGTATGGTC
               atttgat  putative branch site (score: 5)
                                    tgtttttgtaattaaa  TA-rich tract