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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaaaaaaaagcaaacattctccaaattcttgtcaaacaaaatgtcattagaatcaatgttacattgtgttttcatgattcattatttcttcttaatttgcagACAATAGCAAAAGCTGTTGGAGATTGGGTTTATGACAGAACATTGTTTCAGAAGATAGATTGTCCTTACCCTTGTAACCCTACTTGCCACCACAGGGTTT

Basic information

species Arabidopsis thaliana
transcript AT4G19420.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G19420.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA16G17190.3 (Glycine max), 3'ss of exon 13
--gtacaaaaaaaagcaaacattctccaaattcttgtcaaacaaaatgtcattagaatcaatgttacattgtgttttcatgattcattatttcttcttaatttgcagACAATAGCAAAAGCTGTTGGAGATTGGGTTTATGACAGAACATTGTTTCAGAAGATAGATTGTCCTTACCCTTGTAACCCTACTTGCCACCACAGGGTTT
  ||  |||| ||||      ||     || |||  | |     |   | ||||  |||  | || | || | |    |     | |  || | |   | | ||||| |||| ||||| || || || |||||| |||||||  |||     || |   ||||||||||| | |||||||| ||||||||||||||  |  |  |||
atgtttaaaataaag-gggtgttt----aagtctcattactggtaggtttattactatc--ttttcctttatatcaagagctaacttgtttgcataacattgtgcagTCAATTGCAAAGGCAGTGGGTGATTGGTTTTATGATCGAAGGCCCTTCCGTGAGATAGATTGTGCCTACCCTTGCAACCCTACTTGCCATAATCGTATTT

upper sequence: AT4G19420.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv02s0087g00400.t01 (Vitis vinifera), 3'ss of exon 12
gtacaaaaaaaagcaaacattctccaaattcttgtcaaacaaaatgtcattagaatcaatgttacattgtgttttcatgattcattatttcttcttaatttgcagACAATAGCAAAAGCTGTTGGAGATTGGGTTTATGACAGAACATTGTTTCAGAAGATAGATTGTCCTTACCCTTGTAACCCTACTTGCCACCACAGGGTTT
     | |  |  |   ||   | ||        |  |      | ||  |    |      |           | |  ||||    | |    ||    |||||||||| ||||| || || ||||| |||   |||||| | |     || ||||||||||||||| | ||||||||| || ||||||||||  || ||||||
-----acattacccgtccaagttgcagccctagtttcactgctctttctctgcttttttccatttgacaaagcctgaatattctcattcttccattggcatgcagACAATTGCAAAGGCAGTAGGAGACTGGTACTATGACCGGAGTCCATTCCAGAAGATAGATTGTGCCTACCCTTGTGACTCTACTTGCCATAACCGGGTTT
















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|86079949|gb|DR375706.1|DR375706
EST:     AGACACAAACTTCATGGTTCTGGCAAGATTCTCCAATTCTAAMCCGAACG                         ACAATAGCAAAAGCTGTTGGAGATTGGGTTTATGACAGAACATTGTTTCAG
genomic: AGACACAAACTTCATGGTTCTGGCAAGATTCTCCAATTCTAAACCGAACGgtacaaaaaa ... taatttgcagACAATAGCAAAAGCTGTTGGAGATTGGGTTTATGACAGAACATTGTTTCAG
EST: gi|116427942|gb|EG470534.1|EG470534
EST:     AGACACAAACTTCATGGTTCTGGCAAGATTCTCCAATTCTAAACCGAACG                         ACAATAGCAAAAGCTGTTGGAGATTGGGTTTATGACAGAACATTGTTTCAG
genomic: AGACACAAACTTCATGGTTCTGGCAAGATTCTCCAATTCTAAACCGAACGgtacaaaaaa ... taatttgcagACAATAGCAAAAGCTGTTGGAGATTGGGTTTATGACAGAACATTGTTTCAG
EST: gi|116448740|gb|EG491332.1|EG491332
EST:     AGACACAAACTTCATGGTTCTGGCAAGATTCTCCAATTCTAAACCGAACG                         ACAATAGCAAAAGCTGTTGGAGATTGGGTTTATGACAGAACATTGTTTCAG
genomic: AGACACAAACTTCATGGTTCTGGCAAGATTCTCCAATTCTAAACCGAACGgtacaaaaaa ... taatttgcagACAATAGCAAAAGCTGTTGGAGATTGGGTTTATGACAGAACATTGTTTCAG
EST: gi|86076009|gb|DR371766.1|DR371766
EST:     AGACACAAACTTCATGGTTCTGGCAAGATTCTCCAATTCTAAACCGAACG                         ACAATAGCAAAAGCTGTTGGAGATTGGGTTTATGACAGAACATTGTTTCAG
genomic: AGACACAAACTTCATGGTTCTGGCAAGATTCTCCAATTCTAAACCGAACGgtacaaaaaa ... taatttgcagACAATAGCAAAAGCTGTTGGAGATTGGGTTTATGACAGAACATTGTTTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaatcaatgttacattgtgttttcatgattcattatttcttcttaatttgcagACAATAGCAAAAGCTGTTGGAGATTGGGTTTATGACAGAACATTGTTTCAGAAGATAGATTGTCCTTACCCTTGTAACCCTACTTGCCACCACAGGGTTT
                                          tcttaat  putative branch site (score: 3)
                              ttcattatttcttctt  CT-rich tract
                             attcattatttcttct  TA-rich tract