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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgttagttacgtgctaaaattttggaaatatttgataaaaaaaaagtcagctaaatcgccaagttattcacaaagtttctgatttataatgttgatagAGAAGGCGAAAATGGGAGGAAAAGAATGGTACTTTTTTAGCCTCCGGGACCGGAAGTACCCGACGGGAGTGAGGACGAATAGGGCGACGAATACAGGATA

Basic information

species Arabidopsis thaliana
transcript AT2G24430.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G24430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g32260.2 (Oryza sativa), 3'ss of exon 2
attgttagttacgtgctaaaattt-tggaaatatttgataaaaaaaaagtcagctaaatcgccaagttattcacaaagtttctgatttataatgttgat--agAGAAGGCGAAAATGGGAGGAAAAGAATGGTACTTTTTTAGCCTCCGGGACCGGAAGTACCCGACGGGAGTGAGGACGAATAGGGCGACGAATACAGGATA
   |||   |   || | |||| | |||  | ||||  | | |   |      |  ||||   | ||| |    |    || |   | ||||   || |  ||||||||| ||||||||||  || ||||||||||| ||||||||  |||| || |||||||| || || ||| | || ||  | || || ||| | || ||
-aggtt--ctgaatgttcaaatatgtggtcacattttttcacacttacacattcacaatctatatgttctatgtattaattttctctaataaatgtgctccagAGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTAGCCTAAGGGATCGAAAGTACCCAACTGGCGTGCGCACAAACCGAGCAACTAATGCTGGTTA

upper sequence: AT2G24430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G20340.1 (Glycine max), 3'ss of exon 1
--attgttagttacgtgctaaaattttggaaatatttgataaaaaaaaagtcagctaaatcgccaagttattcacaaagtttctgatttataatgttg--atagAGAAGGCGAAAATGGGAGGAAAAGAATGGTACTTTTTTAGCCTCCGGGACCGGAAGTACCCGACGGGAGTGAGGACGAATAGGGCGACGAATACAGGATA
      ||| |||     |   || |   |  ||||      ||  |   |||| ||| |  |    ||| | | |   ||  | | || |     ||  |||||||||||||||||||||  ||||||||||||||| || || ||  | || || |||||||| ||||| || || || ||  | || ||||| ||||| ||
atgaaatta-ttaaacattcctatct--aatttattctgactaattagcatcagttaatttcctctattaat-atatttttattaaattgtttctgtgaaatagAGAAGGCGAAAATGGGACAAAAAGAATGGTACTTCTTCAGTCTAAGAGATCGTAAGTACCCAACGGGTGTTAGAACCAACCGAGCCACGAACACAGGGTA

upper sequence: AT2G24430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0008g02710.t01 (Vitis vinifera), 3'ss of exon 1
-attgttagttacgtgctaaaattttggaaatatttgataaaaaaaaagtcagctaaatcgccaagttattcacaaagtttctgatttataatgttgat-agAGAAGGCGAAAATGGGAGGAAAAGAATGGTACTTTTTTAGCCTCCGGGACCGGAAGTACCCGACGGGAGTGAGGACGAATAGGGCGACGAATACAGGATA
 |||  | || | |    | |   |       ||||  |  ||| ||| |  |  || |  | |  |  |         ||    ||| |  | | ||| || ||||||||||||||||| ||| || ||||| || || |||||| |||||||||| ||||| || ||||| || || ||  | || || || || || ||
aatttcttgtgatgaaagagagcatattcttcattt--tccaaacaaacttggaaaatttcctatatcttctgatctagttaatctttgttctctcgattagGGAAGGCGAAAATGGGAGAAAAGGAGTGGTATTTCTTCAGCCTCAGGGACCGGAAATACCCAACTGGAGTAAGAACAAACCGAGCCACAAACACTGGTTA

upper sequence: AT2G24430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ22540 (Selaginella moellendorffii), 3'ss of exon 1
-------------------------------------------------------------------------------attgtta-gttacgtgctaaaattttggaaatatttgataaaaaaaaagtcagctaaatcgcc------aagttattcacaaagtttctgatttataatgtt---------gatagAGAAGGCGAAAATGGGAGGAAAAGAATGGTACTTTTTTAGCCTCCGGGACCGGAAGTACCCGACGGGAGTGAGGACGAATAGGGCGACGAATACAGGATA
                                                                                ||| |   || | | |      ||   |   | |||  |   |  |  |  |   | | |||      || ||  ||  ||| | |||  ||| |  | ||         |  |||||| || || |||||||  || ||||||||||| |||||| |  ||||||||||||||||||||||  || | |||||| |||| ||  |  | || ||
gtaaggaggaactctcccatcttctctcgcattcgtttctatgatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttggaatcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttcttttttctttcccggcagAGAAAGCAAACATGGGAGAGAAGGAATGGTACTTCTTTAGCTTGAGGGACCGGAAGTACCCGACGGGGATGCGTACGAATCGGGCAACCGAGGCCGGCTA

upper sequence: AT2G24430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ11746 (Selaginella moellendorffii), 3'ss of exon 1
-------------------------------------------------------------------------------attgtta-gttacgtgctaaaattttggaaatatttgataaaaaaaaagtcagctaaatcgcc------aagttattcacaaagtttctgatttataatgtt---------gatagAGAAGGCGAAAATGGGAGGAAAAGAATGGTACTTTTTTAGCCTCCGGGACCGGAAGTACCCGACGGGAGTGAGGACGAATAGGGCGACGAATACAGGATA
                                                                                ||| |   || | | |      ||   |   | |||  |   |  |  |  |   | | |||      || ||  ||  ||| | |||  ||| |  | ||         |  |||||| || || |||||||  || ||||||||||| |||||| |  ||||||| ||||||||||||||  || | |||||| |||| ||  |  | || ||
gtaaggaggaactctctcatcttctctcgcattcgcttctatcatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttggaatcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttcttttttctttcccggcagAGAAAGCAAACATGGGAGAGAAGGAATGGTACTTCTTTAGCTTGAGGGACCGTAAGTACCCGACGGGGATGCGTACGAATCGGGCAACCGAGGCCGGCTA

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|19741486|gb|AU226839.1|AU226839
EST:     ACCAATCGCTGACGTT-ATCTTAACAAGTCCGAGCCATGGGAGCTTCCTG                         AGAAGGCGAAAATGGGAGGAAAAGAATGGTACTTTTTTAGCCTCCGGGACC
genomic: AGCAATCGCTGACGTTGATCTTAACAAGTCCGAGCCATGGGAGCTTCCTGgtacgttaat ... atgttgatagAGAAGGCGAAAATGGGAGGAAAAGAATGGTACTTTTTTAGCCTCCGGGACC
EST: gi|19875211|gb|AU236042.1|AU236042
EST:     AGCAATCGCTGACGTTGATCTTAACAAGTCCGAGCCATGGGAGCTTCCTG                         AGAAGGCGAAAATGGGAGGAAAAGAATGGTACTTTTTTAGCCTCCGGGACC
genomic: AGCAATCGCTGACGTTGATCTTAACAAGTCCGAGCCATGGGAGCTTCCTGgtacgttaat ... atgttgatagAGAAGGCGAAAATGGGAGGAAAAGAATGGTACTTTTTTAGCCTCCGGGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtcagctaaatcgccaagttattcacaaagtttctgatttataatgttgatagAGAAGGCGAAAATGGGAGGAAAAGAATGGTACTTTTTTAGCCTCCGGGACCGGAAGTACCCGACGGGAGTGAGGACGAATAGGGCGACGAATACAGGATA
                                 ttctgat  putative branch site (score: 3)
                                      atttataatgttgata  TA-rich tract