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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcttagccagactatgaacagttttgaaattttctctcattaatccccctcggatttgtctcatgttcgtcatctttttcttgaagTTGGAAGGTAAAACAGTGTTAAAATTTGCGCTGTGTTACGGTTTCCAGAACCTCCAGAATATTGTTCGGAGAGTGAAAACGCGCAAATGCGATTATCAGT

Basic information

species Arabidopsis thaliana
transcript AT4G16440.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G16440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G01120.1 (Glycine max), 3'ss of exon 8
----gtaagttcttagccagactatgaacagttttgaaattttctctcattaatccccctcgga-----tttgtctcatgttcgtcatctttttcttgaagTTGGAAGGTAAAACAGTGTTAAAATTTGCGCTGTGTTACGGTTTCCAGAACCTCCAGAATATTGTTCGGAGAGTGAAAACGCGCAAATGCGATTATCAGT
      ||| |  ||    || |   |  ||  || | | ||  ||  |  |   |  |   ||      |||  |  |||||  ||||| | | | | || |||| || ||||||||||| |||||||| || ||||| ||||||| |||||| ||||| ||||| || | | | |||||  | ||||| |||||||| |
ccataaaagctagtaagaggatttgtaggaggattaagaattattcctaagaggacttcgaagagtactcttgcttactgttctacatctgtctgt-gcagGTGGAGGGAAAAACAGTGTTGAAATTTGCTCTCTGTTATGGTTTCCGGAACCTGCAGAACATTGTACGAAAACTTAAAACTGGGAAATGTGATTATCATT

upper sequence: AT4G16440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G39690.1 (Glycine max), 3'ss of exon 8
gtaagttcttagccagactatga---acagttttgaaattttctctca---ttaatccccctcggatttgt-ctcatgttcgtcatctt-----tttct-tgaagTTGGAAGGTAAAACAGTGTTAAAATTTGCGCTGTGTTACGGTTTCCAGAACCTCCAGAATATTGTTCGGAGAGTGAAAACGCGCAAATGCGATTATCAGT
      |   ||    ||| |     || ||| |  | |   ||  ||    |||     ||  ||   || ||| || |   | | ||     | ||| || || |||| || ||||||||||| |||||||| || ||||| ||||||| |||||| ||||| ||||| || | | | ||||   | ||||| |||||||| |
-----cttggaggagtactcttgcttactgttctagagtaccctgccaaagctaagaggacttagaagagtactcttgcttaccgttttacatctgtctgtgcagGTGGAGGGAAAAACAGTGTTGAAATTTGCTCTCTGTTATGGTTTCCGGAACCTGCAGAACATTGTACGAAAACTTAAAAATGGGAAATGTGATTATCATT
















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|152033990|gb|AU238810.2|AU238810
EST:     TGGAGTTTAAAACTCTCAGAAATTCTGATTTCCGTGAAGTGACTCTTCAA                         TTGGAAGGTAAAACAGTGTTAAAATTTGCGCTGTGTTACGGTTTCCAGAAC
genomic: TGGAGTTTAAAACTCTCAGAAATTCTGATTTCCGTGAAGTGACTCTTCAAgtaagttctt ... tttcttgaagTTGGAAGGTAAAACAGTGTTAAAATTTGCGCTGTGTTACGGTTTCCAGAAC
EST: gi|125149077|gb|EL182422.1|EL182422
EST:     TGGAG-TTAAAACTCTCAGAAATTCTGATTTCCGTGAAGTGACTCTTCAA                         TTGGAAGGTAAAACAGTGTTAAAATTTGCGCTGTGTTACGG
genomic: TGGAGTTTAAAACTCTCAGAAATTCTGATTTCCGTGAAGTGACTCTTCAAgtaagttctt ... tttcttgaagTTGGAAGGTAAAACAGTGTTAAAATTTGCGCTGTGTTACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctctcattaatccccctcggatttgtctcatgttcgtcatctttttcttgaagTTGGAAGGTAAAACAGTGTTAAAATTTGCGCTGTGTTACGGTTTCCAGAACCTCCAGAATATTGTTCGGAGAGTGAAAACGCGCAAATGCGATTATCAGT
      cattaat  putative branch site (score: 3)
                                  ttcgtcatctttttct  putative PPT
     tcattaat  TA-rich tract