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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagcccttttttatcttttgttccaccaacaaaatttttgttgaaatatacgtcaatttactaaaacaactgcagGCTACTAAAATGAGCATGGGAGTGGATGTGTGTATGACCTATGAAAGACGGTTCTACTTTAATCTTCCAGAGGTACAAAAGGCGCTTCATGCGAACCGTA

Basic information

species Arabidopsis thaliana
transcript AT5G42240.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G42240.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA06G12800.1 (Glycine max), 3'ss of exon 6
---------gtcagcccttttttatcttttgttccaccaacaaaa------tttttgttgaaatatacgtcaatttactaaaaca----actgcagGCTACTAAAATGAGCATGGGAGTGGATGTGTGTATGACCTATGAAAGACGGTTCTACTTTAATCTTCCAGAGGTACAAAAGGCGCTTCATGCGAACCGTA
          ||  || ||| |  | | ||| |  |      |||      |||||  | || ||||    |||| | |     |    | |||||||||||||||| ||||| || || ||||| |||||||| ||||||||| | || || || || || || ||||| || ||||| || ||||| |||||||
gtacaatgcctcttccatttctgttttgttgatatatatcttaaaatgttttttttaataaattataaactaattaatttggttactttaatgcagGCTACTAAAATAAGCATAGGTGTAGATGTCTGTATGACTTATGAAAGAAGTTTTTATTTCAACCTCCCTGAGGTTCAGAAGGCTCTCCATGCAAACCGTA

upper sequence: AT5G42240.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA04G41970.1 (Glycine max), 3'ss of exon 6
--------gtcagcccttttttatctt-ttgttccaccaacaaaatttt--tgttgaaat-atacgtcaatttactaaaaca----actgcagGCTACTAAAATGAGCATGGGAGTGGATGTGTGTATGACCTATGAAAGACGGTTCTACTTTAATCTTCCAGAGGTACAAAAGGCGCTTCATGCGAACCGTA
           |   ||||  | |  | ||| |     || ||  ||||  | || |||| |||    |||| | |  |  |    | |||||||||||||||| ||||| || || ||||| |||||||| ||||||||| | || || || || || || ||||| || ||||| || ||||| |||||||
gtactgtgcctatttctttgctgttctattgatattttaaaaagttttttctattaaaattataaactaattaatttgattattttaatgcagGCTACTAAAATAAGCATAGGTGTAGATGTTTGTATGACTTATGAAAGAAGTTTTTATTTCAACCTCCCTGAGGTTCAGAAGGCTCTCCATGCAAACCGTA

upper sequence: AT5G42240.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA14G28120.1 (Glycine max), 3'ss of exon 6
------------------------------gtcagcccttttttatcttttgttccaccaacaaaatttttgttgaaatatacgtcaatttactaaaacaactgcagGCTACTAAAATGAGCATGGGAGTGGATGTGTGTATGACCTATGAAAGACGGTTCTACTTTAATCTTCCAGAGGTACAAAAGGCGCTTCATGCGAACCGTA
                                 |     ||| | |||||  ||          ||| | | |   ||| || || ||||   | |    | ||||||| |||||||| ||  |  | || ||||||||||||||    |||||||| || ||||| ||||| || ||||| |||||||| |||||||| |||||||
gtaggcctcttcaattttgttctggtgatacataatttatttatttctttattttttttgtatgaatctatatgctaat-taagt-aattgctttacttgaatgcagGCAACTAAAATAAGTGTTAGTGTAGATGTGTGTATGACTCTAGAAAGACGTTTTTACTTCAATCTCCCTGAGGTCCAAAAGGCTCTTCATGCAAACCGTA

upper sequence: AT5G42240.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv18s0001g15550.t01 (Vitis vinifera), 3'ss of exon 6
--------------------gtcagcccttttttatctttt-gttccaccaacaaaatttt-tgttgaaatatacgtcaatttactaaaacaactgcagGCTACTAAAATGAGCATGGGAGTGGATGTGTGTATGACCTATGAAAGACGGTTCTACTTTAATCTTCCAGAGGTACAAAAGGCGCTTCATGCGAACCGTA
                     | |     ||||  |||||    |||          | ||  | ||||  ||   | ||   |    | ||| | ||||| ||||| |||||  | ||  | ||||||||||||||||||||||||   ||||| || || ||||| ||||| || ||||| |||||||| || || |
gtactttcttagtttcccccttgaatttcttttcctctttccaatccgttcttgtgctattacgctgaaccatctttaaacaaaactcaccaatttcagGCCACTAAGATGAGTGTTGGGATCGATGTGTGTATGACCTATGAAAGATCTTTCTATTTCAACCTTCCTGAGGTTCAGAAGGCTCTTCATGCAAATCGAA

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|124987172|gb|EL059644.1|EL059644
EST:     CGTCTATCGTCCAGCAAGAGCTGAGGCTCAAGAAAATG                         GCTACTAAAATGAGCATAGGGAGTGGATGTGTGTATGACCTATGAAAGACG
genomic: CGTCTATCGTCCAGCAAGAGCTGAGGCTCAAGAAAATGgtcagccctt ... acaactgcagGCTACTAAAATGAGCAT-GGGAGTGGATGTGTGTATGACCTATGAAAGACG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccaccaacaaaatttttgttgaaatatacgtcaatttactaaaacaactgcagGCTACTAAAATGAGCATGGGAGTGGATGTGTGTATGACCTATGAAAGACGGTTCTACTTTAATCTTCCAGAGGTACAAAAGGCGCTTCATGCGAACCGTA
                                      tactaaa  putative branch site (score: 1)
       aacaaaatttttgttg  TA-rich tract