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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactacgagtgtccaatttacttttcttctgctcttctaattcgccactcgatctgcttggctgtcatcttggtatatttaaatgtaggctcattcttcactacacttactgatagGTTCGAGCTTATGCTGTGAGTGTCCTGGAAAGAGCTGATGATGAAGAGCTTCAGTGTTACTTGCTTCAACTGGTTCAGGCTCTTCGTTTTGAACGCTCTG

Basic information

species Arabidopsis thaliana
transcript AT1G60490.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G60490.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA06G10090.1 (Glycine max), 3'ss of exon 8
gtactacgagtgtccaatttacttttcttctgctcttctaattcgccactcgatctgcttggctgtcatcttggtatatttaaatgtaggctcattcttcactacacttactgatagGTTCGAGCTTATGCTGTGAGTGTCCTGGAAAGAGCTGATGATGAAGAGCTTCAGTGTTACTTGCTTCAACTGGTTCAGGCTCTTCGTTTTGAACGCTCTG
  | | |   |||   | ||| | ||     ||  || | |||   ||||| ||       |  |  || |    || ||| ||    |||   ||||  ||| |  ||| |   |||| || |||||||| || ||||| || |||||||||||||||||||||||||||||||| ||||||||| |||||||||||||||| ||||| || ||||
ccattgcacatgtatcacttaatatt-----gcaattattatttttcactcaat------agtagaaatttatacatctttcaa----ggccgtttctcaactgc-tttattc-cagGTCCGTGCTTATGCAGTTAGTGTTCTTGAAAGAGCTGATGATGAAGAGCTTCAGTGTTATTTGCTTCAATTGGTTCAGGCTCTTCGGTTTGAGCGTTCTG

upper sequence: AT1G60490.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA04G10090.1 (Glycine max), 3'ss of exon 8
gtactacgagtgtccaatttacttttcttctgctcttctaattcgccactcgatctgcttggctgtcatcttggtatatttaa-atgtaggctcattcttcactacacttactgatagGTTCGAGCTTATGCTGTGAGTGTCCTGGAAAGAGCTGATGATGAAGAGCTTCAGTGTTACTTGCTTCAACTGGTTCAGGCTCTTCGTTTTGAACGCTCTG
                 || |  | ||   |  | || | | ||   |   ||  |   |  |    ||   |   ||||||  ||    |  | ||  |||     |||  |   |||| || |||||||| || ||||| || |||||||||||||||||||| ||||||||||| ||||||||| ||||||| |||||||| ||||| || ||||
----------------cttaatatctcaattattttttttactcaataggagaaatttata-cacctatagagaactatttactatacgaggccgtttctcaac-tgcttcattccagGTCCGTGCTTATGCAGTTAGTGTTCTTGAAAGAGCTGATGATGAAGAACTTCAGTGTTATTTGCTTCAATTGGTTCAAGCTCTTCGGTTTGAGCGTTCTG

upper sequence: AT1G60490.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv01s0127g00430.t01 (Vitis vinifera), 3'ss of exon 8
gtactacgagtgtccaatttacttttcttctgctcttctaattcgccactcgatctgcttggctgtcatcttggtata--tttaaatgtaggctcattcttcactacacttactgatagGTTCGAGCTTATGCTGTGAGTGTCCTGGAAAGAGCTGATGATGAAGAGCTTCAGTGTTACTTGCTTCAACTGGTTCAGGCTCTTCGTTTTGAACGCTCTG
                |||||   | ||| | ||  |   ||| |    |  || ||  | | | |  ||     ||   | | |||| |      ||  |    || |      | ||||||| || |||||||| ||||| || |||||||||||||||||||||||||| |||||||| |||||||||||||||||||||||||| || |||||||
----------------attta---tccttatactagttgtatttgatctttaatttgtgttgttatgttccacacatcattctgaatgaataaaattttattttaactcccttcaacagGTTCGTGCATATGCTGTCAGTGTTCTTGAAAGAGCTGATGATGAAGAGCTTCAATGTTACTTACTTCAACTGGTTCAGGCTCTTCGTTTCGAGCGCTCTG

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|116469041|gb|EG511633.1|EG511633
EST:     ATGTATGTGATGCTTTGGAGCTATTGTCTCCTCTATTTGAGAGTGAAGAG                         GTTCGAGCTTATGCTGTGAGTGTCCTGGAAAGAGCTGATGATGAAGAGCTT
genomic: ATGTATGTGATGCTTTGGAGCTATTGTCTCCTCTATTTGAGAGTGAAGAGgtactacgag ... ttactgatagGTTCGAGCTTATGCTGTGAGTGTCCTGGAAAGAGCTGATGATGAAGAGCTT
EST: gi|116411922|gb|EG454514.1|EG454514
EST:     ATGTATGTGATGCTTTGGAGCTATTGTCTCCTCTATTTGAGAGTGAAGAG                         GTTCGAGCTTATGCTGTGAGTGTCCTGGAAAGAGCTGATGATGAAGAGCTT
genomic: ATGTATGTGATGCTTTGGAGCTATTGTCTCCTCTATTTGAGAGTGAAGAGgtactacgag ... ttactgatagGTTCGAGCTTATGCTGTGAGTGTCCTGGAAAGAGCTGATGATGAAGAGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtcatcttggtatatttaaatgtaggctcattcttcactacacttactgatagGTTCGAGCTTATGCTGTGAGTGTCCTGGAAAGAGCTGATGATGAAGAGCTTCAGTGTTACTTGCTTCAACTGGTTCAGGCTCTTCGTTTTGAACGCTCTG
                                          cacttac  putative branch site (score: 2)
            tatatttaaatgta  TA-rich tract