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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttgcgtaaacgtcttcatctagattccgtagcgcattttgttgtcactttcattgtccttgcttcttcagtggtatcacattttcaatttcttaacagGATGGAATGGAGCTTGCAGAGAAGAACGGCATGTTCTTCATTGAGACGTCAGCCAAGACAGCCGATAACATAAATCAACTGTTTGAG

Basic information

species Arabidopsis thaliana
transcript AT3G54840.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G54840.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM5G863105_T01 (Zea mays), 3'ss of exon 2
gtgagtttgcgt-aaacgtcttcatctagattccgtagcgcattttgttgtcactttcattgtccttgcttcttcagtggtatcacattttcaatttcttaacagGATGGAATGGAGCTTGCAGAGAAGAACGGCATGTTCTTCATTGAGACGTCAGCCAAGACAGCCGATAACATAAATCAACTGTTTGAG
  ||   ||       || | |||        | ||    ||  |     |  |  |||    |     |   | | ||  |  |   | |  | || ||  | ||||| |  |||   |||||||||||||   ||||| |||||||||||||||||||||||||| ||||| ||||| ||||||||||||
--gaccatggaccgtccggcctcagggccggactgtccgccagctcaaaatggcgctcaacaactgctatatgttattgacaatatggtgt--acttgttg-cggGATGCACAGGACTATGCAGAGAAGAACAAAATGTTTTTCATTGAGACGTCAGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG

upper sequence: AT3G54840.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 7
gtgagtttgcgtaaacgtcttcatctagattccgtagcgcattttgttgtcactttcat-tgtccttgcttcttcagtggtatcacattttcaatttcttaacagGATGGAATGGAGCTTGCAGAGAAGAACGGCATGTTCTTCATTGAGACGTCAGCCAAGACAGCCGATAACATAAATCAACTGTTTGAG
|| ||  |   |   | |   || ||    |   ||  | | ||  | |   ||   || ||  ||||    |   |       | ||  |  | || ||  |||||||    |||    ||||||||||||   ||||| |||||||||||||| ||||||||||| ||||| ||||| ||||||||||||
gtaagagtatatgctctttgccaactga--tagatattgtagttaatggctgctactatatgatcttgaccatatgg-------atatggtgtacttgttg-cagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG

upper sequence: AT3G54840.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 6
gtgagtttgcgtaaacgtcttcatctagattccgtagcgcattt-tgttgtcactttcattgtccttgcttcttca-gtggtatcacattttcaatttcttaacagGATGGAATGGAGCTTGCAGAGAAGAACGGCATGTTCTTCATTGAGACGTCAGCCAAGACAGCCGATAACATAAATCAACTGTTTGAG
                   |    | | | |  |||    | || |  | | |     ||  || ||  ||  |||  | ||||    ||| |  ||||     ||||||| |  ||   |||||||||||| || ||||| ||||| ||||| || || |||||||| ||||| |||||| |||||||||||
------------------gtagtgcaacactatgtaatatagttgtcatataaacaaaataatcatttttttctcatatagtatgc--tttactgtttccatgaaggatggcactgactatgcagAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG

upper sequence: AT3G54840.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 6
gtgagtttgcgtaaacgtcttcatctagattccgtagcgcattt----tgttgtcactttcattgtccttgcttcttcagtggtatcacattttcaatttcttaacagGATGGAATGGAGCTTGCAGAGAAGAACGGCATGTTCTTCATTGAGACGTCAGCCAAGACAGCCGATAACATAAATCAACTGTTTGAG
                   |    | | | || |||    | ||    | |   ||   | |||||   |  ||||    |  |||    ||| |  ||||     ||||||| |  ||   |||||||||||| |  ||||| ||||| ||||| || || |||||||| ||||| |||||| |||||||||||
------------------gtagtgcaacactctgtaatatagttgtcatataaacaaaataattgtttgtttttctcatata-tatatgctttactgtttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG

upper sequence: AT3G54840.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 6
gtgagtttgcgtaaacgtcttcatctagattccgtagcgcattttgttgtcactttcattgtccttgcttcttcagtggtatcacattttcaatttcttaacagGATGGAATGGAGCTTGCAGAGAAGAACGGCATGTTCTTCATTGAGACGTCAGCCAAGACAGCCGATAACATAAATCAACTGTTTGAG
    ||  | || |   | ||  |||  || |   |||   ||||  | |    ||||       |||||   ||   || |   |||||    ||||| | ||||||| || ||   |||||||||||| || |||||||| ||||| || || || |||||||| ||||||||||| || |||||||||
----gtgagtgtcatactatttgtctgaatgcttcagc---ttttcctat-gtattcacaaaatgtgctttaacacgtgttt---atttta---ttcttga-agGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG

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|164197463|gb|ES118199.1|ES118199
EST:     ACATGAAAAAAGAGAAGTACCTACTGAG                         GATGGAATGGAGCTTGCAGAGAAGAACGGCATGTTCTTCATTGAGACGTCA
genomic: ACATGAAAAAAGAGAAGTACCTACTGAGgtgagtttgc ... ttcttaacagGATGGAATGGAGCTTGCAGAGAAGAACGGCATGTTCTTCATTGAGACGTCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcactttcattgtccttgcttcttcagtggtatcacattttcaatttcttaacagGATGGAATGGAGCTTGCAGAGAAGAACGGCATGTTCTTCATTGAGACGTCAGCCAAGACAGCCGATAACATAAATCAACTGTTTGAG
                                            tttctt  CT-rich tract
                                    attttcaatttcttaa  TA-rich tract