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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcatacgcctttgtgtcaaaggatcttcttcttcttactcggagaagatccagaattttcctctactggaggtttttggtctcattggtttatctgaaattggatagGATGCTGGCAACTGTGATGAATGCAATATTTCTTCAAGCGACAATGGAGAGTATTGGCATCCCAACCCGTGTTCAAACTGCTTTCCGCATGTCGGAAGTC

Basic information

species Arabidopsis thaliana
transcript AT3G18680.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G18680.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g73450.1 (Oryza sativa), 3'ss of exon 4
gtaatcatacgcctttgtgtcaaaggatcttcttcttcttactcggagaagatccagaattttcctctactggaggtttttggtctcattggtttatctgaaattggat--agGATGCTGGCAACTGTGATGAATGCAATATTTCTTCAAGCGACAATGGAGAGTATTGGCATCCCAACCCGTGTTCAAACTGCTTTCCGCATGTCGGAAGTC
             |||     ||| ||     |  ||| |  |   ||    | || |||||  |||  |   |  |  ||   | | ||   |||           ||  || ||| |||| |||||||||||||| |||||||||||||| ||||||||||| ||||| || ||||||||||| |||||||| || || ||||| ||||| 
-----------tgttttaaaaaaaagaagacatcattcctgttataagtgatttcataattt--ctcagcataaaatagttcaccactttatcttactcttttcctaattcagCATGTTGGCTACTGTGATGAATGCCATATTTCTTCAAGCAACAATGGAGAGCATTGGAATACCAACCCGTGTCCAAACTGCATTTCGTATGTCAGAAGTT

upper sequence: AT3G18680.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G149535_T01 (Zea mays), 3'ss of exon 4
gtaatcatacgcctttgtgtcaaaggatcttcttcttcttactcggagaagatccagaattttcctctactggaggtttttg---gtctcattggtttatctgaaattggatagGATGCTGGCAACTGTGATGAATGCAATATTTCTTCAAGCGACAATGGAGAGTATTGGCATCCCAACCCGTGTTCAAACTGCTTTCCGCATGTCGGAAGTC
         || |     | | |   | |||        |      |  || |    | ||||  |   ||  |       |    ||| ||     | ||  || |     || ||| |||| |||||||||||||| |||||||||||||| ||||||||||| || || || || |||||||| |||||||| ||||| ||||| ||||| 
--------gcgtcgcctaggcgac--accttaaaaacactgtgacaaacagttttgtagttttggtaatcttaaaacaacagtacatcttatgaagctttcctaattc----agCATGTTGGCCACTGTGATGAATGCTATATTTCTTCAAGCAACAATGGAGAGCATCGGAATACCGACCCGTGTCCAAACTGCCTTCCGTATGTCAGAAGTT

upper sequence: AT3G18680.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G139462_T04 (Zea mays), 3'ss of exon 3
gtaatcatacgcctttgtgtcaaaggatcttcttcttcttactcggagaagatccagaattttcctctactggaggtttttggtctcattggtttatctgaaattggatagGATGCTGGCAACTGTGATGAATGCAATATTTCTTCAAGCGACAATGGAGAGTATTGGCATCCCAACCCGTGTTCAAACTGCTTTCCGCATGTCGGAAGTC
   |   |||   ||  |     | |   ||||| |  | ||  |  | | |       |  |  |  |      ||      ||| |||    | ||  || |     || |||||||| |||||||||||||| ||||||||||||||||| |||||||| || || || || |||||||| || ||||| ||||| ||||| ||||| 
---actctac-tgttcattctggaaggcattcttgtgataaccagttgtatagttttggtactattaaaacaacagtac---atcttattatgctttcctaattc----agCATGCTGGCCACTGTGATGAATGCTATATTTCTTCAAGCGACGATGGAGAGCATCGGAATACCGACCCGTGTCCAGACTGCCTTCCGTATGTCAGAAGTT

upper sequence: AT3G18680.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G15610.1 (Glycine max), 3'ss of exon 4
gtaatcatacgcctttgtgtcaaaggatcttcttcttcttactcggagaagatccagaattttcctctactggaggtttttggtctcattggtttatctgaaattggatagGATGCTGGCAACTGTGATGAATGCAATATTTCTTCAAGCGACAATGGAGAGTATTGGCATCCCAACCCGTGTTCAAACTGCTTTCCGCATGTCGGAAGTC
   ||  | |   ||  | | |     | | |||    || |||  |    ||  |||| |    || |     | || ||  |    ||| || || |   ||    ||||||| |||| ||||| |||||||| |||||||||||||| |||||||||||||| ||||| || || || || || || || || || ||||| || || 
--catt-tccaatttattatgatccactatgctttgagttgctcaaaatgcatg-agaagtagtatcca----ggcttattactaattttgtttaattt---atcctctagGATGTTGGCCACTGTTATGAATGCTATATTTCTTCAAGCAACAATGGAGAGTATAGGCATTCCTACTCGGGTGCAGACCGCATTTCGTATGTCTGAGGTT

upper sequence: AT3G18680.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G32340.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------------gtaatcatacgcctttgtgtcaa-aggatcttcttcttct-tactcggagaagatccagaattttcctctactggaggtttttgg--tctcattggtttatctgaaattgg---atagGATGCTGGCAACTGTGATGAATGCAATATTTCTTCAAGCGACAATGGAGAGTATTGGCATCCCAACCCGTGTTCAAACTGCTTTCCGCATGTCGGAAGTC
                                                                      || | | ||    |     | |  | ||||  | ||  || ||||  |||  | || | |||           | ||  |   ||  | | | |  |||   | || ||      ||||||| |||| ||||| |||||||| |||||||||||||| |||||||| ||||||||||| || || || || || ||||| || || ||||| || || 
gtgattcccttaatctcttaatttttatcttgaaggttaagtcagggcactgatcgctgatgtgctggttgttaacttagatttccaatttattatgatccacatccactatactttgagttgctc-aaaatgcatgagagaagtagtatccaggctttttactaattttgtttaatttatcctctagGATGTTGGCCACTGTTATGAATGCTATATTTCTTCAAGCAACAATGGAAAGTATTGGCATTCCTACTCGGGTGCAGACTGCATTTCGTATGTCTGAGGTT

upper sequence: AT3G18680.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0044g00890.t01 (Vitis vinifera), 3'ss of exon 5
gtaatcatacgcct-ttgtgtcaaaggatcttcttcttcttactcggagaagatccagaattttcctctactggaggtttttggtctcattggtttatctgaaattggatagGATGCTGGCAACTGTGATGAATGCAATATTTCTTCAAGCGACAATGGAGAGTATTGGCATCCCAACCCGTGTTCAAACTGCTTTCCGCATGTCGGAAGTC
 |  | || ||| | |||| |  | |   | | || |   |  |     ||  |    || | |  | |   | ||    ||| | |            || ||||   ||||||| |||| ||||| |||||||| |||||||||||||| ||||||||||| |||||||||||||| ||||| || ||||| ||||| ||||| ||||| 
ttcttgattcgcgtgttgtatggaggacacctgttgtgtatctttccttaaattatgtaactgtaatttggggtagaaccttgatgt------------tggaattttttagGATGTTGGCTACTGTTATGAATGCTATATTTCTTCAAGCAACAATGGAGAGCATTGGCATCCCAACTCGTGTCCAGACTGCATTCCGAATGTCTGAAGTT

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|116478458|gb|EG521050.1|EG521050
EST:     GTGCAGTGGCCTTGATCGCTCCTCTGCTGATTATATCGG                         GATGCTGGCAACTGTGATGAATGCAATATTTCTTCAAGCGACAATGGAGAG
genomic: GTGCAGTGGCCTTGATCGCTCCTCTGCTGATTATATCGGgtaatcatac ... aattggatagGATGCTGGCAACTGTGATGAATGCAATATTTCTTCAAGCGACAATGGAGAG
EST: gi|116478459|gb|EG521051.1|EG521051
EST:     GTGCAGTGGCCTTGATCGCTCCTCTGCTGATTATATCGG                         GATGCTGGCAACTGTGATGAATGCAATATTTCTTCAAGCGACAATGGAGAG
genomic: GTGCAGTGGCCTTGATCGCTCCTCTGCTGATTATATCGGgtaatcatac ... aattggatagGATGCTGGCAACTGTGATGAATGCAATATTTCTTCAAGCGACAATGGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattttcctctactggaggtttttggtctcattggtttatctgaaattggatagGATGCTGGCAACTGTGATGAATGCAATATTTCTTCAAGCGACAATGGAGAGTATTGGCATCCCAACCCGTGTTCAAACTGCTTTCCGCATGTCGGAAGTC
                                    tttatct  TA-rich tract