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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataatctgccactatctttaccttattttgatcacaaactgttattaatatgctcatctccttttatgtgtgtttgttgtagGTATCTTGTTGTATGAGATGCTTTATGGTCGCACACCTTTCAGGGGTAAGAATAGGCAAAAGACATTTGCCAACATCTTGCACAAAGATCTCACTTTCCC

Basic information

species Arabidopsis thaliana
transcript AT5G58140.3
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G58140.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os04g23890.3 (Oryza sativa), 3'ss of exon 19
--------------gtataatctgccactatctttaccttattttgatcacaaactgttattaatatgctcatctcctttta-tgtgtgtt----tgttgtagGTATCTTGTTGTATGAGATGCTTTATGGTCGCACACCTTTCAGGGGTAAGAATAGGCAAAAGACATTTGCCAACATCTTGCACAAAGATCTCACTTTCCC
              || | || || || |||   ||  || |||      ||   || || ||||| | | |  |||   ||   |   ||    || | |||| ||  | |||||||||||||| ||||| || ||||||||| | || ||||| ||| |||||||||||   |||||  |||||||||| || || || ||
aaccatgagaacttgtttgatatggcattat---tatattgtttgatatgcattatgctaataataagatgacatccagctaacatcaattcccatgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCC

upper sequence: AT5G58140.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA16G19560.1 (Glycine max), 3'ss of exon 21
------gtataa-tctgccact-atctttaccttat--tttgat---cacaaactgttatt-aatatgctcatctccttttatgtgtgttt--gttgtagGTATCTTGTTGTATGAGATGCTTTATGGTCGCACACCTTTCAGGGGTAAGAATAGGCAAAAGACATTTGCCAACATCTTGCACAAAGATCTCACTTTCCC
       ||| | | |  |||| ||  |||  | ||  ||||||   ||||  | | | ||  | ||   |   | | |||   | | ||     | ||||||||||||||||||||||||| |||||||| ||||| ||||| || |||||||| || ||||||||| |||||||||| ||||| ||||| || || ||
aaatagttattactttttcactcattattaagtcatcgtttgattatcacagcccgatgtttgacatttacgatttcgtttccttatcttctgaatatagGTATCTTGTTGTATGAGATGCTCTATGGTCGTACACCATTCAGAGGAAAGAATAGACAGAAGACATTTTCCAACATCTTACACAAGGATCTTACCTTTCC

upper sequence: AT5G58140.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA08G33520.1 (Glycine max), 3'ss of exon 2
-------gtataatctgccactatct-ttaccttatt--ttgatcacaaa----ctgttattaatatgctca--tctccttttatgtgtgtttgttgtagGTATCTTGTTGTATGAGATGCTTTATGGTCGCACACCTTTCAGGGGTAAGAATAGGCAAAAGACATTTGCCAACATCTTGCACAAAGATCTCACTTTCCC
         | | ||  |   |||   |||  | |||  ||||| |  |     || || || | || |||   |||  ||   | | |  |   |  |||||||||||||||||||||||| |||||||| ||||| ||||| || |||||||| || ||||||||| |||| || || ||||| ||||| || || ||
tcttttctcacactcctcttttattaattaagtcattgtttgattatcacatccctatttttgacattctcgattctgtttccttatcttctgaataaagGTATCTTGTTGTATGAGATGCTCTATGGTCGTACACCATTCAGAGGAAAGAATAGACAGAAGACATTTTCCAATATTTTACACAAGGATCTTACCTTTCC

upper sequence: AT5G58140.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv03s0038g04210.t01 (Vitis vinifera), 3'ss of exon 19
-----------gtataatctgcc-actatctt-taccttattttgatca-caaactgttattaatatgctcatctccttttatgtgtgtttg--ttgtagGTATCTTGTTGTATGAGATGCTTTATGGTCGCACACCTTTCAGGGGTAAGAATAGGCAAAAGACATTTGCCAACATCTTGCACAAAGATCTCACTTTCCC
           |  |||| |||   ||      ||   |   |   ||  | |      |||   ||||     |   ||| |   ||||||  ||  ||| || ||  ||||||||||||||||||| || || |||||||| || ||||||||||| ||||||||| |||||||||||||||||||||| ||||| ||
aacctttttctgcttaatttgcttgctggaggatattctgcctaattcttctagtccccattttcatgccttcatttgtttgttcctgtttgattttcagGGATTTTTCTGTATGAGATGCTTTATGGCCGTACTCCTTTCAGAGGAAAGAATAGGCAGAAGACATTTTCCAACATCTTGCACAAAGATCTGACTTTTCC

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|125289699|gb|EL303784.1|EL303784
EST:     TATTGATTGGTGGGCACTGG                         GTATCTTGTTGTATGAGATGCTTTATGGTCGCACACCTTTCAGGGGTAAGA
genomic: TATTGATTGGTGGGCACTGGgtataatctg ... tttgttgtagGTATCTTGTTGTATGAGATGCTTTATGGTCGCACACCTTTCAGGGGTAAGA
EST: gi|125115453|gb|EL165416.1|EL165416
EST:     ATCAC-GGTGCTGGTCATACAAGTGCTATTGATTGGTGGGCACTGG                         GTATCTTGTTGTA
genomic: ATCACGGGTGCTGGTCATACAAGTGCTATTGATTGGTGGGCACTGGgtataatctg ... tttgttgtagGTATCTTGTTGTA
EST: gi|124981268|gb|EL054147.1|EL054147
EST:     ATTGATTGGTGGGCACTGG                         GTATCTTGTTGTATGAGATGCTTTATGGTCGCACACCTTTCAGGGGTAAGA
genomic: ATTGATTGGTGGGCACTGGgtataatctg ... tttgttgtagGTATCTTGTTGTATGAGATGCTTTATGGTCGCACACCTTTCAGGGGTAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatcacaaactgttattaatatgctcatctccttttatgtgtgtttgttgtagGTATCTTGTTGTATGAGATGCTTTATGGTCGCACACCTTTCAGGGGTAAGAATAGGCAAAAGACATTTGCCAACATCTTGCACAAAGATCTCACTTTCCC
               tattaat  putative branch site (score: 2)
        aaactgttattaatat  TA-rich tract