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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAAGGCTCCTTATGTGGCTAAGGCTGACAAGCGCAAGGTTGAGTATGAGAAGAACATGAAAGCCTACAACAAGAAATTGgtaattgtttatttgcatatagaaggctatgttatgtttatattaaccacgttattgagttgtctactctctttatactagtcagtagtcacactattca...

Basic information

species Arabidopsis thaliana
transcript AT1G20696.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20696.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA06G01970.4 (Glycine max), 5'ss of exon 5
GAGAAGGCTCCTTATGTGGCTAAGGCTGACAAGCGCAAGGTTGAGTATGAGAAGAACATGAAAGCCTACAACAAGAAA----TTGgtaattgtttatttgcatat-----------agaaggctatgttatgt-ttatattaaccacgttattgagttgtctactctctttatactagtcagtagtcacactattca--------------------------
|| || || ||||||||||| ||| |||| ||  | || || ||||| ||||||||||||| |||||| |||||||||    |||||   | |||  |  ||| |             |||  | ||| || | || |  | | ||    |  ||   ||  | | | | | || | ||| ||| | |  || |||                           
GAAAAAGCACCTTATGTGGCAAAGTCTGAGAAAAGGAAAGTGGAGTACGAGAAGAACATGAGAGCCTATAACAAGAAACAGgttggttcatctttggtgacatgttattatttacagaaagaatctgtaatttattgttctcatcagcccaaggaaa-gttgaatatgtgtttattggtctgtaatga-gctgttctcataggcttttgtttcatgttgtcag

upper sequence: AT1G20696.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv18s0122g01190.t01 (Vitis vinifera), 5'ss of exon 6
GAGAAGGCTCCTTATGTGGCTAAGGCTGACAAGCGCAAGGTTGAGTATGAGAAGAACATGAAAGCCTACAACAAGAAATTGgtaattgtttatttgcatatagaaggctatgttatgtttatattaaccacgttattgagttgtctactctcttta-tactagtcagtagtcacactattca-
||||||||||| ||||| || || || || ||||| || || || || |||||||||||||||||||| ||||| |||  |||| ||  |  |||  || ||     |||   |     || | |             | |||| |    | || | ||  |     ||        ||||  
GAGAAGGCTCCCTATGTAGCGAAAGCAGAAAAGCGGAAAGTAGAATACGAGAAGAACATGAAAGCCTATAACAAAAAACAGgtattt--tactttaaatgtatgctcctagtattcaagtaaaatggttcttcatccaaattgtttctcttgttcagtataaaattatatctgattcattcgt
















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|164099572|gb|ES123437.1|ES123437
EST:     CCTACAACAAGAAATTG                         GAGGAAGGCCCTAAGGAAGATGAGGAATCTGACAAGTTCAGTTTCAGAGGT
genomic: CCTACAACAAGAAATTGgtaattgttt ... gtggtttcagGAGGAAGGCCCTAAGGAAGATGAGGAATCTGACAAGT-CAGTTTCAGAGGT
EST: gi|163966015|gb|ES068334.1|ES068334
EST:     AGCGCAAGGTTGAGTATGAGAAGAACATGAAAGCCTACAACAAGAAATTG                         GAGGAAGGCCC
genomic: AGCGCAAGGTTGAGTATGAGAAGAACATGAAAGCCTACAACAAGAAATTGgtaattgttt ... gtggtttcagGAGGAAGGCCC
EST: gi|164017531|gb|ES076639.1|ES076639
EST:     CCTACAACAAGAAATTG                         GAGGAAGGCCCTAAGGAAGATGAGGAATCTGACAAGTCAGTTTCAGAGGTT
genomic: CCTACAACAAGAAATTGgtaattgttt ... gtggtttcagGAGGAAGGCCCTAAGGAAGATGAGGAATCTGACAAGTCAGTTTCAGAGGTT
EST: gi|301502423|gb|HO207963.1|HO207963
EST:     AGCGCAAGGTTGAGTATGAGAAGAACATGAAAGCCTACAACAAGAAATTG                         GAGGAAGGCCCTAAGGAAGATGAGGAATCTGACAAGTCAGTTTCAGAGGTT
genomic: AGCGCAAGGTTGAGTATGAGAAGAACATGAAAGCCTACAACAAGAAATTGgtaattgttt ... gtggtttcagGAGGAAGGCCCTAAGGAAGATGAGGAATCTGACAAGTCAGTTTCAGAGGTT
EST: gi|164154747|gb|ES162659.1|ES162659
EST:     AGCGCAAGGTTGAGTATGAGAAGAACATGAAAGCCTACAACAAGAAATTG                         GAGGAAGGCCCTAAGGAAG
genomic: AGCGCAAGGTTGAGTATGAGAAGAACATGAAAGCCTACAACAAGAAATTGgtaattgttt ... gtggtttcagGAGGAAGGCCCTAAGGAAG
EST: gi|164134739|gb|ES062939.1|ES062939
EST:     CCTACAACAAGAAATTG                         GAGGAAGGCCCTAAGGAAGATGAGGAATCTGACAAGTCAGTTTCAGAGGTT
genomic: CCTACAACAAGAAATTGgtaattgttt ... gtggtttcagGAGGAAGGCCCTAAGGAAGATGAGGAATCTGACAAGTCAGTTTCAGAGGTT
EST: gi|124929923|gb|EL007424.1|EL007424
EST:     AGCGCAAGGTTGAGTATGAGAAGAACATGAAAGCCTACAACAAGAAATTG                         GAGGAAGGCCCTAAGGAAGATGAGGAAT
genomic: AGCGCAAGGTTGAGTATGAGAAGAACATGAAAGCCTACAACAAGAAATTGgtaattgttt ... gtggtttcagGAGGAAGGCCCTAAGGAAGATGAGGAAT
EST: gi|164181036|gb|ES068800.1|ES068800
EST:     AGCGCAAGGTTGAGTATGAGAAGAACATGAAAGCCTACAACAAGAAATTG                         GAGGAAGGCCCTAAGGAAGATGAGGAATCTGACAAGTCAGTT
genomic: AGCGCAAGGTTGAGTATGAGAAGAACATGAAAGCCTACAACAAGAAATTGgtaattgttt ... gtggtttcagGAGGAAGGCCCTAAGGAAGATGAGGAATCTGACAAGTCAGTT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAAGGCTCCTTATGTGGCTAAGGCTGACAAGCGCAAGGTTGAGTATGAGAAGAACATGAAAGCCTACAACAAGAAATTGgtaattgtttatttgcatatagaaggctatgttatgtttatattaaccacgttattgagttgtctactctctttatactagtcagtagtcacactattca

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA