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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtaattaaggaggtatttagagcaaattgtgatccttattagttatgtagatctgattatatgaatctgatattggttattgaattttgtatattacagGGTTTGTGTTGTTTCTCTCGCTTATGATTGATAGACTACACCATTACATTAGAGAGCTTCGTTTGTTGAGGAAGACAATGGAGACTGCAAAGAAGCAGAA

Basic information

species Arabidopsis thaliana
transcript AT5G42570.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G42570.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G46370.1 (Glycine max), 3'ss of exon 1
-agtaattaaggaggtatttagagcaaattgtgatccttattagttatgtagatctgattatatgaatctgatattggttattgaattttgtatat-tacagGGTTTGTGTTGTTTCTCTCGCTTATGATTGATAGACTACACCATTACATTAGAGAGCTTCGTTTGTTGAGGAAGACAATGGAGACTGCAAAGAAGCAGAA
   |   | |     ||||||| |||  || |  |  || ||  |||  || || | ||||| |   |||   ||| | | ||  |  |   || | | ||||||||||  |||| ||||| || |||||||||||||| ||||||||||| ||||||||||| |   | |||||||| |||||  |    ||||| || | 
ggttggatgattctttatttagtgcagtttttatttattttttatta-ataaatat-attatttagttcttgaatttgatctttcacatataatgtgtgcagGGTTTGTACTGTTCCTCTCTCTGATGATTGATAGACTGCACCATTACATAAGAGAGCTTCGGTCACTCAGGAAGACCATGGAAGCCATTAAGAAACAAAG

upper sequence: AT5G42570.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G10400.1 (Glycine max), 3'ss of exon 1
-agtaattaaggaggtatttagagcaaattgtgatccttattagttat--gtagatctgattatatgaatctgatattggt-tattgaattttgtatattacagGGTTTGTGTTGTTTCTCTCGCTTATGATTGATAGACTACACCATTACATTAGAGAGCTTCGTTTGTTGAGGAAGACAATGGAGACTGCAAAGAAGCAGAA
    | ||    |  | ||||   |  |||||  |  || ||   |||   ||||| |  |  |  |  | |||  ||| | | ||| || |  | | |  |||||||| || |||| ||||| || |||||||||||| | ||||||||||| ||||||||||| |   | |||||||| |||||  ||   ||||| || | 
cgtgagttggatatttcttta---cttattgtagtttttttttcctattaatagatatattatttagtttttgaacttgatcttttgcatctaatgtgt-gcagGGTTTCTGCTGTTCCTCTCTCTGATGATTGATAGATTGCACCATTACATAAGAGAGCTTCGGTCACTCAGGAAGACCATGGAAGCTATTAAGAAACAAAG

upper sequence: AT5G42570.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G38590.1 (Glycine max), 3'ss of exon 1
agtaattaaggaggtatttagagcaaattgtgatccttattagttatgtagatctgattatatgaatctgatattggttattgaattttgtatatt---acagGGTTTGTGTTGTTTCTCTCGCTTATGATTGATAGACTACACCATTACATTAGAGAGCTTCGTTTGTTGAGGAAGACAATGGAGACTGCAAAGAAGCAGAA
           |  ||| | || ||| ||||     ||    | | | |   |   || |||    |   || |   || ||||  | || | ||     ||||||||||| ||||  | || || ||||| |||||| | ||||||||||| ||||||||||| ||  |||||||| | |||||| |||| ||||| |||| 
---tgcacgctaaatatatggaccaatttgtttgatttgaagggtttctttcttgtataatagttgtggcatttgatttgttgacatatgaagatgtgagcagGGTTTGTGCTGTTCTTGTCTCTGATGATAGATAGATTGCACCATTACATAAGAGAGCTTCGGTTACTGAGGAAGGCCATGGAGGCTGCTAAGAAACAGAG

upper sequence: AT5G42570.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv12s0059g00810.t01 (Vitis vinifera), 3'ss of exon 1
agtaattaaggaggtatttagagcaaatt--gtgatccttattagttatgtagatctgattatatgaatctgatattggttattgaatt--ttgtata-ttacagGGTTTGTGTTGTTTCTCTCGCTTATGATTGATAGACTACACCATTACATTAGAGAGCTTCGTTTGTTGAGGAAGACAATGGAGACTGCAAAGAAGCAGAA
    ||| |  |    ||||   || |||   |   || |   | || | |       ||| | |    ||||| ||| ||     | |  || | || || |||||||  || |||| ||| | || ||||| |||||||| |||||||||||| |||||||||||||  | |||||| | |||||| ||| ||||||||| ||
--agattcacca---ttttaattcacatttgatatgccatccaatttgtttgataaccattctcttttcctgattttgatttcaagagtagttatttacttgcagGGTTCTTGCTGTTCCTCGCACTGATGATAGATAGACTTCACCATTACATTCGAGAGCTTCGTTTACTCAGGAAGGCCATGGAGGCTGAAAAGAAGCAAAA

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|124974413|gb|EL047974.1|EL047974
EST:     CACTGATCAAGTCCTTGCGTCTAAGCATCTTCTCGAAGCTTCTCTTATGG                         GGTTTGTGTTGTTTCTCTCGCTTATGATTGATAGACTACA
genomic: CACTGATCAAGTCCTTGCGTCTAAGCATCTTCTCGAAGCTTCTCTTATGGgtataaatca ... tatattacagGGTTTGTGTTGTTTCTCTCGCTTATGATTGATAGACTACA
EST: gi|125223568|gb|EL237653.1|EL237653
EST:     TGCGTCTAAGCATCTTCTCGAAGCTTCTCTTATGG                         GGTTTGTGTTGTTTCTCTCGCTTATGATTGATAGACTACACCATTACATTA
genomic: TGCGTCTAAGCATCTTCTCGAAGCTTCTCTTATGGgtataaatca ... tatattacagGGTTTGTGTTGTTTCTCTCGCTTATGATTGATAGACTACACCATTACATTA
EST: gi|125041242|gb|EL113511.1|EL113511
EST:     CACTGATCAAGTCCTTGCGTCTAAGCATCTTCTCGAAGCTTCTCTTATGG                         GGTTTGTGTTGTTT
genomic: CACTGATCAAGTCCTTGCGTCTAAGCATCTTCTCGAAGCTTCTCTTATGGgtataaatca ... tatattacagGGTTTGTGTTGTTT
EST: gi|116457531|gb|EG500123.1|EG500123
EST:     CACTGATCAAGTCCTTGCGTCTAAGCATCTTCTCGAAGCTTCTCTTATGG                         GGTTTGTGTTGTTTCTCTCGCTTATGATTGATAGACTACACCATTACATTA
genomic: CACTGATCAAGTCCTTGCGTCTAAGCATCTTCTCGAAGCTTCTCTTATGGgtataaatca ... tatattacagGGTTTGTGTTGTTTCTCTCGCTTATGATTGATAGACTACACCATTACATTA
EST: gi|116480246|gb|EG522838.1|EG522838
EST:     CACTGATCAAGTCCTTGCGTCTAAGCATCTTCTCGAAGCTTCTCTTATGG                         GGTTTGTGTTGTTTCTCTCGCTTATGATTGATAGACTACACCATTACATTA
genomic: CACTGATCAAGTCCTTGCGTCTAAGCATCTTCTCGAAGCTTCTCTTATGGgtataaatca ... tatattacagGGTTTGTGTTGTTTCTCTCGCTTATGATTGATAGACTACACCATTACATTA
EST: gi|301501179|gb|HO206719.1|HO206719
EST:     CACTGATCAAGTCCTTGCGTCTAAGCATCTTCTCGAAGCTTCTCTTATGG                         GGTTTGTGTTGTTTCTCTCGCTTATGATTGATAGACTACACCATTACATTA
genomic: CACTGATCAAGTCCTTGCGTCTAAGCATCTTCTCGAAGCTTCTCTTATGGgtataaatca ... tatattacagGGTTTGTGTTGTTTCTCTCGCTTATGATTGATAGACTACACCATTACATTA
EST: gi|124817456|gb|EH902322.1|EH902322
EST:     CACTGATCAAGTCCTTGCGTCTAAGCATCTTCTCGAAGCTTCTCTTATGG                         GGTTTGTGTTGTTTCTCTCGCTTATG
genomic: CACTGATCAAGTCCTTGCGTCTAAGCATCTTCTCGAAGCTTCTCTTATGGgtataaatca ... tatattacagGGTTTGTGTTGTTTCTCTCGCTTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtagatctgattatatgaatctgatattggttattgaattttgtatattacagGGTTTGTGTTGTTTCTCTCGCTTATGATTGATAGACTACACCATTACATTAGAGAGCTTCGTTTGTTGAGGAAGACAATGGAGACTGCAAAGAAGCAGAA
                    atctgat  putative branch site (score: 4)
                         atattggttattgaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtaattaaggaggtatttagagcaaattgtgatccttattagttatgtagatctgattatatgaatctgatattggttattgaattttgtatattacagGGTTTGTGTTGTTTCTCTCGCTTATGATTGATAGACTACACCATTACATTAGAGAGCTTCGTTTGTTGAGGAAGACAATGGAGACTGCAAAGAAGCAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - gagcaaa