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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttccaaattaaattagtagaaagctacatagaccagtcttatggagtacttataacaacaaaaaaaatgaaaatattcaattggttactaaatggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTAAGAAAGATCGAGGCAAAGCCGATTCTCCGATATACACTATGCAGATTTG

Basic information

species Arabidopsis thaliana
transcript AT3G15840.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G15840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G03360.2 (Glycine max), 3'ss of exon 4
ttccaaattaaattagtagaaagct-acatagaccagtcttatggagtacttataacaacaaaaaaaatgaaaatattcaattggttactaaatggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTAAGAAAGATCGAGGCAAAGCCGATTCTCCGATATACACTATGCAGATTTG
  | | | |   ||  ||||  |   |  |  |   ||| ||   | |  ||         | |    |   ||    | | ||     |||    | ||||||| ||||| || ||||| ||||| ||||| |||||||| || |||||||  ||||||||||||||||| ||| | || |||||  | || ||||| ||
-actatactgctttcttagattgtagaggttaagatgtcatacttattcgtttcggtggtcatattttttccaactgactagtgaaatttaatccattcagGAGGTTTTAATCAGCCAATTATGTGCGGTGGTGAGCCAAGGGCCATGCTTAGAAAAGATCGAGGCAAAGCTGATGCCCCAATATATTCCATTCAGATATG

upper sequence: AT3G15840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G22740.1 (Glycine max), 3'ss of exon 4
ttccaaattaaattagtagaaagctacatagaccagtcttatggagtacttata-acaacaaaaaaaatgaaaatattcaattggttactaaa-------tggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTAAGAAAGATCGAGGCAAAGCCGATTCTCCGATATACACTATGCAGATTTG
  | | | |   ||  ||||    |     |   | |   |||   |||||||      |       ||     | | ||| ||| || ||||          | ||||||| ||||| || ||||| ||||||||||| |||||||| || |||||||  ||| ||||||||||||| ||| | || |||||  | || ||||| ||
--ctatacttctttcttaga---ttgtggtggttaat---atgtcatacttattcgtttcgctggtcatctttttttccaactggctagtaaaatttcatccattcagGAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTAGAAAATATCGAGGCAAAGCTGATGCCCCAATATATTCCATTCAGATATG

upper sequence: AT3G15840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv09s0002g06980.t01 (Vitis vinifera), 3'ss of exon 4
-ttccaaattaaat-tagtagaaagctacatagaccagtcttatggagtacttataacaacaaaaaaaatgaaaatattcaattggtta-ctaaatggt-gcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTAAGAAAGATCGAGGCAAAGCCGATTCTCCGATATACACTATGCAGATTTG
   |   || |||| | ||| | |     |||   || ||  |   |  |  |  ||||  | | ||| |     |||| | ||| | | ||  |   | |||||||||||||| || || |||||||||||||| || ||||| ||||||||||| ||||  ||||| ||||| |||  ||| ||||| ||||| ||||| ||
gcccaccatgaaatctggtaaataatgctata---cattcgaacaaaccaaat-caacagaatagaaagtttgtttattaacttgttgaactgtacacttgcagGAGGATTTAATCAGCCCATCATGTGTGGTGGTGAACCAAGGGCAATGCTTAAAAAAGCCCGAGGAAAAGCTGATCGTCCCATATATACTATCCAGATATG

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|47828825|gb|CK118509.1|CK118509
EST:     AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG                         GAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
genomic: AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACGgtgagtttct ... aatggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
EST: gi|47828827|gb|CK118511.1|CK118511
EST:     AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG                         GAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
genomic: AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACGgtgagtttct ... aatggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
EST: gi|116420760|gb|EG463352.1|EG463352
EST:     AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG                         GAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
genomic: AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACGgtgagtttct ... aatggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
EST: gi|47828708|gb|CK118392.1|CK118392
EST:     AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG                         GAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
genomic: AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACGgtgagtttct ... aatggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
EST: gi|124727942|gb|EH819344.1|EH819344
EST:     GACTATGGGGTTGCTTTCAACG                         GAGGATTTAACCAACCTAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTT
genomic: GACTATGGGGTTGCTTTCAACGgtgagtttct ... aatggtgcagGAGGATTTAACCAACC-AATCATGTGTGGTGGGGAGCCAAGAGCAATGCTT
EST: gi|116441102|gb|EG483694.1|EG483694
EST:     AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG                         GAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
genomic: AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACGgtgagtttct ... aatggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
EST: gi|124706136|gb|EH797538.1|EH797538
EST:     GAAGACTATGGGGTTGCTTTCAACG                         GAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
genomic: GAAGACTATGGGGTTGCTTTCAACGgtgagtttct ... aatggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
EST: gi|47831953|gb|CK121637.1|CK121637
EST:     AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG                         GAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
genomic: AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACGgtgagtttct ... aatggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
EST: gi|47830759|gb|CK120443.1|CK120443
EST:     AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG                         GAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
genomic: AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACGgtgagtttct ... aatggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
EST: gi|47832287|gb|CK121971.1|CK121971
EST:     AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG                         GAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
genomic: AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACGgtgagtttct ... aatggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
EST: gi|125202456|gb|EL217410.1|EL217410
EST:     AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG                         GAGGATTTAACCAACCAATCATGTGTGGTGGG
genomic: AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACGgtgagtttct ... aatggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGG
EST: gi|116479685|gb|EG522277.1|EG522277
EST:     AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG                         GAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
genomic: AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACGgtgagtttct ... aatggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
EST: gi|116479684|gb|EG522276.1|EG522276
EST:     AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG                         GAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
genomic: AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACGgtgagtttct ... aatggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
EST: gi|124873658|gb|EH955303.1|EH955303
EST:     AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG                         GAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAA
genomic: AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACGgtgagtttct ... aatggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAA
EST: gi|116441100|gb|EG483692.1|EG483692
EST:     AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG                         GAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
genomic: AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACGgtgagtttct ... aatggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
EST: gi|116428971|gb|EG471563.1|EG471563
EST:     AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACG                         GAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA
genomic: AGCTGCAAGCAAACTCACTCTTAACGAAGACTATGGGGTTGCTTTCAACGgtgagtttct ... aatggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacttataacaacaaaaaaaatgaaaatattcaattggttactaaatggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTAAGAAAGATCGAGGCAAAGCCGATTCTCCGATATACACTATGCAGATTTG
                                        tactaaa  putative branch site (score: 1)
              aaaaaaaatgaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttccaaattaaattagtagaaagctacatagaccagtcttatggagtacttataacaacaaaaaaaatgaaaatattcaattggttactaaatggtgcagGAGGATTTAACCAACCAATCATGTGTGGTGGGGAGCCAAGAGCAATGCTTAAGAAAGATCGAGGCAAAGCCGATTCTCCGATATACACTATGCAGATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT