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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtagaagtctctgaacttgtaaagtttcaacatgctacttgtgaagtatatgtctaacgtatgccaaatgtgtggtcttattatctctgtttcagTGTTTGTATGGTGGTGCACCAAAGGGCCCTCAGTTGAGGGATTTAGAAAGAGGAGCAGATATCGTGGTTGCAACTCCTGGGAGATTGAATGATATCCTTG

Basic information

species Arabidopsis thaliana
transcript AT3G01540.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G01540.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g07740.2 (Oryza sativa), 3'ss of exon 7
gtatgtagaagtctctgaacttgtaaagtttcaacatgc-tacttgtgaagtatatgtctaacgtatgccaaatgtgtggtcttattatctctgtttcagTGTTTGTATGGTGGTGCACCAAAGGGCCCTCAGTTGAGGGATTTAGAAAGAGGAGCAGATATCGTGGTTGCAACTCCTGGGAGATTGAATGATATCCTTG
    |||     |||  | ||| ||    |     |||| |  |||||   ||||    | | ||   | || |||    | |||||        |  ||||||| ||||| ||||| || || || |||||| | || ||| ||||  | || ||||| || ||||||||||||||||| ||||||||||| ||  | |
----gtacgttcctcctatcttttactcatctgttatgcgtttttgtgtcctataaagttgatgtcatctaattgtacctttttatt--------tgaagTGTTTATATGGAGGTGCTCCTAAAGGTCCTCAGCTAAGAGATCTAGAGCGTGGTGCAGACATTGTGGTTGCAACTCCTGGAAGATTGAATGACATTTTAG

upper sequence: AT3G01540.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0066g01020.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtagaagtctctgaacttgtaaagtttcaacatgctacttgtgaagtatatgtctaacgtatgccaaatgtgtggtcttatt-atctctgtttc---agTGTTTGTATGGTGGTGCACCAAAGGGCCCTCAGTTGAGGGATTTAGAAAGAGGAGCAGATATCGTGGTTGCAACTCCTGGGAGATTGAATGATATCCTTG
|| |||      ||   ||||  |||    |     ||||  ||  |||  ||   | |      |||  | |||  | ||| |||  | | ||| |    ||||||||||||| || ||||||||||| || |||||||| ||| |||| ||||||||||||||||||||||| ||||||||  | ||||||||||| || |
gtttgtta----cttgcaactcttaatacctt--tttgctgtttaggaaaaatgattgttttaattgctga-tgttagttctcatttgtttttgtcttttaagTGTTTGTATGGAGGAGCACCAAAGGGTCCCCAGTTGAGAGATCTAGACAGAGGAGCAGATATCGTGGTTGCTACTCCTGGCCGCTTGAATGATATTCTGG
















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|124738261|gb|EH829663.1|EH829663
EST:     AGGTCATCAAGAATTTCGTGTACG                         TGTTTGTATGGTGGTGCACCAAAGGGCCCTCAGTTGAGGGATTTAGAAAGA
genomic: AGGTCATCAAGAATTTCGTGTACGgtatgtagaa ... tctgtttcagTGTTTGTATGGTGGTGCACCAAAGGGCCCTCAGTTGAGGGATTTAGAAAGA
EST: gi|124984053|gb|EL056743.1|EL056743
EST:     TCCAAGAAGAAGCTGTTAAATTTGGGAGGTCATCAAGAATTTCGTGTACG                         TGTTTGTATGGTGGTGCACCAAAGGGCCCTCAGTT
genomic: TCCAAGAAGAAGCTGTTAAATTTGGGAGGTCATCAAGAATTTCGTGTACGgtatgtagaa ... tctgtttcagTGTTTGTATGGTGGTGCACCAAAGGGCCCTCAGTT
EST: gi|125301320|gb|EL315405.1|EL315405
EST:     TCCAAGAAGAAGCTGTTAAATTTGGGAGGTCATCAAGAATTTCGTGTACG                         TGTTTGTATGGTGGTG
genomic: TCCAAGAAGAAGCTGTTAAATTTGGGAGGTCATCAAGAATTTCGTGTACGgtatgtagaa ... tctgtttcagTGTTTGTATGGTGGTG
EST: gi|125199320|gb|EL214274.1|EL214274
EST:     TTGGGAGGTCATCAAGAATTTCGTGTACG                         TGTTTGTATGGTGGTGCACCAAAGGGCCCTCAGTTGAGGGATTTAGAAAGA
genomic: TTGGGAGGTCATCAAGAATTTCGTGTACGgtatgtagaa ... tctgtttcagTGTTTGTATGGTGGTGCACCAAAGGGCCCTCAGTTGAGGGATTTAGAAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaagtatatgtctaacgtatgccaaatgtgtggtcttattatctctgtttcagTGTTTGTATGGTGGTGCACCAAAGGGCCCTCAGTTGAGGGATTTAGAAAGAGGAGCAGATATCGTGGTTGCAACTCCTGGGAGATTGAATGATATCCTTG
           gtctaac  putative branch site (score: 2)
                                           tctctgtttc  putative PPT
                                   tcttattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtagaagtctctgaacttgtaaagtttcaacatgctacttgtgaagtatatgtctaacgtatgccaaatgtgtggtcttattatctctgtttcagTGTTTGTATGGTGGTGCACCAAAGGGCCCTCAGTTGAGGGATTTAGAAAGAGGAGCAGATATCGTGGTTGCAACTCCTGGGAGATTGAATGATATCCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT