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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacaacttaaatgcttgttagttgttatgtggaacctgaatttcttaattttctgctacatctggtgatataagtgatgccggtaacattagatgtgtttttgtattacggtgatagtgaaaacccttaaattctgaacttgtaagGACTTGCTGGATGCACTGAACCAACTAGAAGAAGGGCTAAAAGACAAGATCAAGAAATTGAGTTCCTTTGATAAATATAAGCAAGAGGTGCTCCTTGGCC

Basic information

species Arabidopsis thaliana
transcript AT3G42050.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G42050.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv16s0039g01610.t01 (Vitis vinifera), 3'ss of exon 10
gtaagacaacttaaatgcttgttagttgttatgtggaacctgaatttcttaatttt-ctgctacatctggtgatataagtgatgccggtaacattagatgtgtttttgtattacggtgatagtgaaaacccttaaattctgaacttgtaagGACTTGCTGGATGCACTGAACCAACTAGAAGAAGGGCTAAAAGACAAGATCAAGAAATTGAGTTCCTTTGATAAATATAAGCAAGAGGTGCTCCTTGGCC
                                          |  | ||  ||||  |||  | |   | | ||||  || |   |   |   |    |||  ||   ||| |   |  |  |    |   |  |||| |   |     ||||| || |||| || ||||| |||||||| |||||||| ||||  || || ||||||||||| || |||||||| || || ||||| || ||||||||||
------------------------------------------acctactccatttggctgtcaaactcgattatatgtgttagatctcaagtct---gtgttcttcactatcatcatt-tcttattgattttggaattttatgc-----agGACCTGATGGAGGCTCTGAATCAACTAGATGAAGGGCTGAAAGCTAACATTAAGAAATTGAGCTCGTTTGATAAGTACAAACAAGAAGTCCTCCTTGGCC
















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|86031301|gb|DR327054.1|DR327054
EST:     GACTCCCACATATTATCCACAGTCTAAAAACACAAGCATGGAGTGACGAG                         GACTTGCTGGATGCACTGAACCAACTAGAAGAAGGGCTAAAAGACAAGATC
genomic: GACTCCCACATATTATCCACAGTCTAAAAACACAAGCATGGAGTGACGAGgtaagacaac ... aacttgtaagGACTTGCTGGATGCACTGAACCAACTAGAAGAAGGGCTAAAAGACAAGATC
EST: gi|124925944|gb|EL003863.1|EL003863
EST:     GACTCCCACATATTATCCACAGTCTAAAAACACAAGCATGGAGTGACGAG                         GACTTGCTGGATGCACTGAACCAACTAGAAGAAGGGCTAAAAGACAAGA
genomic: GACTCCCACATATTATCCACAGTCTAAAAACACAAGCATGGAGTGACGAGgtaagacaac ... aacttgtaagGACTTGCTGGATGCACTGAACCAACTAGAAGAAGGGCTAAAAGACAAGA
EST: gi|124784886|gb|EH874569.1|EH874569
EST:     TTATCCACAGTCTAAAAACACAAGCATGGAGTGACGAG                         GACTTGCTGGATGCACTGAACCAACTAGAAGAAGGGCTAAAAGACAAGATC
genomic: TTATCCACAGTCTAAAAACACAAGCATGGAGTGACGAGgtaagacaac ... aacttgtaagGACTTGCTGGATGCACTGAACCAACTAGAAGAAGGGCTAAAAGACAAGATC
EST: gi|164206935|gb|ES059481.1|ES059481
EST:     CTAAAAACACAAGCATGGAGTGACGAG                         GACTTGCTGGATGCACTGAACCAACTAGAAGAAGGGCTAAAAGACAAGATC
genomic: CTAAAAACACAAGCATGGAGTGACGAGgtaagacaac ... aacttgtaagGACTTGCTGGATGCACTGAACCAACTAGAAGAAGGGCTAAAAGACAAGATC
EST: gi|125229979|gb|EL244064.1|EL244064
EST:     TTATCCACAGTCTAAAAACACAAGCATGGAGTGACGAG                         GACTTGCTGGATGCACTGAACCAACTAGAAGAAGGGCTAAAAGACAAGATC
genomic: TTATCCACAGTCTAAAAACACAAGCATGGAGTGACGAGgtaagacaac ... aacttgtaagGACTTGCTGGATGCACTGAACCAACTAGAAGAAGGGCTAAAAGACAAGATC
EST: gi|124737838|gb|EH829240.1|EH829240
EST:     TATTATCCACAGTCTAAAAACACAAGCATGGAGTGACGAG                         GACTTGCTGGATGCACTGAACCAACTAGAAGAAGGGCTAAAAGACAAGATC
genomic: TATTATCCACAGTCTAAAAACACAAGCATGGAGTGACGAGgtaagacaac ... aacttgtaagGACTTGCTGGATGCACTGAACCAACTAGAAGAAGGGCTAAAAGACAAGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtgtttttgtattacggtgatagtgaaaacccttaaattctgaacttgtaagGACTTGCTGGATGCACTGAACCAACTAGAAGAAGGGCTAAAAGACAAGATCAAGAAATTGAGTTCCTTTGATAAATATAAGCAAGAGGTGCTCCTTGGCC
      tttttgtatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagacaacttaaatgcttgttagttgttatgtggaacctgaatttcttaattttctgctacatctggtgatataagtgatgccggtaacattagatgtgtttttgtattacggtgatagtgaaaacccttaaattctgaacttgtaagGACTTGCTGGATGCACTGAACCAACTAGAAGAAGGGCTAAAAGACAAGATCAAGAAATTGAGTTCCTTTGATAAATATAAGCAAGAGGTGCTCCTTGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG