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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaataagatgagatttatacatactatgctaagtggggattaaggtcaattggtttgtctaggtaaaaacccattaattgttttggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT

Basic information

species Arabidopsis thaliana
transcript AT1G78900.2
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 18
-----gtaaataagatgagat-ttatacatactatgctaagtggggattaaggtcaattggtttgtctaggtaaaaacccattaattgttttggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT
     |   ||| ||| |  |  |  |  |  ||| |||       | | |    |     || |  |   |   |||   | |  ||  |   ||| |||||| || ||| | | |||||| ||||| || || ||||| || ||||| |||||||||||||| || |||||||| ||||| ||| | ||
aatttgaccataggatcaagtgctggatttggtat-ctataaaactaatgaaagaatgacattggattttcttttaacatgtgatgtgact-aaatatacagGCAGTAGAGCGTGGAGCTGGTATGGATGGACAGAAGATAACTTACACCCTTATCAAGCATCGGTTGGGAGATCTGTTCTATCGTCTTGT
















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|116484152|gb|EG526744.1|EG526744
EST:     CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
EST: gi|116484817|gb|EG527409.1|EG527409
EST:     CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
EST: gi|116423655|gb|EG466247.1|EG466247
EST:     CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
EST: gi|116423878|gb|EG466470.1|EG466470
EST:     CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
EST: gi|124935587|gb|EL012560.1|EL012560
EST:     TTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: TTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
EST: gi|116423877|gb|EG466469.1|EG466469
EST:     CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
EST: gi|116467266|gb|EG509858.1|EG509858
EST:     CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
EST: gi|116484141|gb|EG526733.1|EG526733
EST:     CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
EST: gi|116452176|gb|EG494768.1|EG494768
EST:     CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
EST: gi|164015096|gb|ES097749.1|ES097749
EST:     GATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: GATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
EST: gi|124745663|gb|EH836475.1|EH836475
EST:     GTAACATTATCCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAAGATTA
genomic: GTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAA-GATTA
EST: gi|86077026|gb|DR372783.1|DR372783
EST:     CCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGWGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: CCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
EST: gi|116436722|gb|EG479314.1|EG479314
EST:     CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
EST: gi|116424281|gb|EG466873.1|EG466873
EST:     CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
EST: gi|116452175|gb|EG494767.1|EG494767
EST:     CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
EST: gi|116456041|gb|EG498633.1|EG498633
EST:     CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
EST: gi|116433583|gb|EG476175.1|EG476175
EST:     CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
EST: gi|125058515|gb|EL127281.1|EL127281
EST:     CGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGACCAACCAG                         GCGGTTGAGAGAGCAGCT
genomic: CGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAG-CCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCT
EST: gi|116423654|gb|EG466246.1|EG466246
EST:     CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
EST: gi|116451304|gb|EG493896.1|EG493896
EST:     CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
EST: gi|116424219|gb|EG466811.1|EG466811
EST:     CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
EST: gi|116468179|gb|EG510771.1|EG510771
EST:     CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG                         GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT
genomic: CCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgtaaataaga ... ggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaggtcaattggtttgtctaggtaaaaacccattaattgttttggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT
                                cattaat  putative branch site (score: 3)
                                 attaattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaataagatgagatttatacatactatgctaagtggggattaaggtcaattggtttgtctaggtaaaaacccattaattgttttggatacacagGCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC