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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggttcattcacttaacaaccatcatcatttcgttaccctgattaatttggtgggtataatgttcagGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGAGAAA

Basic information

species Arabidopsis thaliana
transcript AT3G23640.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23640.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os07g23880.1 (Oryza sativa), 3'ss of exon 2
------------------------gtgggttcattcacttaacaacca-tcatcatttcgttaccc-tgattaatttggtgggtataatgttca---gGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGAGAAA
                        ||  ||   |||   |||   | | |  | |  |  ||||      || || | |||  |||  | | ||   |||||||||||||||||| ||||||||||| | |||  | ||||||||||| ||||| |||||||| ||||||||  | | |||||| ||   |||| |  
gtacgttatctgcttgaagaaattgtttgtcatttcttgtaaattctagttcttagctgtttacaaacatttgatctcgtgt-tatgttttccactagGTTTTTACTTGGAACACAGATGCATGGGGTTTTGGGCCAGGAACCACTTCATTATATCAGTCACACCCTTGGGTTTTGGCTGTCCTCCCTGATGGAAAGG

upper sequence: AT3G23640.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os07g23944.1 (Oryza sativa), 3'ss of exon 2
gtgggttcattcacttaacaacca-tcatcatttcgttaccctgattaatttggt---gggtataatgttcagGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGAGAAA
||  ||    |   | |  ||  | |||| |      |      || |||||| |    |  | | || | ||||| ||||||||||||| ||||||||||  |||||| | |||||||| ||  |||| |||||||| ||||||||||| | ||| |||||   |||  |  
gtatgtcatatttttgagaaattagtcattaaccttctgtttccataaatttgatctatgaaacattggttagGTTATTACTTGGAACACGGATGCATGGGATTATGGTCCAGGAACCACATCACTATATCAGTCACACCCTTGGGTACTGGCTGTTCTTCCTGATGGGAAGG

upper sequence: AT3G23640.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G14810.1 (Glycine max), 3'ss of exon 2
-------------gtgggttcattcacttaacaaccatcatcatttcgttaccctgat--taatttggtgggtataatgttcagGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGAGAAA
              |||  |  ||  |||   ||  |   | ||||  ||| |  | |  | ||  | |   | | || | |||||||| || |||||||| ||||||||||| |||||  ||||||| || || || ||||| |||||||| |||||  |||  || ||||| | ||| ||  
gtaagtcaatcttatggaatt-ttgtctttttaaaaagatttattt-attatctgggtgctgatcagttaaatttcatttgcagGTTTTCACATGGAACACAGATGCATGGGGTTATGGCCCTGGAACTACATCCTTGTACCAATCACATCCATGGGTGTTAGCAGTTCTTCCTAATGGCGAGG

upper sequence: AT3G23640.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0033g01410.t01 (Vitis vinifera), 3'ss of exon 3
--------gtgggttcattcacttaacaaccatcatcatttcgttaccctgattaat--ttggtgggtataatgttcagGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGAGAAA
        ||  ||  | |  || | ||   | | |  || |  | |    | || |  |       |||    |  |||||||||| |||||||| ||||||||||| |||||||||||||| || || || |||||||||||||||||||| |||| ||| ||||||| ||| ||  
gtaagacagtttgtatagtttctcatcatgaagccttgttccagttctacaagtattgataaacttatattccatgtagGTTTTTACGTGGAACACAGATGCATGGGGTTATGGTTCTGGAACAACATCCTTGTACCAGTCACATCCTTGGGTTCTAGCTGTTCTTCCAAATGGGGAGG

upper sequence: AT3G23640.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0087g00060.t01 (Vitis vinifera), 3'ss of exon 3
--------gtgggttcattcacttaacaaccatcatcatttcgttaccctgattaatt-tggtgggtataatgttcagGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGAGAAA
        ||  ||  | |  || | ||   | | |  | ||  | |    |  | |  |      |||    |  |||||||||| |||||||  | ||||||||| | || ||||||||| || || || |||||||||||||||||||| |||| ||| ||||||| ||| ||  
gtaagacagtttgtatagtttctcatcatgaagctttgtgtcagttctacaagcattgataacttatattccatgtagGTTTTTACGTGGAACATAGCTGCATGGGGTTTTGATTCTGGAACGACATCCTTGTACCAGTCACATCCTTGGGTTCTAGCTGTTCTTCCAAATGGGGAGG

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|116479211|gb|EG521803.1|EG521803
EST:     TTTATGGGACGGGAGAAGTTAGTGGTCAGTTGGAGAGAACAGGCAAACGG                         GTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCG
genomic: TTTATGGGACGGGAGAAGTTAGTGGTCAGTTGGAGAGAACAGGCAAACGGgtgggttcat ... taatgttcagGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaacaaccatcatcatttcgttaccctgattaatttggtgggtataatgttcagGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGAGAAA
                            gattaat  putative branch site (score: 3)
                           tgattaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggttcattcacttaacaaccatcatcatttcgttaccctgattaatttggtgggtataatgttcagGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA