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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgtttttgttcatattttggctttggttgttgagtaaagctaatgaggggaatgtcactttatattcagtatttaaacttttgagcttccctgtcatgcttttcatcattgtgctgatgattgcagATCGCTCAAACATTTCGCGACAAGAAAATTCCTTCTGACGTGATATGGATGGATATTGACTACATGGATGGTTTCCGTTGTTTCACATTCGACAAG

Basic information

species Arabidopsis thaliana
transcript AT3G23640.2
intron # 6
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 6
lower sequence: LOC_Os07g23880.1 (Oryza sativa), 3'ss of exon 5
gtcagtgtttttgttcatattttggctttggttgttgagtaaagctaatgaggggaatgtcactttatattcagtatttaaacttttgagcttccctgtcatgctttt-catcattgtgctgatgattgcagATCGCTCAAACATTTCGCGACAAGAAAATTCCTTCTGACGTGATATGGATGGATATTGACTACATGGATGGTTTCCGTTGTTTCACATTCGACAAG
                  | ||      |  ||| |  || |            |||||    || |   |   || |     |  |||   |   | |||||||  | |||  || |  |     |  ||| | | |  ||||||||| || ||    ||||||| ||| ||| | ||||||||||||||||| |||||||||||  | || |||||||| || |  
------------------agttcaatcctcattgctttgtca------------gaatgcattttgaggcttgataat-gttttactgatgatatgt-tcatgctgatacatagttattttttgcttcacagGTTGTTAGAACATTTCGAGAGAAAGGTATTCCTTGTGATGTGGTCTGGATGGATATTGACTATATGGATGGTTTTAGATGCTTCACATTTGATAGT

upper sequence: AT3G23640.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os07g23944.1 (Oryza sativa), 3'ss of exon 5
gtcagtgtttttgttcatattttggctttggttgttgagtaaagcta-atgaggggaatgtcactttatattcagtatttaaacttttgagcttccctgtcatgcttttcat-cattgtgctgatgattgcagATCGCTCAAACATTTCGCGACAAGAAAATTCCTTCTGACGTGATATGGATGGATATTGACTACATGGATGGTTTCCGTTGTTTCACATTCGACAAG
                                 |||||||   |  | |||   |    ||||    | ||| | | |  |||      |||     |||  |     | ||   || |  |     |||||| | | | |||||||| | || |     ||||||| ||| ||  |||||||||||||||| ||||||||||||||  | || || || ||   |   
--------------------------------agttgagttgggaaagatgctagaggggtcaagc-acatttattttgaaaagggcccagcgatgatgttttaacactgatatgtttttttttctgttgcagGTTGTTAAAACATTTAGAGAAAGAGGCATTCCTTGTGATGTTGTATGGATGGATATTGATTACATGGATGGTTTTAGGTGCTTTACGTTTAGC---

upper sequence: AT3G23640.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: AC203753.4_FGT006 (Zea mays), 3'ss of exon 1
gtcagtgtttttgttcatattttggctttggttgttgagtaaagctaatgaggggaatgtcactttatattcagtatttaaacttttgagcttccctgtcatgcttttcatcattgtgctgatgattgcagATCGCTCAAACATTTCGCGACAAGAAAATTCCTTCTGACGTGATATGGATGGATATTGACTACATGGATGGTTTCCGTTGTTTCACATTCGACAAG
           | | |||||||      |||||  |   | | ||  || ||   | | | ||   |||||   || | ||   || | | | |   || ||   || | ||                ||| | | |  ||||||| | || ||   |||||||| ||| ||  | ||||||||||||||||| |||||||||||  | || ||||| || || |  
---------gctttacatatttgtcacatggttcattt-tgaggc--ataagaatactttgaca--atattttatactgaa---ttagtgttgcttggttatttattgcttc--------------cacagGTTGTTAGAACATTTAGGGAGAAAGGAATTCCTTGTGATGTTGTCTGGATGGATATTGACTATATGGATGGTTTTAGGTGCTTCACGTTTGATAGT

upper sequence: AT3G23640.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G14810.1 (Glycine max), 3'ss of exon 5
gtcagtgtttttgttcatattttggctttggttgttgagtaaagctaatgaggggaatgtcactttatattcagtatttaaacttttgagcttccctgtcatgcttttcatcattg--tgctgatgattgcagATCGCTCAAACATTTCGCGACAAGAAAATTCCTTCTGACGTGATATGGATGGATATTGACTACATGGATGGTTTCCGTTGTTTCACATTCGACAAG
                           |   | | | |  ||   |  |  |   | | | |||||   ||  ||  ||||  ||||       | |||  ||  ||   |  ||      | |   |||||| | ||  ||||||| ||  | ||||  || |||| ||| ||| | ||||||||||| || |||||||||||||| ||||||||||| || ||||||
---------------------------tgcatcgct-atcaactttgttttgtatattctaacttt---tttggttattaattttttagaag--catgttttgtcttgacttgttaacaattaaaatttgcagGTTGCAAAAACATTCCGGAAAAAGAGCATACCTTGTGATGTGGTGTGGATGGATATCGATTACATGGATGGTTTTCGTTGTTTCACCTTTGACAAG

upper sequence: AT3G23640.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv02s0033g01410.t01 (Vitis vinifera), 3'ss of exon 6
gtcagtgtttttgttcatattttggctttggttgttgagtaaagctaatgaggggaatgtcactttatattcagtatttaaacttttgagcttccctgtcatgcttttcatcattgtgctgatgattgcagATCGCTCAAACATTTCGCGACAAGAAAATTCCTTCTGACGTGATATGGATGGATATTGACTACATGGATGGTTTCCGTTGTTTCACATTCGACAAG
                        |   | ||| ||    |  |||        | |   |  |||| | |  | | || |     | |  ||  |||      ||  |         || ||  || ||| | || | |||||| || || |||  ||| |||| ||| || ||||||||||||||||| |||||||||||||| || |||||||| || ||  ||
-----------------------agagcttgtt-ttacacactgctctgactttgtagaaccttttaaactttgaacttcattccctcaaattttctgctgaatttacc-------cactcatacttacagGTTGCCCGAACATTCCGTGAGAAGGGAATACCTTGTGATGTCATATGGATGGATATTGATTACATGGATGGTTTTCGCTGTTTCACTTTTGATCAG

upper sequence: AT3G23640.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv02s0087g00060.t01 (Vitis vinifera), 3'ss of exon 6
gtcagtgtttttgttcatattttggctttggttgttgagtaaagctaatgaggggaatgtcactttatattcagtatttaaacttttgagcttccctgtcatgcttttcatcattgtgctgatgattgcagATCGCTCAAACATTTCGCGACAAGAAAATTCCTTCTGACGTGATATGGATGGATATTGACTACATGGATGGTTTCCGTTGTTTCACATTCGACAAG----
                        ||||    | ||    |  ||||||     | |   |  |||| | |  | | || |     | |  ||  |||        |||||       || ||  |||||| | || | |||||| || || |||  ||| |||| ||| || ||||||||||||||||| |||||||||||||| || |||||||| || ||  ||    
---------------------agagctt---cttttacacactgctaatactttgtagaaccttttaaactttgaacttcattccctcaaattttctg-------cttcatttacccactcatacttgcagGTTGCCCGAACATTCCGTGAGAAGGGAATACCTTGTGATGTCATATGGATGGATATTGATTACATGGATGGTTTTCGCTGTTTCACTTTTGATCAGGCAA

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|124800017|gb|EH889682.1|EH889682
EST:     CGAGTAGCCGAG                         ATCGCTCAAACATTTCGCGACAAGAAAATTCCTTCTGACGTGATATGGATG
genomic: CGAGTAGCCGAGgtcagtgttt ... atgattgcagATCGCTCAAACATTTCGCGACAAGAAAATTCCTTCTGACGTGATATGGATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaacttttgagcttccctgtcatgcttttcatcattgtgctgatgattgcagATCGCTCAAACATTTCGCGACAAGAAAATTCCTTCTGACGTGATATGGATGGATATTGACTACATGGATGGTTTCCGTTGTTTCACATTCGACAAG
                                        tgctgat  putative branch site (score: 3)
                            ttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgtttttgttcatattttggctttggttgttgagtaaagctaatgaggggaatgtcactttatattcagtatttaaacttttgagcttccctgtcatgcttttcatcattgtgctgatgattgcagATCGCTCAAACATTTCGCGACAAGAAAATTCCTTCTGACGTGATATGGATGGATATTGACTACATGGATGGTTTCCGTTGTTTCACATTCGACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA