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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatatttcattttgattgattatgcggttcatagttgtagaaactttgcaaaactatgtaccaatgcttgtttaacttgtcatgcagGTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAAGGATGCAAATCAGTTGCCGCAGGAATGAATGCAATGGACTTGCGAAGAGGTATTTC

Basic information

species Arabidopsis thaliana
transcript AT3G23990.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 4
--------gtaagata--tttcattttgattg-attatgcggtt-catagttgtagaaactttgcaaaactatgtaccaatgcttgtttaacttgtcatgcagGTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAAGGATGCAAATCAGTTGCCGCAGGAATGAATGCAATGGACTTGCGAAGAGGTATTTC
        ||||   |  | |||  ||| | | |||||    |    ||| ||  |  ||  || || | |||     |  |    ||| | ||||  |||||| || || || ||||| ||||| || || || |||||| | ||||| |||||||||||||| || |||||||||||||||||| || |  | |||||   
tgaagactgtaaaccaactatcagcttgctggtattatctaataatttaggtgctgttaccatgaaagaatat---tgagggaacatttcaattgttttgcagGAACCACGTGCGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAGTTGCGGCTGGAATGAATGCAATGGACCTGAGGCGTGGTATAAG

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 4
----gtaagata--tttcattttgat--tgattatgcggttcatagttgtagaaactttg-caaaactatgtaccaatgcttgtttaacttgtcatgcagGTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAAGGATGCAAATCAGTTGCCGCAGGAATGAATGCAATGGACTTGCGAAGAGGTATTTC
     |||  |   | |||  ||| |  |  |||| |  |   ||| ||| |  ||  || || ||   ||    |  |    ||| | ||||| |||||| || || |||||||| ||||| || || || |||||| | ||||| ||||||||| | || || |||||||||||||||||| || |  | |||||   
gactataaactgactatcagcttgctggtatttatccaataattaggtgttgttaccgtgacagaatattgagggagggagcatttcaattgtcttgcagGAACCACATGTGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAATCGCGGCTGGAATGAATGCAATGGACCTGAGGCGGGGTATAAG

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 4
gtaagatatttcattt-tgattgattatgcggttcatagttgtagaaact--ttgcaaaactatgtaccaatgcttgtttaacttgtcatg-cagGTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAAGGATGCAAATCAGTTGCCGCAGGAATGAATGCAATGGACTTGCGAAGAGGTATTTC
||||| ||||  ||   |  | |||||| |  |    | |  |    | |   | |     ||| ||  ||||   ||  ||  |    || |||| || |||||||||||  | || ||    || |||||| | |||||||| ||||||||||| || ||||||||||| |||||| || || |||||||   
gtaagctattatatccatactggattatactttattaaatcttcagcattggctactttgttat-taataatgagggtacaatctaatttggcagGAACCACTTGTGCTACAATTCTTACTAAAGCAATATTTACGGAAGGATGTAAATCAGTTGCAGCTGGAATGAATGCGATGGACCTGAGACGAGGTATAAA

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 4
----------gtaag-atatttcattttgattgattatgcggttcatagttgtagaaactttgcaa--aactatgtaccaatgcttgtttaac-ttgtcat--gcagGTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAAGGATGCAAATCAGTTGCCGCAGGAATGAATGCAATGGACTTGCGAAGAGGTATTTC
           ||    || |   || |  || ||| |    |    ||   |    ||||||  |  ||  |  |   |||  |     ||| || | ||  ||||| || |||||||||||  | |||||    || |||||| | ||||| || ||||||||||| || ||||||||||| |||||| || || |||||||   
gtaagccattatatccgtactgggttatactttattgttaaatcttcagcattgactactttgttattaaacaaatggtaataatgagggaacattctaattggcagGAACCACTTGTGCTACAATTCTCACTAAAGCAATATTTACGGAAGGGTGTAAATCAGTTGCAGCTGGAATGAATGCGATGGACCTGAGACGAGGTATAAA

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 4
---------gtaagatatttcattttgattgattatgcggttcatagttgtagaaactttgcaaaac-tatgtaccaatgcttgtttaacttgtcatgcagGTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAAGGATGCAAATCAGTTGCCGCAGGAATGAATGCAATGGACTTGCGAAGAGGTATTTC
          || || | | |||  |  |  |   ||    |     || |      | ||  | || ||  |   |   ||| |||    ||   | ||||||| || ||||| || ||||| ||||| || |||||| | ||||| ||||| || ||||| || |||||||||||||||||| |  |||| ||||| ||
agaatggttttatgacaatgcatacttgtctacgttgtctctgtggtttattttgtttctgttacacatagatctgatcccttatttttgatgat-ttcagGTACCACCTGTGCCACAGTCCTTACCCGAGCAATATTTACTGAAGGGTGCAAGTCGGTTGCTGCTGGAATGAATGCAATGGACCTAAGAAGGGGTATCTC

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------------------------------------------gtaagatatttcattttgattgattatgcggttcatagttgtagaaactttgcaaaactatgtaccaatgcttgtttaacttgtcatgcagGTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAAGGATGCAAATCAGTTGCCGCAGGAATGAATGCAATGGACTTGCGAAGAGGTATTTC
                                                                                                         ||  ||| |||  ||  ||||||  |  |     |     | |   | ||  |||  || |  |           ||  |||  |||||| || |||||||| || || |||||||| ||||| ||||  || ||||| || |||||||| || || ||||||||||||||||| || || |||||   
gtaaagtcccggttctatctaaatttggagatatcgctcttacacgcatagttcctggacccattctttttattttgtacgaaggcttggggaattatttttgaaaatttatgtcacctt--ttgatttcggcgaattgatccacacaccttctgtgaaaacatttggctgactcgaaagaatatgttttgcagGGACAACTTGTGCAACGGTGCTCACCCGAGCTATTTTTGTTGAGGGATGTAAGTCAGTTGCAGCTGGCATGAATGCAATGGACTTACGTAGGGGTATCAA

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------------------------------------gtaagatatttcattttgattgattatgcggttcatagttgtagaaac------tttgca---aaactatgtaccaatgcttgtttaacttgtcatgcagGTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAAGGATGCAAATCAGTTGCCGCAGGAATGAATGCAATGGACTTGCGAAGAGGTATTTC
                                                                                                    | | ||||     |||||    |  | |||| | |||||  ||        || | |     |  || |  | |   |||  | |     | |||||| || |||  ||| || || ||||| || ||||| ||||| ||||| ||||||||||| || || || ||||| |||||||||||||| || || ||   
gcaagtgctctgtgtcatataatttgtgaagtttgagttcttagtcaggagcattattttcttgaatattgcagggtctaccgtattcaatctaatgacgacacatttagacgtgattatagacactgttcgtggttgtttaactatccgattcgtactgggatcatttggctaacattggctgaaacaccctgcagGAACCACTGCTGCAACAGTGCTCACACGAGCTATTTTTGCTGAAGGGTGCAAATCAGTAGCAGCTGGTATGAACGCAATGGACTTGCGCAGGGGCATCAA

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------------------------------------gtaagatatttcattttgattgattatgc--ggttcatagttgtagaaactttgcaaaactatgtaccaatgcttgtttaacttgtcatgcagGTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAAGGATGCAAATCAGTTGCCGCAGGAATGAATGCAATGGACTTGCGAAGAGGTATTTC
                                                                                               ||     |  |||    | ||    |||    |  |||  ||||   ||  |||||   | |  ||  |  |    |||     |  |||||| || |||||||| || || |||||||| || || ||||  || || |||||||||||||| || || ||||| ||||||||| | || |||||||||  
gtatatgcctaatcccagttgactgtgtgaacctcgttctgatgcatgatttcaacctactttttcattttgtatgaatctatggaatactcttatacagattaacatcagcactggccttgccaaatcaataaatgtatctacagtgcaatgat-ttcactgactcgaagtta-tgaattttgcagGAACAACTTGTGCAACAGTGCTCACCCGAGCAATTTTTGTTGAGGGCTGCAAATCAGTTGCAGCTGGCATGAACGCAATGGACCTACGTAGAGGTATTAG

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|86027480|gb|DR323233.1|DR323233
EST:     TAGTCTTGTGAAGCAGGTTGCAAATGCTACTAATGATGTTGCTGGTGATG                         GTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAA-GATGCA
genomic: TAGTCTTGTGAAGCAGGTTGCAAATGCTACTAATGATGTTGCTGGTGATGgtaagatatt ... tgtcatgcagGTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAAGGATGCA
EST: gi|164016731|gb|ES211907.1|ES211907
EST:     TAATGATGTTGCTGGTGATG                         GTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAAGGATGCA
genomic: TAATGATGTTGCTGGTGATGgtaagatatt ... tgtcatgcagGTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAAGGATGCA
EST: gi|86027481|gb|DR323234.1|DR323234
EST:     TAGTCTTGTGAAGCAGGTTGCAAATGCTACTAATGATGTTGCTGGTGATG                         GTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAA-GATGCA
genomic: TAGTCTTGTGAAGCAGGTTGCAAATGCTACTAATGATGTTGCTGGTGATGgtaagatatt ... tgtcatgcagGTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAAGGATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgtagaaactttgcaaaactatgtaccaatgcttgtttaacttgtcatgcagGTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAAGGATGCAAATCAGTTGCCGCAGGAATGAATGCAATGGACTTGCGAAGAGGTATTTC
                                     gtttaac  putative branch site (score: 3)
                 aaaactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatatttcattttgattgattatgcggttcatagttgtagaaactttgcaaaactatgtaccaatgcttgtttaacttgtcatgcagGTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAAGGATGCAAATCAGTTGCCGCAGGAATGAATGCAATGGACTTGCGAAGAGGTATTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG