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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaagccttgttatctaattgtctttattgaccatctgacacctttttagaacaccatgctctgatgtgagtgaatattagactattagagtatacttatctgccactagatctcaagactactagctatgtatcagGTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAG

Basic information

species Arabidopsis thaliana
transcript AT3G54840.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os10g30520.1 (Oryza sativa), 3'ss of exon 3
gtaagtaaagccttgttatctaattgtctttattgaccatctgacacctttttagaa-caccatgctctgatgtgagtgaatattagactat-tagagtatacttatctgccactagatctcaagactactagctatgtatcagGTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAG
                            |  |     ||  |||    |||||| |     | ||  | || |  |    || | |  ||   || | |||   | | | | | |   | |      || ||  |   | | |||| |||||||| || || || ||||| |||||  | || ||| | || || || ||||| |||||||||||||||||||| || || ||||||||
---------------------------gtgaaacagacacttgattattttttacaggtttcctgtacagaggacacaccatttgattctccctataatatggct-tattctattctgttt--gttttattaaatgaat-ttagGTGACTGTTGGTGCATCATTTTTGTCACAAACATTGGCGTTGGAGGATTCCACAACAGTAAAGTTTGAAATATGGGATACTGCTGGTCAGGAGAG

upper sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 3
gtaagtaaagccttgttatctaattgtctt-tattgaccatctgacacctttttagaacaccatgctctgatgtgagtgaatattagactattagagtat-acttatctgcc--actagatctcaagactactag-ctatgta---tcagGTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAG
    |||||    |||||| || |  | || | || |   | | |     ||||     |  ||  | |      |   ||||||    | ||    | | | ||||       | | | ||| |    |  ||| || ||||   | |||||||||||||||| || || ||||| ||||| |||||  ||||||||||||| ||||| |||||||||||||||||||| || || || |||||
----gtaaatatatgttatttagtacttttatttttattttttaatgtaattttttt-taatatagtttatgacaaaaaaatattgtcgtcttgatatgttaattattccatggaattgttcttatatgttttagactttgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG

upper sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 3
gtaagtaaagccttgttatctaattgtctttattg-accatctgacac--ctttttagaacaccatgctctgatgtgagtgaatattagactattagagtatacttatctgccactagat-ctcaagactactag-ctatgta---tcagGTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAG
    |||||    ||||   |   |   ||||||  |   | | | |    ||||   || |   |  | |||| | | |   | || | || ||   ||  | |  ||       |  | || |    |  ||| || ||||   | |||||||||||||||| || || ||||| ||||| |||||  ||||||||||||| ||||| |||||||||||||||||||| || || || |||||
----gtaaatatatgttgcttcggtacttttattttattttttaatataatttttcttaatatggt-ttatgatataaat---tttttgtctttttatgttaattattccatggaaattttcttatatgttttagactctgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG

upper sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 3
-------------------gtaagtaaagccttgt-tatctaattgtctttattgaccatctgacacctttttagaac--accatgctctgatgtgagtgaatattagactatt-----agagtatac-----ttatctgccactagatct--caagactactagctatgtat-----cagGTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAG
                    ||  | | |   ||   || |  || |     || |  || | | |   | ||  | |      ||  |  |||   || |  || |  |   |     | | || |      |||| |     ||||| |    ||| |  | | | |  ||     ||||| ||||| ||||| || |||||||| ||||| || || |||||||| ||||| ||||| ||||||||||||||||| || || || || |||||
gtaagaaatatacatagctatatattatgtgatgcacattttttttttcccttttattatattaaattctgttcaaccttgttttgtgccaatggatgttagcatcaatcctctcatgcaaaatacatggatgttatttcatgatagatttacttagattggttgatcttaataacttcagGTGACTGTAGGAGCTTCATTCTTGTCACAAACAATTGCCTTGCAAGATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAG

upper sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ26700 (Selaginella moellendorffii), 3'ss of exon 3
gtaagtaaagccttgttatctaattgtctttattgaccatctgacacctttttagaacaccatgctctgatgtgagtgaatattagactattagagtatacttatctgccactagatctcaagactactagctatgtatcagGTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAG-----
                                                                                       | | ||| |  |  | || ||    |  || |  | |      ||||     ||||| |||||||| || || || ||||| |||||||||||  | |||||||| | |||||| |||||||| |||||||| || |||||||| |||||     
--------------------------------------------------------------------------------------gcaagtagtgctt-ttaatgtgtttatt-attttgatatggt--gcta-----cagGTTACTGTTGGTGCTTCTTTTTTGTCGCAAACTATAGCTCTCCAAGACTCGAGCACAGTTAAGTTTGAGATATGGGACACCGCAGGACAAGAGAGATATG

upper sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ26987 (Selaginella moellendorffii), 3'ss of exon 3
gtaagtaaagccttgttatctaattgtctttattgaccatctgacacctttttagaacaccatgctctgatgtgagtgaatattagactattagagtatacttatctgccactagatctcaagactactagctatgtatcagGTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAG-----
                                                                                               |||       ||   | |   | |      |        ||   ||||| |||||||| || || || ||||| |||||||||||  | |||||||| | |||||| |||||||| |||||||| || |||||||| |||||     
-----------------------------------------------------------------------------------------------gtaagtagtgcttttaatgtgtttattattttgatatggtgctacagGTTACTGTTGGTGCTTCTTTTTTGTCGCAAACTATAGCTCTCCAAGACTCGAGCACAGTTAAGTTTGAGATATGGGACACCGCAGGACAAGAGAGATATG

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|164114252|gb|ES140566.1|ES140566
EST:     CCTTCGATTTGTACGTGGTCAGTTTGACGCAACATCTTAAG                         GTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTC
genomic: CCTTCGATTTGTACGTGGTCAGTTTGACGCTACATC-TAAGgtaagtaaag ... tatgtatcagGTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTC
EST: gi|124794348|gb|EH884027.1|EH884027
EST:     TACGTGGTCAGTTTGACGCTACATCTAAG                         GTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCT
genomic: TACGTGGTCAGTTTGACGCTACATCTAAGgtaagtaaag ... tatgtatcagGTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCT
EST: gi|19875441|gb|AU236272.1|AU236272
EST:     GTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG                         GTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCT
genomic: GTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAGgtaagtaaag ... tatgtatcagGTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattagagtatacttatctgccactagatctcaagactactagctatgtatcagGTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAG
         tatacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaaagccttgttatctaattgtctttattgaccatctgacacctttttagaacaccatgctctgatgtgagtgaatattagactattagagtatacttatctgccactagatctcaagactactagctatgtatcagGTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA