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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatctcttaacactaaggacctctctttttaatctaagtgtttcaattttgatgataaactttttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTTCCTGACAAAGGCAAGGAAATACACTTTCTTCAAGCCAAAATTCATCTTC

Basic information

species Arabidopsis thaliana
transcript AT3G56940.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------------------------------------------------------------gtaagatct---cttaacactaaggacctctctttttaatc-------taagtgtttcaattttgatg-----ataaactttttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTTCCTGACAAAGGCAAGGAAATACACTTTCTTCAAGCCAAAATTCATCTTC
                                                                                                       || || |   ||| |   | ||| | ||  |||  | ||       ||||   ||||| |    ||     || |  | |  |   ||||||||||||||||||  ||||||||||||||||||| || ||  | || ||| |||| ||||| ||||| ||||| ||||||||||| || |||||||||
gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagcttcagttttagggcgtccatttcaactcaattgagtaagcaattcaactgaattgtctgcatgatttatgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC

upper sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
----------gtaagatctcttaacactaaggacctctctttttaatctaagtgtttcaattttgatgataaactttttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTTCCTGACAAAGGCAAGGAAATACACTTTCTTCAAGCCAAAATTCATCTTC
               |||||||  ||   |            || | || |  ||||||  | ||||  |  |||   | |   |||||||||||||||||  ||||||| ||||||||||| || ||  |||| |||||||| ||||| ||||| ||||| ||||||||||| || |||||||||
gtacgcacctaccttatctcttttcatccattcggggagaaattcagctgaaagtttca--tgtgatt-tgcactcactgtt-tagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC

upper sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G043109_T01 (Zea mays), 3'ss of exon 2
----------------------------gtaagatctcttaacactaaggacctctctttttaatctaagtgtttcaattttgatgataaactttttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTTCCTGACAAAGGCAAGGAAATACACTTTCTTCAAGCCAAAATTCATCTTC
                             | ||          | | | ||   |       |||  |  ||    || ||| ||| | |  |    |  | ||||| |||||||||||  ||||||| ||||||||||| || ||  |||| ||||| || ||||| ||||| ||||| ||||||||||| || |||||||||
catgcatgttttcctgattgtgttcaatttgaggctctagggtaatgatgagggcatggagaaattcagctga---aagtttcatg-tgatttgcactgtgtagGTTTTTGAACAAGGGTCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTCACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC

upper sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 2
------------gtaagatctcttaacactaaggacctctcttt----ttaatctaagtgtttcaattttgatg-ataaactttttttg-------gcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTTCCTGACAAAGGCAAGGAAATACACTTTCTTCAAGCCAAAATTCATCTTC
             |     || | |    |||  | |  |||||    ||    |   | | |   || |  || || | ||  |||||       ||||||| ||||||||||| || ||||||||||| |||||||| || ||||||||| |||| || || || |||||||| || ||||||||||| || ||||||
gtatggaaacgccttgtgcctttaatttttaattatccttctttgattttctatttgatatcttgtttgtagtgcatgacctcattttgattctgtgcagGTTTTTGAACAAGGGTTTATCTGATTTCAATTTGGCTCTGGACTTGGGTTTCTTGACCAAAGCTAGAAAATACACATTTTTCAAGCCAAAGTTTATCTTC

upper sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0040g00390.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------------------------------------gtaagatctcttaacactaaggacctctctttttaatctaagtgtttcaattttgatgataaactttttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTTCCTGACAAAGGCAAGGAAATACACTTTCTTCAAGCCAAAATTCATCTTC
                                                                    |||   |        | ||         ||||||   ||  || | || |    |        |  | | |||| ||  ||||||| || || ||||||||||| |||||| | || ||||| ||||| |||||||| || || ||||| || || ||||| || |||||||||
gtatgcaaacaactctctgcccttctcccttcctcactcatggtcatatgcatcatagtttgcagaacaagtaatacagctgttgagttttatagcttttaactgaaaagtctgaaataaacttcatgttctgctgttgcagATTTCTGAACAAAGGTTTATCTGATTTCAATTTGGCTTTGGACTTGGGGTTCCTCACAAAGGCTAGAAAGTACACCTTTTTTAAGCCCAAGTTCATCTTC

upper sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ30397 (Selaginella moellendorffii), 3'ss of exon 2
gtaagatctcttaacactaaggacctctctttttaatctaagtgtttcaattttgatgataaacttttt-ttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTTCCTGACAAAGGCAAGGAAATACACTTTCTTCAAGCCAAAATTCATCTTC
                 ||||  |     || | | |   |       |   | ||| ||   || | | ||   |||||| ||||||| ||||| || || || ||||||||||| ||| | || || ||||| || ||  |||| ||||| |||||||||||| | |||||||||
----------------gtaagttctcagtttctcagttggaaaaaa--agcatcgatcatttcctatatgttcatagGTTCCTGAACAAAGGATTATCCGACTTTAACTTGGCTCTGGATCTTGGATTTCTGACCAAAGCCCGGAAGTACACCTTCTTCAAGCCACAGTTCATCTTC

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|125045547|gb|EL117816.1|EL117816
EST:     AGATGAAGCAAGACATGCCGG                         GTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTT
genomic: AGATGAAGCAAGACATGCCGGgtaagatctc ... tttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTT
EST: gi|164072961|gb|ES131766.1|ES131766
EST:     GATGAAGCAAGACATGCCGG                         GTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTT
genomic: GATGAAGCAAGACATGCCGGgtaagatctc ... tttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTT
EST: gi|125191269|gb|EL206223.1|EL206223
EST:     GTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAAGCAAGACATGCCGG                         GTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCT
genomic: GTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAAGCAAGACATGCCGGgtaagatctc ... tttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCT
EST: gi|125026028|gb|EL098297.1|EL098297
EST:     GTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAAGCAAGACATGCCGG                         GTTCTTGAACAAGGGATTGTCTGAT
genomic: GTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAAGCAAGACATGCCGGgtaagatctc ... tttttggcagGTTCTTGAACAAGGGATTGTCTGAT
EST: gi|124739769|gb|EH830931.1|EH830931
EST:     GTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAAGCAAGACATGCCGG                         GTTCTTGAACAAGGGATTGTCTGATTTCAA
genomic: GTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAAGCAAGACATGCCGGgtaagatctc ... tttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAA
EST: gi|86076552|gb|DR372309.1|DR372309
EST:     GTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAAGCAAGACATGCCGG                         GTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTT
genomic: GTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAAGCAAGACATGCCGGgtaagatctc ... tttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTT
EST: gi|164159392|gb|EL976250.1|EL976250
EST:     GAGATGAAGCAAGACATGCCGG                         GTTCTTGAACAAGGGATTGTCTGATT-CAACTTGGCTCTTCGATTTGGGTT
genomic: GAGATGAAGCAAGACATGCCGGgtaagatctc ... tttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTT-GATTTGGGTT
EST: gi|124734990|gb|EH826392.1|EH826392
EST:     TGTCTAGAGATGAAGCAAGACATGCCGG                         GTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTT
genomic: TGTCTAGAGATGAAGCAAGACATGCCGGgtaagatctc ... tttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTT
EST: gi|164020420|gb|ES081793.1|ES081793
EST:     GATGAAGCAAGACATGCCGG                         GTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTT
genomic: GATGAAGCAAGACATGCCGGgtaagatctc ... tttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTT
EST: gi|124907492|gb|EH981572.1|EH981572
EST:     TGGCTGAGATCTTCTCTTCTTATGTCTAGAGATGAAGCAAGACATGCCGG                         GTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCT
genomic: TGGCTGAGATCTTCTC-TCTTATGTCTAGAGATGAAGCAAGACATGCCGGgtaagatctc ... tttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCT
EST: gi|124926764|gb|EL004560.1|EL004560
EST:     CTTATGTCTAGAGATGAAGCAAGACATGCCGG                         GTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTACTTAGATTTGGGT
genomic: CTTATGTCTAGAGATGAAGCAAGACATGCCGGgtaagatctc ... tttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCT-CTT-GATTTGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacctctctttttaatctaagtgtttcaattttgatgataaactttttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTTCCTGACAAAGGCAAGGAAATACACTTTCTTCAAGCCAAAATTCATCTTC
                                          cttttttt  CT-rich tract
                       tttcaattttgatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatctcttaacactaaggacctctctttttaatctaagtgtttcaattttgatgataaactttttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTTCCTGACAAAGGCAAGGAAATACACTTTCTTCAAGCCAAAATTCATCTTC

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