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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcaactttagcatacgtaaatcgttagtagtaatttctagattgatagaggttcgagaccttaaaaggtgatgaatatttggtgggttttgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCGGGTATTAGTGGTGCTCCACAGG

Basic information

species Arabidopsis thaliana
transcript AT1G14400.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G14400.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g08960.1 (Oryza sativa), 3'ss of exon 1
agcaactttagcatacgtaaatcgttagtagtaatttctaga---ttgatagaggttcgagaccttaaaaggtgatgaatatttggtgggttttgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCGGGTATTAGTGGTGCTCCACAGG-----
      | | || || |||  | || |   ||||  |  |||   |   |  |||||    |          | | |  |||||||||    ||| |   || | ||   | |  |||||||||||||||||||||||||| ||||||||||||||  |  ||  ||| || || || || || || ||||| || |||||||     
-attggtctggc-ta-gtaggt-gtcatgggtaaactaaagaatctcagtgtaggtttcccattccttctattta-gcttatttggtga--cttggtatctacacagGGTGAAT-ATGTCGACGCCAGCAAGGAAGAGGTTGATGAGGGATTTCAAACGACTGATGCAGGATCCTCCAGCTGGCATAAGTGGGGCCCCACAGGACAAC

upper sequence: AT1G14400.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G110983_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------agcaactttagcatacgtaaatcgttagtagtaatttctagattgatagaggttcgagaccttaaaaggtgatgaatatttggtgggttttgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCGGGTATTAGTGGTGCTCCACAGG
                                               | | | |||   |          || |       | ||| ||||||     | || | |    | | |||    ||  |  |  | |||     || || |   | |||||||||| || || ||||||||| | ||||||||||||||| |||||  ||| ||||| || || || || ||||| || || ||||
gtagttttttccctcaaattttgttcgagttgttaatcctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgat-gatagattcgtgcgatccttttggctcatg----ttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG

upper sequence: AT1G14400.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 1
-----agcaactttagcatacgtaaatcgttagtagtaatttctagattgatagaggttcgagaccttaaaaggtgatgaatatttggtgggttttgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCGGGTATTAGTGGTGCTCCACAGG
         | | | |||   |          || |       | ||| ||||||     | || | |    | | |||    ||  |  |  | |||     || || |   | |||||||||| || || ||||||||| | ||||||||||||||| |||||  ||| ||||| || || || || ||||| || || ||||
ctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgat-gatagattcgtgcgatccttttggctcatg----ttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG

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|116430003|gb|EG472595.1|EG472595
EST:     GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACG                         AAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
genomic: GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACGgtaccatttt ... tgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
EST: gi|86023409|gb|DR319162.1|DR319162
EST:     GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACG                         AAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGNNNNATTTC
genomic: GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACGgtaccatttt ... tgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
EST: gi|86023416|gb|DR319169.1|DR319169
EST:     GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACG                         AAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
genomic: GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACGgtaccatttt ... tgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
EST: gi|116452457|gb|EG495049.1|EG495049
EST:     GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACG                         AAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
genomic: GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACGgtaccatttt ... tgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
EST: gi|86023414|gb|DR319167.1|DR319167
EST:     GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACG                         AAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
genomic: GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACGgtaccatttt ... tgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
EST: gi|125236797|gb|EL250882.1|EL250882
EST:     CAACGAGATCTGTTTCCACG                         AAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
genomic: CAACGAGATCTGTTTCCACGgtaccatttt ... tgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
EST: gi|301501590|gb|HO207130.1|HO207130
EST:     GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACG                         AAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
genomic: GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACGgtaccatttt ... tgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
EST: gi|116452451|gb|EG495043.1|EG495043
EST:     GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACG                         AAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
genomic: GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACGgtaccatttt ... tgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
EST: gi|116452452|gb|EG495044.1|EG495044
EST:     GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACG                         AAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
genomic: GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACGgtaccatttt ... tgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
EST: gi|86023411|gb|DR319164.1|DR319164
EST:     GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACG                         AAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
genomic: GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACGgtaccatttt ... tgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
EST: gi|86023408|gb|DR319161.1|DR319161
EST:     GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACG                         AAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
genomic: GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACGgtaccatttt ... tgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
EST: gi|86023410|gb|DR319163.1|DR319163
EST:     GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACG                         AAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
genomic: GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACGgtaccatttt ... tgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
EST: gi|116452475|gb|EG495067.1|EG495067
EST:     GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACG                         AAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
genomic: GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACGgtaccatttt ... tgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
EST: gi|164175968|gb|ES188444.1|ES188444
EST:     CTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACG                         AAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
genomic: CTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACGgtaccatttt ... tgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
EST: gi|86023412|gb|DR319165.1|DR319165
EST:     GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACG                         AAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
genomic: GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACGgtaccatttt ... tgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
EST: gi|116452456|gb|EG495048.1|EG495048
EST:     GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACG                         AAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
genomic: GACCTCTTCTCTCCGCGATCTTTACCTCAACAACGAGATCTGTTTCCACGgtaccatttt ... tgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
EST: gi|124809242|gb|EH894948.1|EH894948
EST:     CGAGATCTGTTTCCACG                         AAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC
genomic: CGAGATCTGTTTCCACGgtaccatttt ... tgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagaggttcgagaccttaaaaggtgatgaatatttggtgggttttgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCGGGTATTAGTGGTGCTCCACAGG
 gattgat  putative branch site (score: 4)
                                          ttttgttt  putative PPT
                                          ttttgtttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcaactttagcatacgtaaatcgttagtagtaatttctagattgatagaggttcgagaccttaaaaggtgatgaatatttggtgggttttgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCGGGTATTAGTGGTGCTCCACAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - cgagacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatttgg