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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgagcagtgatgatatcatatcaacccattccaatctctccttacttaaatcctacacttacggtaatatctataatacttttgtagACACAACACAAGATGGAAATGGACAAGAGGGACGGTAAGTTCGGGCCACAGCCAATGGCAGTGCCTCCGGCTCAGCAAATGTCACGGTTTGATCAAGCCA

Basic information

species Arabidopsis thaliana
transcript AT4G23470.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G23470.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os03g03180.1 (Oryza sativa), 3'ss of exon 7
gtacgagcagtgatgatatcatatcaacccattccaatctctccttacttaaatcctac--acttacggtaatatctataatacttttgtagACACAACACAAGATGGAAATGGACAAGAGGGACGGTAAGTTCGGGCCACAGCCAATGGCAGTGCCTCCGGCTCAGCAAATGTCACGGTTTGATCAAGCCA
     | ||   || ||||| |        |||     ||| |  | |||||    | |  |   |   ||    ||  ||| | | || |||| |||||||| || |||||||||||||| || || |||||||| |||||||| ||||||||||||||    ||||||||||| ||  | |||||  | |
--gtaaacatacataatatctttggtgattattta---ctcactcttcttaacctttgcgtatccatcttatccactgaaatgcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAGCCCATGGCAGTGCCTCCAATGCAGCAAATGTCGCGCATCGATCAGCCTA

upper sequence: AT4G23470.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G060564_T02 (Zea mays), 3'ss of exon 6
gtacgagcagtgatgatatcatatcaacc----cattccaatctctccttacttaaatcct-aca-------cttacggtaatatctataatacttttgtagACACAACACAAGATGGAAATGGACAAGAGGGACGGTAAGTTCGGGCCACAGCCAATGGCAGTGCCTCCGGCTCAGCAAATGTCACGGTTTGATCAAGCCA
  |  |    |  |  | |  |  |||||       ||    ||||  | |   ||| ||| |||       |||  || | |      ||| |   || |||| || |||||  | ||||||||||||||||| || |||||| | |||||||| ||||||||||| ||||  || |||||||||||  | |||||  | |
--ataactcattcttttcttctcgcaaccttactgatcagggctcttgtgaaccaaaccctcacatatccttcttgtggcattgaaataaatgcaaatgcagACGCAGCACAAAGTCGAAATGGACAAGAGGGATGGAAAGTTCAGCCCACAGCCTATGGCAGTGCCCCCGGTGCAACAAATGTCACGCATCGATCAGCCTA

upper sequence: AT4G23470.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G060564_T03 (Zea mays), 3'ss of exon 7
--gtacgagcagtgatgatatcatatcaaccc----attccaatctctccttacttaaatcct-aca-------cttacggtaatatctataatacttttgtagACACAACACAAGATGGAAATGGACAAGAGGGACGGTAAGTTCGGGCCACAGCCAATGGCAGTGCCTCCGGCTCAGCAAATGTCACGGTTTGATCAAGCCA
   ||  |    |  |  | |  |  |||||       ||    ||||  | |   ||| ||| |||       |||  || | |      ||| |   || |||| || |||||  | ||||||||||||||||| || |||||| | |||||||| ||||||||||| ||||  || |||||||||||  | |||||  | |
gtatataactcattcttttcttctcgcaaccttactgatcagggctcttgtgaaccaaaccctcacatatccttcttgtggcattgaaataaatgcaaatgcagACGCAGCACAAAGTCGAAATGGACAAGAGGGATGGAAAGTTCAGCCCACAGCCTATGGCAGTGCCCCCGGTGCAACAAATGTCACGCATCGATCAGCCTA

upper sequence: AT4G23470.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G060564_T01 (Zea mays), 3'ss of exon 6
--------------------------------------------------------------------------------------------------------gtacgagcagtgatgatatcatatcaaccc----attccaatctctccttacttaaatcct-aca-------cttacggtaatatctataatacttttgtagACACAACACAAGATGGAAATGGACAAGAGGGACGGTAAGTTCGGGCCACAGCCAATGGCAGTGCCTCCGGCTCAGCAAATGTCACGGTTTGATCAAGCCA
                                                                                                         ||  |    |  |  | |  |  |||||       ||    ||||  | |   ||| ||| |||       |||  || | |      ||| |   || |||| || |||||  | ||||||||||||||||| || |||||| | |||||||| ||||||||||| ||||  || |||||||||                
taaggccgcccttaactgtctttttgcaaatctccatagcaaatgtctcagttctgataatcctatgccacattcttttgcagggtttgtgcatgtatgcaggtatataactcattcttttcttctcgcaaccttactgatcagggctcttgtgaaccaaaccctcacatatccttcttgtggcattgaaATAAATGCAAATGCAGACGCAGCACAAAGTCGAAATGGACAAGAGGGATGGAAAGTTCAGCCCACAGCCTATGGCAGTGCCCCCGGTGCAACAAATGTCA----------------

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|125015062|gb|EL087331.1|EL087331
EST:     CTGCACGGTTTGCGCATGTATGCAG                         ACACAACACAAGATGGAAA
genomic: CTGCACGGTTTGCGCATGTATGCAGgtacgagcag ... acttttgtagACACAACACAAGATGGAAA
EST: gi|124717629|gb|EH809031.1|EH809031
EST:     TGCACGGTTTGCGCATGTATGCAG                         ACACAACACAAGATGGAAATGGACAAGAGGGACGGTAAGTTCGGGCCACAG
genomic: TGCACGGTTTGCGCATGTATGCAGgtacgagcag ... acttttgtagACACAACACAAGATGGAAATGGACAAGAGGGACGGTAAGTTCGGGCCACAG
EST: gi|116434599|gb|EG477191.1|EG477191
EST:     CTGCACGGTTTGCGCATGTATGCAG                         ACACAACACAAGATGGAAATGGACAAGAGG
genomic: CTGCACGGTTTGCGCATGTATGCAGgtacgagcag ... acttttgtagACACAACACAAGATGGAAATGGACAAGAGG
EST: gi|301501098|gb|HO206638.1|HO206638
EST:     CTGCACGGTTTGCGCATGTATGCAG                         ACACAACACAAAGATGGAAATG
genomic: CTGCACGGTTTGCGCATGTATGCAGgtacgagcag ... acttttgtagACACAACACAA-GATGGAAATG
EST: gi|124720550|gb|EH811952.1|EH811952
EST:     CTGCACGGTTTGCGCATGTATGCAG                         ACACAACACAAGATGGAAA
genomic: CTGCACGGTTTGCGCATGTATGCAGgtacgagcag ... acttttgtagACACAACACAAGATGGAAA
EST: gi|125134662|gb|EL175419.1|EL175419
EST:     CTGCACGGTTTGCGCATGTATGCAG                         ACACAACACAAGATGGAAATGGACAAGAGGGACGGTAAGCTCGGGCCACAG
genomic: CTGCACGGTTTGCGCATGTATGCAGgtacgagcag ... acttttgtagACACAACACAAGATGGAAATGGACAAGAGGGACGGTAAGTTCGGGCCACAG
EST: gi|124993508|gb|EL065777.1|EL065777
EST:     CTGCACGGTTTGCGCATGTATGCAG                         ACACAACACAAGATGGAAATGGACAAGAGGGACGGTAAG
genomic: CTGCACGGTTTGCGCATGTATGCAGgtacgagcag ... acttttgtagACACAACACAAGATGGAAATGGACAAGAGGGACGGTAAG
EST: gi|125206972|gb|EL221926.1|EL221926
EST:     CGGTTTGCGCATGTATGCAG                         ACACAACACAAGATGGAAATGGACAAGAGGGACGGTAAGTTCGGGCCACAG
genomic: CGGTTTGCGCATGTATGCAGgtacgagcag ... acttttgtagACACAACACAAGATGGAAATGGACAAGAGGGACGGTAAGTTCGGGCCACAG
EST: gi|124929398|gb|EL006946.1|EL006946
EST:     CTGCACGGTTTGCGCATGTATGCAG                         ACACAACACAAGATGGAAATGGACAAGAGGGACGGTAAGTTCGGGACCACA
genomic: CTGCACGGTTTGCGCATGTATGCAGgtacgagcag ... acttttgtagACACAACACAAGATGGAAATGGACAAGAGGGACGGTAAGTTCGGG-CCACA
EST: gi|116434598|gb|EG477190.1|EG477190
EST:     CTGCACGGTTTGCGCATGTATGCAG                         ACACAACACAAGATGGAAATGGACAAGAGG
genomic: CTGCACGGTTTGCGCATGTATGCAGgtacgagcag ... acttttgtagACACAACACAAGATGGAAATGGACAAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctctccttacttaaatcctacacttacggtaatatctataatacttttgtagACACAACACAAGATGGAAATGGACAAGAGGGACGGTAAGTTCGGGCCACAGCCAATGGCAGTGCCTCCGGCTCAGCAAATGTCACGGTTTGATCAAGCCA
                       cacttac  putative branch site (score: 2)
                                            tactttt  putative PPT
                                taatatctataatact  TA-rich tract