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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgaataaatatctcgttttccatccttgtcttgtccttaataaccttatatatctctgcaagtcatatttagacactatattcccttattttgatcgatgcagAGAGATGATCCAGCACAGACCCTACACTCAAAAAGTGGACGTGTATAGTTTTGGAATCGTGCTGTGGGAGTTGATTACAGGTCTGTTACCGTTCCAGAAC

Basic information

species Arabidopsis thaliana
transcript AT4G31170.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G31170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S69_199V6.2 (Physcomitrella patens), 3'ss of exon 3
gtaagttgaataaatatctcgttttccatccttgtcttgtccttaataaccttatatatctctgcaagtcatatttagacactatattcccttattttgatcgatgcagAGAGATGATCCAGCACAGACCCTACACTCAAAAAGTGGACGTGTATAGTTTTGGAATCGTGCTGTGGGAGTTGATTACAGGTCTGTTACCGTTCCAGAAC
 || ||    ||   ||   |      |  |      |       |  |    | |   | |      |  | ||||||  ||| ||    |  |  |  |   | ||| |||||||| |||||||||||||||| ||| || ||||||||||| || |||||  | ||  |||||||| |  | ||||| |||||||| ||||| || 
-taggtc---tatgcattatgaacaagacacaaaaaataaaagagaggaagaaaaaagccaccttttatattgtttaga-gctaaat----tggtggttgttactacagGGAGATGATTCAGCACAGACCCTACAATCATAAGGTGGACGTGTACAGCTTTGGCGTTGTTTTGTGGGAGCTTGTGACAGGCCTGTTACCCTTCCAAAAT

upper sequence: AT4G31170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S120_103V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaagttgaataaatatctcgttttccatccttgtcttgtccttaataaccttatatatctctgcaagtcatatttagacactatattcccttattttgatcgatgcagAGAGATGATCCAGCACAGACCCTACACTCAAAAAGTGGACGTGTATAGTTTTGGAATCGTGCTGTGGGAGTTGATTACAGGTCTGTTACCGTTCCAGAAC
      ||| | |   | | || ||     | | | | |   || |    |  || | ||  | ||   ||||||         ||         || || |  ||||| |||||||||||||||| ||| |||| ||| ||||||||||| || || |||||  | ||  | |||||| |  | ||||| ||||| || || || || 
-----ctgattcag-gtgttgtgttttgggcatctttagaggttcaggttcaaatgt-tcgattcattgcatattagtgagagctaagttggaccttggaac--tgcagGGAGATGATCCAGCACAAACCTTACAATCACAAAGTGGACGTCTACAGCTTTGGTGTGGTCTTATGGGAGCTTGTGACAGGCCTGTTGCCCTTTCAAAAT

upper sequence: AT4G31170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ13809 (Selaginella moellendorffii), 3'ss of exon 1
gtaagttgaataaatatctcgttttccatccttgtcttgtccttaataaccttatatatctctgcaagtcatatttagacactatattcccttattttgatcgatgcagAGAGATGATCCAGCACAGACCCTACACTCAAAAAGTGGACGTGTATAGTTTTGGAATCGTGCTGTGGGAGTTGATTACAGGTCTGTTACCGTTCCAGAAC
       | |     || ||  | | | | ||  ||  ||  |   |   |||      |||   | |  | | ||  |  |   | |  |   |||   ||  ||||||||||||||||||||||| |  ||||| || || |||||||| || || ||||| || |||||||||||| | || |||||  || ||||||||||||||
-------gtaagcgcatttctctcttcgttctcttcgcgttttcg-tgttctt-----cctccata-gctagacttcaaagcctcactaacc-gtttcattcattgcagAGAGATGATCCAGCACAGGCTTTACACGCACAAGGTGGACGTTTACAGCTTTGGCATTGTGCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC

upper sequence: AT4G31170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ28993 (Selaginella moellendorffii), 3'ss of exon 1
gtaagttgaataaatatctcgttttccatccttgtcttgtccttaataaccttatatatctctgcaagtcatatttagacactatattcccttattttgatcgatgcagAGAGATGATCCAGCACAGACCCTACACTCAAAAAGTGGACGTGTATAGTTTTGGAATCGTGCTGTGGGAGTTGATTACAGGTCTGTTACCGTTCCAGAAC
       | |     || ||  | | | | ||  ||  ||  |   |   |||      |||   | |  | | ||  |  |   | |  |   |||   ||  ||||||||||||||||||||||| |  ||||| || || |||||||| || || ||||| || || ||||||||| | || |||||  || ||||||||||||||
-------gtaagcgcatttctctcttcgttctcttcgcgttttcg-tgttctt-----cctccata-gctagacttcaaagcctcactaacc-gtttcattcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTTTGGCATTGTCCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC

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|124843781|gb|EH928218.1|EH928218
EST:     CAAACCGAAGGGATGACACCAGAGACTGGAACTTACAGATGGATGGCACC                         AGAGATGATCCAGCACAGACCCTACACT
genomic: CAAACCGAAGGGATGACACCAGAGACTGGAACTTACAGATGGATGGCACCgtaagttgaa ... atcgatgcagAGAGATGATCCAGCACAGACCCTACACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatctctgcaagtcatatttagacactatattcccttattttgatcgatgcagAGAGATGATCCAGCACAGACCCTACACTCAAAAAGTGGACGTGTATAGTTTTGGAATCGTGCTGTGGGAGTTGATTACAGGTCTGTTACCGTTCCAGAAC
                                        ttttgat  putative branch site (score: 4)
                                     ttattttgat  TA-rich tract