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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaaagagtattacgcttgaatctcttgaaacgttgcaaaaaccggttttctgatgatgatttgaatccattgtgaatgtgcagGCATGTAAGAAACTTAACAAAATCGAGTTATCAGAATGCGAGATTTACGCATCTTGTGAGCCATGTCCGATGTGCTTCGGAGCCATCCATCTCTCGAGAC

Basic information

species Arabidopsis thaliana
transcript AT5G28050.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G28050.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g14150.5 (Oryza sativa), 3'ss of exon 2
---------------------------------------------gtaagaaaa-gagtattacgcttgaatctcttg------aaacgttg-------caaaaaccggttttctgatgatgatttgaatc--cattgtg---aatgtgcagGCATGTAAGAAACTTAACAAAATCGAGTTATCAGAATGCGAGATTTACGCATCTTGTGAGCCATGTCCGATGTGCTTCGGAGCCATCCATCTCTCGAGAC
                                              | |||| | | ||||  || |||   || |||      |||| | |        |  |  |  ||||| |||    | |   ||   | || ||   ||| | ||||| || || || ||    ||||||||| | ||||| || || |||||||| |||||||||||||| || |||||||| || ||  | ||||||||  |  
gtgaaatgctttatttatctgtcactgctcgtaaatcatttgttcatgagaatatgtgtatc-cgtttgggccttttgcgtgttaaacttcgaattgtttaccacaccattttcggatagctactcacattgtcgttctgttaaattttcagGCTTGCAAAAAGCTCGGAAAAATCGAGCTCTCAGATTGTGAAATTTACGCGTCTTGTGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGGA
















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|125259041|gb|EL273126.1|EL273126
EST:     TGAAATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAG                         GCATGTAAGAAACTTAAACAAAATCGAGTTATCAGAAT
genomic: TGAAATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAGgtaagaaaag ... gaatgtgcagGCATGTAAGAAACTTAA-CAAAATCGAGTTATCAGAAT
EST: gi|301501150|gb|HO206690.1|HO206690
EST:     TGAAATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAG                         GCATGTAAGAAACTTAACAAAATCGAGTTATCAGAATGCGAGATTTACGCA
genomic: TGAAATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAGgtaagaaaag ... gaatgtgcagGCATGTAAGAAACTTAACAAAATCGAGTTATCAGAATGCGAGATTTACGCA
EST: gi|301502126|gb|HO207666.1|HO207666
EST:     AATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAG                         GCATGTAAGAAACTTAACAAAATCGAGTTATCAGAATGCGAGATTTACGCA
genomic: AATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAGgtaagaaaag ... gaatgtgcagGCATGTAAGAAACTTAACAAAATCGAGTTATCAGAATGCGAGATTTACGCA
EST: gi|124884110|gb|EH963012.1|EH963012
EST:     TACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAG                         GCATGCAAGAAACTTAACAAAATCGAGTTATCAGAATGCGAGAT
genomic: TACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAGgtaagaaaag ... gaatgtgcagGCATGTAAGAAACTTAACAAAATCGAGTTATCAGAATGCGAGAT
EST: gi|125126733|gb|EL171800.1|EL171800
EST:     TGCTGAAGTCACTGCCATTAGAGAG                         GCATGTAAGAAACTTAACAAAATCGAGTTATCAGAATGCGAGATTTACGCA
genomic: TGCTGAAGTCACTGCCATTAGAGAGgtaagaaaag ... gaatgtgcagGCATGTAAGAAACTTAACAAAATCGAGTTATCAGAATGCGAGATTTACGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacgttgcaaaaaccggttttctgatgatgatttgaatccattgtgaatgtgcagGCATGTAAGAAACTTAACAAAATCGAGTTATCAGAATGCGAGATTTACGCATCTTGTGAGCCATGTCCGATGTGCTTCGGAGCCATCCATCTCTCGAGAC
                   ttctgat  putative branch site (score: 3)
                              atttgaat  TA-rich tract