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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgatttttcctccatttattcctctttgtccaatgatgctttttcgcataatgcaagatagtaactaatatctcagattgatcttttcattggaaatttatgcgttgtttcttctttattactcttcagGGGCATGTGAAGGTTCTCTAGCGTGTTCAACCTGCCATGTGATTGTTATG

Basic information

species Arabidopsis thaliana
transcript AT4G21090.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G21090.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os07g01930.1 (Oryza sativa), 3'ss of exon 5
gtacgatttttcctccatttattcctctttgtccaatgatgctttttcgcataatgcaagatagtaactaatatctcagattgatcttttcattggaaatttatgcgttgtttcttctttattactcttcagGGGCATGTGAAGGTTCTCTAGCGTGTTCAACCTGCCATGTGATTGTTATG
                         | ||  |    ||||| | |||  |||  | || | || | |||| |      || |||| |||| |||| |  |     | | || |  | |||      || |||| |||||||||||||| || |||||||||||||| ||||| || ||||||
------------------------ttattgattacttgatgttatttgacatgtttcatg-tattgactatt------gactgat-ttttaattgtagttagtaacttggtctagtattttgggtactgcagGAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATG

upper sequence: AT4G21090.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os09g26650.1 (Oryza sativa), 3'ss of exon 4
gtacgatttttcctccatttattcctctttgtccaatgatgctttttcgcataatgcaagatagtaactaatatctcagattgatcttttcattggaaatttatgcgttgtttcttctttattactcttcagGGGCATGTGAAGGTTCTCTAGCGTGTTCAACCTGCCATGTGATTGTTATG
                              || |||  ||| |||| |      | ||     |  || | ||    |  |  || |||||      |   | ||  |||   | | ||          ||||||||||||| || ||||| || ||||| || |||||||||||||| | |
------------------------------gtacaaaaatgattttcctagc--tccatttctggtaccactaaaataactgtattttttctaatatatcatctgaattgccccctgttgtcatgataacagGGGCATGTGAGGGCTCTCTTGCATGTTCGACATGCCATGTGATTGTAACG
















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|125321845|gb|EL335930.1|EL335930
EST:     AAGCTGCTCATGAAAATGATATAGAACTCGAAG                         GGGCATGTGAAGGTTCTCTAGCGTGTTCAACCTGACCATGTGATTGTTATG
genomic: AAGCTGCTCATGAAAATGATATAGAACTCGAAGgtacgatttt ... tactcttcagGGGCATGTGAAGGTTCTCTAGCGTGTTCAACCTG-CCATGTGATTGTTATG
EST: gi|19874920|gb|AU235751.1|AU235751
EST:     AGGAATGAACATCCTTGAAGCTGCTCATGAAAATGATATAGAACTCGAAG                         GGGCATGTGAAGGGTCTCTAGCGTGTTCAACCTGNCATGTGATTGTTATG
genomic: AGGAATGAACATCCTTGAAGCTGCTCATGAAAATGATATAGAACTCGAAGgtacgatttt ... tactcttcagGGGCATGTGAAGGTTCTCTAGCGTGTTCAACCTGCCATGTGATTGTTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattgatcttttcattggaaatttatgcgttgtttcttctttattactcttcagGGGCATGTGAAGGTTCTCTAGCGTGTTCAACCTGCCATGTGATTGTTATG
 gattgat  putative branch site (score: 4)
                              ttgtttcttctttatt  putative PPT
                                 tttcttctttatta  TA-rich tract