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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagctgctatagattcttcttctttttgaacactgtgagatgtgtttttacaattgctggtgatctagatttggttgcatttgtgacttgttcgataaattaagtcagggtcgttaatcgatagtctgtgtagatcttcttcatgttttgaggcttggtgtgactattaatgcagACTTTTCTCTCCGGAGGCGGCTTGTGAAGTGATCGAAGCAGAAAGACATTCCCATGTTTTCTATGAGGCTGAACCTGATATCTGGATGGTTATG

Basic information

species Arabidopsis thaliana
transcript AT1G16020.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G16020.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G34400.1 (Glycine max), 3'ss of exon 1
gtcagctgctatagattcttcttctttttgaacactgtgagatgtgtttttacaattgctggtgatctagatttggttgcatttgtgacttgttcgataaattaagtcagggtcgttaatcgatagtctgtgtagatcttcttcat-gttttgaggcttggtgtga-ctattaatgcagACTTTTCTCTCCGGAGGCGGCTTGTGAAGTGATCGAAGCAGAAAGACATTCCCATGTTTTCTATGAGGCTGAACCTGATATCTGGATGGTTATG
                                                                                                              | | |||  |       |  ||   ||||     ||  ||||     ||| |     ||   | | |||| | ||||| || ||||| || || || || |||||||||||||||||||| ||||||||||| ||||| ||||| ||||||||||| || |||
--------------------------------------------------------------------------------------------------------------gtttgtttgttaggttaccctgcttatctctcaaattattttactaattgattcattctgcaattccagAATCTTCTCGCCAGAGGCTGCCTGCGACGTCATCGAAGCAGAAAGACATTCTCATGTTTTCTACGAGGCCGAACCCGATATCTGGATAGTCATG

upper sequence: AT1G16020.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G05260.2 (Glycine max), 3'ss of exon 1
gtcagctgctatagattcttcttctttttgaacactgtgagatgtgtttttacaattgctggtgatctagatttggttgcatttgtgacttgttcgataaattaagtcagggtcgttaatcgatagtctgtgtagatcttcttcatgttttgaggcttggtgtgactattaatgcagACTTTTCTCTCCGGAGGCGGCTTGTGAAGTGATCGAAGCAGAAAGACATTCCCATGTTTTCTATGAGGCTGAACCTGATATCTGGATGGTTATG------
                                                                                                     ||   |        |  |||  || ||| | |   |    | ||| | || |   || |||   ||   | |||||| | |||||||| ||  | ||||| || || |||||||| ||||| ||||| ||||||||||| ||||| ||||| ||||||||||| || ||       
----------------------------------------------------------------------------------------------------gtttctttctatctttctatc--tactct-tattacttcattccatttattta---tttgtgct-cttcaattgcagAATCTTCTCTCCAGACTCTGCTTGCGAGGTCATCGAAGCTGAAAGGCATTCTCATGTTTTCTACGAGGCCGAACCCGATATCTGGATAGTCATTGTTCGT

upper sequence: AT1G16020.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G05260.1 (Glycine max), 3'ss of exon 1
gtcagctgctatagattcttcttctttttgaacactgtgagatgtgtttttacaattgctggtgatctagatttggttgcatttgtgacttgttcgataaattaagtcagggtcgttaatcgatagtctgtgtagatcttcttcatgttttgaggcttggtgtgactattaatgcagACTTTTCTCTCCGGAGGCGGCTTGTGAAGTGATCGAAGCAGAAAGACATTCCCATGTTTTCTATGAGGCTGAACCTGATATCTGGATGGTTATG
                                                                                                     ||   |        |  |||  || ||| | |   |    | ||| | || |   || |||   ||   | |||||| | |||||||| ||  | ||||| || || |||||||| ||||| ||||| ||||||||||| ||||| ||||| ||||||||||| || || 
----------------------------------------------------------------------------------------------------gtttctttctatctttctatc--tactct-tattacttcattccatttattta---tttgtgct-cttcaattgcagAATCTTCTCTCCAGACTCTGCTTGCGAGGTCATCGAAGCTGAAAGGCATTCTCATGTTTTCTACGAGGCCGAACCCGATATCTGGATAGTCATT

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|19874695|gb|AU235526.1|AU235526
EST:     ACGCAGTTATCAGTGATCGGGCTCAGTGAAGGGCTTATTACTTTTACTAG                         ACTTTTCTCTCCGGAGGCGGCTTGTGAAGTGATCGAAGCAGAAAGACATTC
genomic: ACGCAGTTATCAGTGATCGGGCTCAGTGAAGGGCTTATTACTTTTACTAGgtcagctgct ... attaatgcagACTTTTCTCTCCGGAGGCGGCTTGTGAAGTGATCGAAGCAGAAAGACATTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagtctgtgtagatcttcttcatgttttgaggcttggtgtgactattaatgcagACTTTTCTCTCCGGAGGCGGCTTGTGAAGTGATCGAAGCAGAAAGACATTCCCATGTTTTCTATGAGGCTGAACCTGATATCTGGATGGTTATG
                                            tattaat  putative branch site (score: 2)
                                          actattaat  TA-rich tract