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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtactgcttttattacctaaaacatccataaatgttttagcgattttcttatacttttctttacctttctctagCTATTTCACCAACACACTTATTCTTCCGGTTATCAATGGGCCTACAGAGGGGCTTGCACTTATATTTGTCAGCCACTTCTTCACAGCCATCGTCG

Basic information

species Arabidopsis thaliana
transcript AT1G13560.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G13560.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G14210.1 (Glycine max), 3'ss of exon 8
-----------------gtaagtactgcttttattacctaa-aacatccataaatgttttagcgattttc-ttatacttttctttacctttc---tctagCTATTTCACCAACACACTTATTCTTCCGGTTATCAATGGGCCTACAGAGGGGCTTGCACTTATATTTGTCAGCCACTTCTTCACAGCCATCGTCG
                   ||||  ||   ||      ||  || ||   || |     |||  || ||  ||||  |||   |    |||    |  |||||||||||||| |||||||| || || ||||| ||||||||||||||||| |||    | ||||   || | ||||| ||||| || ||||| |
tttcatagcattagccacaaagtgttgtaattgcagtataggaatattgttagacagactaggaatattgattatgttttcaatgttgttttggatgcagCTATTTCACCAATACACTTATACTGCCTGTTATAAATGGGCCTACAGAGGGTCTTATGATAATATACATCTGTCACTTTTTCACTGCTATCGTGG

upper sequence: AT1G13560.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G08720.1 (Glycine max), 3'ss of exon 8
---------------------gtaagtactgcttttattacctaaaacatccataaatgttttagcgattttcttatacttttctttacctttctc----tagCTATTTCACCAACACACTTATTCTTCCGGTTATCAATGGGCCTACAGAGGGGCTTGCACTTATATTTGTCAGCCACTTCTTCACAGCCATCGTCG
                      | | |||| | | | | || || |   |   || |     |||  || ||  | | ||||||  |    || |      || ||||||||||| |||||||| || || ||||| ||||||||||||||||| |||    | ||||   || | ||||| ||||| || ||||| |
acttttggcatgattgtatattttaatactacatatttcacatatactgt---tagacagactaggaatattgattttcttttcaatgttgttttggatgcagTTATTTCACCAATACACTTATACTGCCTGTTATAAATGGGCCTACAGAGGGTCTTATGATAATATACATCTGTCACTTTTTCACTGCTATCGTGG
















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|124969857|gb|EL043728.1|EL043728
EST:     TGGTTCTGGGTTATTTCAGCTATTCCATTTTATGGAGCTACATGGGAACA                         CTATTTCACCAACACACTTATTCTTCCGGTTATCAATGGGCCTACAGAGGG
genomic: TGGTTCTGGGTTATTTCAGCTATTCCATTTTATGGAGCTACATGGGAACAgtaagtactg ... ctttctctagCTATTTCACCAACACACTTATTCTTCCGGTTATCAATGGGCCTACAGAGGG
EST: gi|86070080|gb|DR365837.1|DR365837
EST:     TGGTTCTGGGTTATTTCAGCTATTCCATTTTATGGAGCTACATGGGAACA                         CTATTTCACCAACACACTTATTCTTCCGGTTATCAATGGGCCTACAGAGGG
genomic: TGGTTCTGGGTTATTTCAGCTATTCCATTTTATGGAGCTACATGGGAACAgtaagtactg ... ctttctctagCTATTTCACCAACACACTTATTCTTCCGGTTATCAATGGGCCTACAGAGGG
EST: gi|86070077|gb|DR365834.1|DR365834
EST:     TGGTTCTGGGTTATTTCAGCTATTCCATTTTATGGAGCTACATGGGAACA                         CTATTTCACCAACACACTTATTCTTCCGGTTATCAATGGGCCTACAGAGGG
genomic: TGGTTCTGGGTTATTTCAGCTATTCCATTTTATGGAGCTACATGGGAACAgtaagtactg ... ctttctctagCTATTTCACCAACACACTTATTCTTCCGGTTATCAATGGGCCTACAGAGGG
EST: gi|86070081|gb|DR365838.1|DR365838
EST:     TGGTTCTGGGTTATTTCAGCTATTCCATTTTATGGAGCTACATGGGAACA                         CTATTTCACCAACACACTTATTCTTCCGGTTATCAATGGGCCTACAGAGGG
genomic: TGGTTCTGGGTTATTTCAGCTATTCCATTTTATGGAGCTACATGGGAACAgtaagtactg ... ctttctctagCTATTTCACCAACACACTTATTCTTCCGGTTATCAATGGGCCTACAGAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacatccataaatgttttagcgattttcttatacttttctttacctttctctagCTATTTCACCAACACACTTATTCTTCCGGTTATCAATGGGCCTACAGAGGGGCTTGCACTTATATTTGTCAGCCACTTCTTCACAGCCATCGTCG
 acctaaa  putative branch site (score: 3)
                        ttttcttatacttttc  putative PPT
                       attttcttatactttt  TA-rich tract