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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtactcaaaatttattcagccttgaccctctctatgtagtgatgcagcgtggcttatgctgaagttgatcaggattcttatgccgttgcttgtttaaagtacagGACTTACCTCGGACATTTCCTGGTCATCCTGCTCTAGATGATGATGGTAGAAATGCTCTACGGCGTTTGCTTACTGCTTATGCTAGGCATAATCCTTCTG

Basic information

species Arabidopsis thaliana
transcript AT3G55020.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g38950.2 (Oryza sativa), 3'ss of exon 4
--------------------------------gtagtactcaaaatttattcagccttgaccctctctatgtagtgatgcagcgtggct-tatgctgaagttgatcaggattcttat--gccgttgcttgtttaaagtacagGACTTACCTCGGACATTTCCTGGTCATCCTGCTCTAGATGATGATGGTAGAAATGCTCTACGGCGTTTGCTTACTGCTTATGCTAGGCATAATCCTTCTG
                                 || ||   |||  |  ||     | ||  ||     | |  | ||  |||||   | | ||   ||  |||  || |  | |||  ||| || || |  |    |||||||||| ||| | || ||||| |||||||||||| |||| || ||||| ||||||||| |  | |||||||||   ||||||||||| || |||||  | |
gtaggtcactgagtccaaatttccttttttttttaatataaaaagctagttttat-tggaggctaggatttttcttatttagcgtttttatctggaaaatctgacaagaagccgtatctgccatttctgggctcct-tacagGACTTGCCTAGAACTTTTCCAGGTCATCCTGCTTTAGACGAGGATGGAAGAAATGCTTTGAGACGTTTGCTTCTAGCTTATGCTAGACACAATCCAGCAG

upper sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G094951_T01 (Zea mays), 3'ss of exon 4
gtagtactcaaaatttattcagccttgaccctctctatgtagtgatgcagcgtggcttatgctgaagttgatcaggattcttatgccgttgcttgtttaaagtacagGACTTACCTCGGACATTTCCTGGTCATCCTGCTCTAGATGATGATGGTAGAAATGCTCTACGGCGTTTGCTTACTGCTTATGCTAGGCATAATCCTTCTG
||||   |  |     |||    |  ||   |||   |||| |  | |         ||| |||  ||  |    || ||  ||   |   |||| |     || ||||||| ||  | || |||||||||||||||||| ||||||| ||||| ||||||||| |  | || |||||||  |||||||| |  || ||||| || |
gtagctgtttatggacattttcacgggattatct---tgtattttttcgataaaa--tatactgctgt--actgagagtccaatat-gcatcttgatcct--tatagGACTTGCCCAGAACTTTTCCTGGTCATCCTGCTTTAGATGAGGATGGAAGAAATGCTTTGAGACGCTTGCTTATAGCTTATGCGAAACACAATCCATCAG

upper sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G051050_T01 (Zea mays), 3'ss of exon 4
gtagtactcaaaatttattca-gccttgaccctctctatgtagt---gatgcagcgtggc-ttatgctg--aagttgatcaggattcttatgccgttgcttgtttaaagtacagGACTTACCTCGGACATTTCCTGGTCATCCTGCTCTAGATGATGATGGTAGAAATGCTCTACGGCGTTTGCTTACTGCTTATGCTAGGCATAATCCTTCTG
||||   |  |  |  |||    |   ||  | |  | | |  |   |||  |   |     | |||||  ||||  |  || | ||  ||   ||  |||   |     | |||| || ||  | || |||||||||||||||||| ||||||| ||||| ||||||||| |  | || |||||||  |||||||| |  || || || || |
gtagctgtttatgtacattttcacggggaagcaccttgtattttttggataaaatatactgctgtgctggaaagtctaatag-actccaatat-gtaccttccct----catagGATTTGCCCAGAACTTTTCCTGGTCATCCTGCTTTAGATGAGGATGGAAGAAATGCTTTGAGACGCTTGCTTATAGCTTATGCGAAACACAACCCATCAG

upper sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 4
gta-gtactcaaaatttattcagccttgaccctctctatgtagtgatgc----agcgtggct-tatgctgaagttga---tcaggattcttatgccgttgcttgtttaaagtacagGACTTACCTCGGACATTTCCTGGTCATCCTGCTCTAGATGATGATGGTAGAAATGCTCTACGGCGTTTGCTTACTGCTTATGCTAGGCATAATCCTTCTG
|||  | ||    || | |||| ||||     |||  ||   |||||       |  || || | |    |||||     | || | ||   |  | ||||||||||   |  |||||  | ||||| ||||||||||||||||||||||| || || ||||||||||||||| |  | || || |||||||| |||||| | ||||| || || |
gtatatgcttttgatat-ttcacccttattgttcttaatactgtgatattattggtatgactctttaaacaagtttcttcttagtagtccattatcattgcttgttt---gcgcagGATCTGCCTCGAACATTTCCTGGTCATCCTGCTCTGGACGAGGATGGTAGAAATGCTTTGAGACGATTACTTACTGCATATGCTCGACATAACCCCTCAG

upper sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 4
gtagt-actcaaaatttattcagccttgaccctctctatgtagtgatgc----agcgtggc-ttatgctgaagttga---tcaggattcttatgccgttgcttgtttaaagtacagGACTTACCTCGGACATTTCCTGGTCATCCTGCTCTAGATGATGATGGTAGAAATGCTCTACGGCGTTTGCTTACTGCTTATGCTAGGCATAATCCTTCTG
||| |  ||    || | |||| ||||     |||  ||   |||||       |  || |  | |    |||||     | || | |||  |  | ||||||||||   || |||||  | ||||| ||||||||||||||||||||| | || || ||||||||||||||| |  | || || |||||||| |||||| | ||||| || || |
gtatttgcttttgatat-ttcatccttattgttcttaatactgtgatattattggtatgacactttaaacaagtttcttcttagtagtctattatcattgcttgttt---gtgcagGATCTGCCTCGAACATTTCCTGGTCATCCTGCTTTGGACGAGGATGGTAGAAATGCTTTGAGACGATTACTTACTGCATATGCTCGACATAACCCCTCAG

upper sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------gtagtactcaaaatttat-----tcagccttgaccctctctatgt--agtgatgcagcgtggcttatgctgaagttgat---caggattcttatgccgttgcttg-----tttaaagtacagGACTTACCTCGGACATTTCCTGGTCATCCTGCTCTAGATGATGATGGTAGAAATGCTCTACGGCGTTTGCTTACTGCTTATGCTAGGCATAATCCTTCTG
                           ||||||||||  | | |     ||||   |  || |   ||  |  |   ||     ||   |  | || |  |  |    |||||||       |             ||  || | ||||| || ||||| ||||| || |||||||||||||||||||| ||||||||||||||| |  ||||||| ||||| || |||||| | || || || ||||
gtcattacatgcatatgctttgaaatttagtactcaatttctttgattttcaggtgttgcctttgttaaatccaaaaatctcaagtcattgttactaatctctaaatgcaggatttactgatcaaaaaaaaaaaatttctaaatgcagGATTTGCCTCGAACATTCCCAGGTCATCCTGCTCTAGATGAGGATGGTAGAAATGCTTTGAGGCGTTTACTTACGGCATATGCTCGACACAACCCCTCTG

upper sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ22778 (Selaginella moellendorffii), 3'ss of exon 3
gtagtactcaaaatttattcagccttgaccctctctatgtagtgatgcagcgtggcttatgctgaagttgatcaggattcttatgccgttgcttgtttaaagtacagGACTTACCTCGGACATTTCCTGGTCATCCTGCTCTAGATGATGATGGTAGAAATGCTCTACGGCGTTTGCTTACTGCTTATGCTAGGCATAATCCTTCTG
                                                   ||    ||   |||   |     | |   | |   || || ||  |    ||  |||||||||| || || |||||||||||||| ||||||||||| |||||| | || ||  | ||  |  |  | ||||| || ||  | |||||||||  ||
---------------------------------------------------gtactataccatgatagtataatgtaaattcagttcgatgttttct---ggtgtagGACTTACCGCGAACTTTTCCTGGTCATCCAGCTCTAGATGAAGATGGTCGGAACGCATTGCGCAGGCTTTTGACTGCATACGCACGACATAATCCTGATG

upper sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ30863 (Selaginella moellendorffii), 3'ss of exon 3
gtagtactcaaaatttattcagccttgaccctctctatgtagtgatgcagcgtggcttatgctgaagttgatcaggattcttatgccgttgcttgtttaaagtacagGACTTACCTCGGACATTTCCTGGTCATCCTGCTCTAGATGATGATGGTAGAAATGCTCTACGGCGTTTGCTTACTGCTTATGCTAGGCATAATCCTTCTG
                                                   ||    ||   |||   |     | |   | |   || || ||  |    ||  |||||||||| || || |||||||||||||| ||||||||||| |||||| | || ||  | ||  |  |  | ||||| || ||  | |||||||||   |
---------------------------------------------------gtactataccatgatagtataatgtaaattcagttcgatgttttct---ggtgtagGACTTACCGCGAACTTTTCCTGGTCATCCAGCTCTAGATGAAGATGGTCGGAACGCATTGCGCAGGCTTTTGACTGCATACGCACGACATAATCCTGACG

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|124760160|gb|EH850290.1|EH850290
EST:     TACAGAATCTATTGCTGTTGTGGAAAAATGGAAAGGACAGATAGAAAAG                         GACTTACCTCGGACATTTCCTGGTCATCCTGCTCTAGATGATGATGGTA
genomic: TACAGAATCTATTGCTGTTGTGGAAAAATGGAAAGGACAGATAGAAAAGgtagtactca ... taaagtacagGACTTACCTCGGACATTTCCTGGTCATCCTGCTCTAGATGATGATGGTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcttatgctgaagttgatcaggattcttatgccgttgcttgtttaaagtacagGACTTACCTCGGACATTTCCTGGTCATCCTGCTCTAGATGATGATGGTAGAAATGCTCTACGGCGTTTGCTTACTGCTTATGCTAGGCATAATCCTTCTG
             agttgat  putative branch site (score: 5)
                                       cttgttt  putative PPT
                                        ttgtttaaa  TA-rich tract