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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtgggggattcaaaaataatagatgaagccaaatgatcgattgtaaacgtaacaatgactttgtattgcagAGTGCCATTGGTGAGGGTATGACTCGCAGGGACCACTCTGATGTTTCTAATCAA

Basic information

species Arabidopsis thaliana
transcript AT4G38510.5
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 12
-------------------------gtaagtgtgggggattcaaaaataatagatgaagccaaatgatcgattgtaaacgtaacaatgactttgta----ttgcagAGTGCCATTGGTGAGGGTATGACTCGCAGGGACCACTCTGATGTTTCTAATCAA
                           |  |     || |||| ||    || |||   | | |   || |||       ||| ||     |  ||    ||||||||||| ||||||||||||||||| ||  | ||||| || ||||| ||||| || 
gtgagattactcatcaatataaatttcacataaactggtttcataacagttacatgctacaataatttccatttgcgttctaagaactgtctaataattcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAACCAG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 12
gtaagtgtgggggattcaaaaataatag-atgaagccaaatgatcgattgtaaacgtaacaatgactttgtattgcagAGTGCCATTGGTGAGGGTATGACTCGCAGGGACCACTCTGATGTTTCTAATCAA
|||||    |     |  |   |   || ||  |     | | |   ||||||  | | || | |     |  |||||||||| ||||||||||| ||||| || || ||||| || ||||| |||||||| 
gtaagataagttttctgtatgttttcagcatttatgttgaaggttagttgtaa--gaaccacttaacaactcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 12
--------------------------------------------------------------------------------------------------gtaagtgtgggggattcaaaaa-------taatagatgaagccaaatgatcgattgtaaacgtaacaatgactttgtat----------tgcagAGTGCCATTGGTGAGGGTATGACTCGCAGGGACCACTCTGATGTTTCTAATCAA-
                                                                                                    ||        || ||   ||       |  | | | ||||   || | |  |  ||     || | | | ||| ||           |||||||||||||||||||||| ||||| || | ||| || |||||||| || || ||  
taaggttaatcttgttcgtttgatgtcaaaatggcaccaacagataaatttgtgacgttttggatgggtgagtggtgcctaccactggattccatccaacaatcactaaagactctgcaacttgttttcctggctaaagcagcattacccttattagttcaaaaagtaaatttttaaggtttgcttatgcagaGTGCCATTGGTGAGGGAATGACACGAAAGGATCATTCTGATGTGTCCAACCAGG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 13
-------------------------------------gtaagtg-tgggggattcaaaaataatagatgaagccaaatgatcga--ttgtaaacgta-acaatgactttgtattgcagAGTGCCATTGGTGAGGGTATGACTCGCAGGGACCACTCTGATGTTTCTAATCAA
                                       ||||| |      ||    | |  ||  | | || || || |  |   | |||  ||  |  ||   |   |  |||||||||| ||||||||||| |||||| | ||||| || |||||||| || || || 
gtaaggataatcttgcttgtttgatatctaggtgctttaaagtgataaatattttctgattcttaattaatgcaaagtggttcacgctctaatggtgcatcattggtcacttctgcagAGTGCTATTGGTGAGGGAATGACTAGAAGGGATCATTCTGATGTGTCCAACCAG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 12
------------------------gtaagtgtgggggattcaaaaataatagatgaagccaaatgatcgattgtaaacgtaacaatgactttgtattgcagAGTGCCATTGGTGAGGGTATGACTCGCAGGGACCACTCTGATGTTTCTAATCAA
                         ||||   || |  ||   ||||   || |    | ||  |    |    |     ||   ||    | |  |||||||||||||||||||||| ||||| || ||||| ||  | ||||| || ||||| 
gtaaccttgcttattgcataagccctaagctcggagattttttaaatggaagttctgac-aaggggcttacatcatgtaaaatgttggtaat-tcctgcagAGTGCCATTGGTGAGGGGATGACCCGTAGGGATCATGCCGATGTATCCAATCAG

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|164031420|gb|EL996362.1|EL996362
EST:     TGTCTCGTCTCATGAAG                         AGTGCCATTGGTGAGGGTATGACTCGCAGGGACCACTCTGATGTTTCTAAT
genomic: TGTCTCGTCTCATGAAGgtaagtgtgg ... tgtattgcagAGTGCCATTGGTGAGGGTATGACTCGCAGGGACCACTCTGATGTTTCTAAT
EST: gi|116450403|gb|EG492995.1|EG492995
EST:     ATCTACCCTCCGATCAATGTCCTGCCATCTTTGTCCCGTCTCATGAAG                         AGTGCCATTGGTGAGG
genomic: ATCTACCCTCCGATCAATGTCTTGCCATCTCTGTCTCGTCTCATGAAGgtaagtgtgg ... tgtattgcagAGTGCCATTGGTGAGG
EST: gi|116450411|gb|EG493003.1|EG493003
EST:     ATCTACCCTCCGATCAATGTCTTGCCATCTCTGTCTCGTCTCATGAAG                         AGTGCCATTGGTGAGG
genomic: ATCTACCCTCCGATCAATGTCTTGCCATCTCTGTCTCGTCTCATGAAGgtaagtgtgg ... tgtattgcagAGTGCCATTGGTGAGG
EST: gi|164216891|gb|ES019661.1|ES019661
EST:     AGATCTACCCTCCGATCAATGTCTTGCCATCTCTGTCTCGTCTCATGAAG                         AGTGCCATTGGTGAGGGTATGACTCGCAGGG
genomic: AGATCTACCCTCCGATCAATGTCTTGCCATCTCTGTCTCGTCTCATGAAGgtaagtgtgg ... tgtattgcagAGTGCCATTGGTGAGGGTATGACTCGCAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatagatgaagccaaatgatcgattgtaaacgtaacaatgactttgtattgcagAGTGCCATTGGTGAGGGTATGACTCGCAGGGACCACTCTGATGTTTCTAATCAA
                              acgtaac  putative branch site (score: 3)
                       attgtaaa  TA-rich tract