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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatatatatgtacatgtttcaaatgaattttaatttgattttgtctaatcattatgcaaaatatttaacttttttataaaataataatttacagAGTCCAGATGGTGATGTAATAGATTGTGTACCCAAAAGAAAGCAGCCAGCTTTGGATCATCCACTCTTAAAGCATCACAAGATTCAG

Basic information

species Arabidopsis thaliana
transcript AT5G18460.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G18460.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G41280.1 (Glycine max), 3'ss of exon 1
-----------gttatatatatgtacatgt---------------ttcaaatgaattttaatttgattttgt-----ctaatcattatg--caaaatattt---------aacttttttataaaataataat--ttacagAGTCCAGATGGTGATGTAATAGATTGTGTACCCAAAAGAAAGCAGCCAGCTTTGGATCATCCACTCTTAAAGCATCACAAGATTCAG
           | || |||| ||||  |||               ||||  |   |  |  |||| |||| |      ||||||| ||    | |||||||         ||   | ||  |   |||| ||  || |||||||||||||||||| | ||||||||||| |  |||||||| || |||||||| ||||| || || |||||| ||||||||||||||
gtaattaatatgctaaatatgtgtatgtgtcaatggttgaaaatgttcatgtttttccttttttgtttttctatataataatcatcattattagaatattttcattgataaatgatgttgaatcttaattattatttcagAGTCCAGATGGTGATCTCATAGATTGTGTCCATAAAAGAAAACAACCAGCTTTAGATCACCCCCTTTTAAAGAATCACAAGATTCAG

upper sequence: AT5G18460.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G43900.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------gttatatatatgtaca---tgtttcaaatgaattttaatttgattttgtc-taatcattat---------------gcaaaatatttaacttttttataaaataataattta--cagAGTCCAGATGGTGATGTAATAGATTGTGTACCCAAAAGAAAGCAGCCAGCTTTGGATCATCCACTCTTAAAGCATCACAAGATTCAG
                                                            ||||||||| ||||     | |||  |   || |  ||  || |  |  ||||||| ||               |  || || || ||  |  |  |   || || || |  |||||||||||||||||| | ||||||||||| |  |||||||| || |||||||| ||||| || || |||||| |||||||||| |||
gtaattaatatgctaaatatgtgtatgtatcaatggttgaaaatgttaatgagtatagactatatatatatacaaaaaatgtcattttttttctttttctatatactaataatcatcattagaatattttcattgataagtacttgacgatgctgaatcttattatttcattcagAGTCCAGATGGTGATCTCATAGATTGTGTCCATAAAAGAAAACAACCAGCTTTAGATCACCCCCTTTTAAAGGATCACAAGATCCAG

upper sequence: AT5G18460.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G36380.1 (Glycine max), 3'ss of exon 1
-----------------------------------------------------gttatatatatgtacatgtttcaaatga--attttaat-ttgattttgtc--taatcattatgcaaaatatttaa----cttttttataaaataataatttacagAGTCCAGATGGTGATGTAATAGATTGTGTACCCAAAAGAAAGCAGCCAGCTTTGGATCATCCACTCTTAAAGCATCACAAGATTCAG
                                                     | |    |   ||  | |||| |||||   |  | ||| ||| |||| ||  |  | |||||    || | | |     ||||  | |   ||  |||||  |||||||||||||| ||| | ||||||||||| | ||||||||| || |  ||||| ||||| || || |||||| |||||||||| |||
gtaatattactgttaccattaatgttatatttgtactatagtttttagcgtacgctgatcagtggttgaggttttaaatggccacataaatgttggttttttccttctttattatatgtaacagtaagtattctttgctgtcggattgtaatt-gcagAGTCCAGATGGAGATCTTATAGATTGTGTTCACAAAAGAAAACAACTGGCTTTAGATCACCCCCTTTTAAAGAATCACAAGATCCAG

upper sequence: AT5G18460.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G31140.1 (Glycine max), 3'ss of exon 1
--------------------gttatatatatgtacatgtttcaaatgaattttaatttgattttg----tctaatcattatgcaaa-----atatttaactttttt------ataaaataataatt------------tacagAGTCCAGATGGTGATGTAATAGATTGTGTACCCAAAAGAAAGCAGCCAGCTTTGGATCATCCACTCTTAAAGCATCACAAGATTCAG
                     |||| ||| |      ||||  | || |  || ||  |   |||    | ||||    |   |||      | |||  | || ||      ||  || | ||| |            | |||||||||||||| ||| | ||||||||| | | ||||||||| || |  ||||| ||||| || || |||||| |||||||||| |||
gtaacattattactattaatattatttatgtactatagttttcattgtacgttgatcagtggttgagattttaatggccacataaatgttggtttttgcccttctttattatatgtaacagtaagtattcttttgtattgcagAGTCCAGATGGAGATCTTATAGATTGTATTCACAAAAGAAAACAACTGGCTTTAGATCACCCCCTTTTAAAGAATCACAAGATCCAG

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|116435457|gb|EG478049.1|EG478049
EST:     TCCAAAAGCACTTGAACAAGATCAACAAGTCTCCTGTCTTCACCATTCAG                         AGTCCAGATGGTGATGTAATAGATTGTGTACCCAAAAGAAAGCAGCCAGCT
genomic: TCCAAAAGCACTTGAACAAGATCAACAAGTCTCCTGTCTTCACCATTCAGgttatatata ... taatttacagAGTCCAGATGGTGATGTAATAGATTGTGTACCCAAAAGAAAGCAGCCAGCT
EST: gi|86052896|gb|DR348653.1|DR348653
EST:     TCCAAAAGCACTTGAACAAGATCAACAAGTCTCCTGTCTTCACCATTCAG                         AGTCCAGATGGTGATGTAATAGATTGTGTACCCAAAAGAAAGCAGCCAGCT
genomic: TCCAAAAGCACTTGAACAAGATCAACAAGTCTCCTGTCTTCACCATTCAGgttatatata ... taatttacagAGTCCAGATGGTGATGTAATAGATTGTGTACCCAAAAGAAAGCAGCCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtctaatcattatgcaaaatatttaacttttttataaaataataatttacagAGTCCAGATGGTGATGTAATAGATTGTGTACCCAAAAGAAAGCAGCCAGCTTTGGATCATCCACTCTTAAAGCATCACAAGATTCAG
                       atttaac  putative branch site (score: 3)
           attatgcaaaatattt  TA-rich tract