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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgttagatatatgagggctccctagaatctgcctccactacatagtataaatctttcatctcttttgcaaaaaatagATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCATGATCCTGTTCTTCCCCTTAACATCGAG

Basic information

species Arabidopsis thaliana
transcript AT5G17530.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G17530.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 16
-------------------------------------gtgagtgt-tagatatatgagggctccctagaatc---tgcctccactacatagtataaatctttcatctcttttgcaaaaaatagATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCATGATCCTGTTCTTCCCCTTAACATCGAG
                                     ||   | | | |||||||      |  || |  |    |  ||   ||   |  |     | |         |||  |  |   || |  | ||||| || | |||||| |||||  |  |  |  | || |||||||| || |||||||||||||||||||||
gtatgtcattattctttgcttgttttcacaagtttgagtatatatcttgatatatctaccttttcttgggtaaagtagctgggctttcttattgctgtatcatgctatatttttactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG

upper sequence: AT5G17530.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 15
---------------gtgagtgttagatat---atgagggctccctagaatctgcctccactacatagtataaatctttcatctcttttgcaaaaaatagATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCATGATCCTGTTCTTCCCCTTAACATCGAG
               |  | | |  ||  |   | ||  | |    ||  ||||  || |    ||| | ||   ||| |      |   |   ||  || |||| ||||| |||| |||||||||||||||||| ||| | || |||||||||||||| |||||||||||||| |||
caatgagacccttctgcaaatttctgacctgcaacgattggtttgcagtttctgtttctatattataatttattacttgctcaatctaatcttcaaccagGTCCGAGTTTCTGGCTATGGTGGATGGTTTCTTCTTAGATTATCACTCCATGATCCTGTACTTCCCCTTAACATTGAG

upper sequence: AT5G17530.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA10G35490.2 (Glycine max), 3'ss of exon 15
-----------gtgagtgttagatatatgagggctccctagaatctgcctccact--acatagtataaatc-tttcatctcttttgcaaa----aaatagATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCATGATCCTGTTCTTCCCCTTAACATCGAG
           |  | |    ||  |   | |  |   | |  |  |  ||   |    ||| | ||| |  |||| | |||  |  ||     ||  || |||| ||||| |||| |||||||||||| ||||| ||| | || |||||||||||||| |||||||||||||| |||
gacacccttgtgcaaattcctgacctgcaatgattggtttgcttgagtttctgttttgtatattttaatttatttcttgtctgatctaatcttcaaccagGTCCGAGTTTCTGGCTATGGTGGATGGTTCCTTCTTAGATTATCACTCCATGATCCTGTACTTCCCCTTAACATTGAG

upper sequence: AT5G17530.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv13s0019g04370.t01 (Vitis vinifera), 3'ss of exon 16
----------------gtgagtgtt--agatatatgagggctccctagaatctgcctccactacatagtataaatctttcatctcttttgcaaaaaatagATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCATGATCCTGTTCTTCCCCTTAACATCGAG
                ||   | ||  | |  | |      | | ||   |  |  |  |  |  |   |   || ||||  || |  |      || || | || | ||| |||||||| |||||||| ||||| ||||| || || ||||| |||||||||||||||||||| |||
ttttctgacccatcttgtagctttttcaaaattgttttcttttcttatttttaggttttaaaagttcaaactcatttttccactttgcttgtgtgaacagGTTCGAGCTTCTGGCTTTGGGGGATGGTTCCTTCTAAGACTCTCCCTTCATGACCCTGTTCTTCCCCTTAACATTGAG

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|86075023|gb|DR370780.1|DR370780
EST:     CAATAGAAACAAATCCAAATCTTATAATAGCTCCAGTTAACTACGAAGGG                         ATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCAT
genomic: CAATAGAAACAAATCCAAATCTTATAATAGCTCCAGTTAACTACGAAGGGgtgagtgtta ... caaaaaatagATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCAT
EST: gi|116416532|gb|EG459124.1|EG459124
EST:     CAATAGAAACAAATCCAAATCTTATAATAGCTCCAGTTAACTACGAAGGG                         ATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCAT
genomic: CAATAGAAACAAATCCAAATCTTATAATAGCTCCAGTTAACTACGAAGGGgtgagtgtta ... caaaaaatagATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCAT
EST: gi|116416533|gb|EG459125.1|EG459125
EST:     CAATAGAAACAAATCCAAATCTTATAATAGCTCCAGTTAACTACGAAGGG                         ATCCGCGTTTCGGGCTTTGGTGGATGGNNNNNNNNCAGACTTTCTCTCCAT
genomic: CAATAGAAACAAATCCAAATCTTATAATAGCTCCAGTTAACTACGAAGGGgtgagtgtta ... caaaaaatagATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCAT
EST: gi|116424751|gb|EG467343.1|EG467343
EST:     CAATAGAAACAAATCCAAATCTTATAATAGCTCCAGTTAACTACGAAGGG                         ATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCAT
genomic: CAATAGAAACAAATCCAAATCTTATAATAGCTCCAGTTAACTACGAAGGGgtgagtgtta ... caaaaaatagATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCAT
EST: gi|86023635|gb|DR319388.1|DR319388
EST:     CAATAGAAACAAATCCAAATCTTATAATAGCTCCAGTTAACTACGAAGGG                         ATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCAT
genomic: CAATAGAAACAAATCCAAATCTTATAATAGCTCCAGTTAACTACGAAGGGgtgagtgtta ... caaaaaatagATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCAT
EST: gi|86023634|gb|DR319387.1|DR319387
EST:     CAATAGAAACAAATCCAAATCTTATAATAGCTCCAGTTAACTACGAAGGG                         ATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCAT
genomic: CAATAGAAACAAATCCAAATCTTATAATAGCTCCAGTTAACTACGAAGGGgtgagtgtta ... caaaaaatagATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCAT
EST: gi|124857155|gb|EH941592.1|EH941592
EST:     ATAGCTCCAGTTAACTACGAAGGG                         ATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCAT
genomic: ATAGCTCCAGTTAACTACGAAGGGgtgagtgtta ... caaaaaatagATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaatctgcctccactacatagtataaatctttcatctcttttgcaaaaaatagATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCATGATCCTGTTCTTCCCCTTAACATCGAG
                             tctttcatctcttttg  CT-rich tract
                   atagtataaatcttt  TA-rich tract