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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgtttatatttggaacacacacaggatgtttagctttgttcatacttgctctgctcttaaaatgtgtttgttgtggaccttggcacagATCATAAACAGCGACAACGTGCAAGAGGCAGCGAGAGAGACTGATGGATATTTCATAAAGAGCGGAATTGTAACGGTTATCAAAGACGCCTTAATCCCAA

Basic information

species Arabidopsis thaliana
transcript AT5G48300.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 8
--------gttagtgtttatatttggaacacacacaggatgtttagctttgttcat-acttgctctgctcttaaaatgtgtttgttgtggaccttggcacagATCATAAACAGCGACAACGTGCAAGAGGCAGCGAGAGAGACTGATGGATATTTCATAAAGAGCGGAATTGTAACGGTTATCAAAGACGCCTTAATCCCAA
        | |      |  ||   ||||  | |||  ||| |  ||  |||| ||  | |    |  |  | ||   | | || | ||   ||||  |||||| || ||   ||||||  | ||||| ||  | || |||||||||||||| ||||| || || || ||||| || || ||||| |||||||||||||| |
tttccagagatgaccagttgatactgaactga-acaaaatgatgtgcaatgtttattgcattaattaatgatcaatcttatatgatctgttgcttg-tacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATACTTCATCAAAAGTGGCATTGTCACTGTGATCAAGGACGCCTTAATCCCTA

upper sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 8
gttagtgtttatatttggaacacacacaggatgttt----agctttgttcatacttgct----ctgctcttaaaatgtgtttgttgt--------------ggaccttggca---cagATCATAAACAGCGACAACGTGCAAGAGGCAGCGAGAGAGACTGATGGATATTTCATAAAGAGCGGAATTGTAACGGTTATCAAAGACGCCTTAATCCCAA
|||    |||  |||       ||   |  || |||    |  || |||      || |     |||| | |  ||| | ||||  |              | |  |||  |   |||||||| || || || || |||||||| || || || || || |||||||||||||| ||||||||||| || ||||| ||||| || |||||  | || |
gttgtgattttaattaacttagcatggattatttttcatcaatttcgttttctactggtaatgttgctatgatgatgaggttgtgattttaatttagcgaagaaatttgttatttcagATCATCAATAGTGATAATGTGCAAGAAGCGGCAAGGGAAACGGATGGATATTTCATTAAGAGCGGAATAGTCACGGTAATCAAGGATGCCTTGCTTCCTA
















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|125244505|gb|EL258590.1|EL258590
EST:     CGACAAAAACGACACGTATCGGTGACAATGTCAAG                         ATCATAAACAGCGACAACGTGCAAGAGGCAGCGAGAGAGACTGATGGATAT
genomic: CGACAAAAACG-CACGTATCGGTGACAATGTCAAGgttagtgttt ... cttggcacagATCATAAACAGCGACAACGTGCAAGAGGCAGCGAGAGAGACTGATGGATAT
EST: gi|86075039|gb|DR370796.1|DR370796
EST:     TCAAAAGGGCCATCATCGACAAAAACGCACGTATCGGTGACAATGTCAAG                         ATCATAAACAGCGACAACGTGCAAGAGGCAGCGAGAGAGACTGATGGATAT
genomic: TCAAAAGGGCCATCATCGACAAAAACGCACGTATCGGTGACAATGTCAAGgttagtgttt ... cttggcacagATCATAAACAGCGACAACGTGCAAGAGGCAGCGAGAGAGACTGATGGATAT
EST: gi|86084119|gb|DR379878.1|DR379878
EST:     TCAAAAGGGCCATCATCGACAAAAACGCACGTATCGGTGACAATGTCAAG                         ATCATAAACAGCGACAACGTGCAAGAGGCAGCGAGAGAGACTGATGGATAT
genomic: TCAAAAGGGCCATCATCGACAAAAACGCACGTATCGGTGACAATGTCAAGgttagtgttt ... cttggcacagATCATAAACAGCGACAACGTGCAAGAGGCAGCGAGAGAGACTGATGGATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgttcatacttgctctgctcttaaaatgtgtttgttgtggaccttggcacagATCATAAACAGCGACAACGTGCAAGAGGCAGCGAGAGAGACTGATGGATATTTCATAAAGAGCGGAATTGTAACGGTTATCAAAGACGCCTTAATCCCAA
                     tcttaaaat  TA-rich tract