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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatatgatcctaggtctctttgtttcttttgctagatcaagctagagtagttgacttaaggtgtgttgggttaaattgattaacagGGAAAGTGAATACGCAGCATGGACCCTTGTCAATGGATATGCACTTAACCACGTCACGATTTCTGTTCATCGGCTTAAATCTCATCTAAACAAAATCAAG

Basic information

species Arabidopsis thaliana
transcript AT1G07040.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G07040.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os10g32680.3 (Oryza sativa), 3'ss of exon 4
--------------------------------------------------------------------------------------------------------gtacatatgatcctaggtctctttgtttcttttgctagatcaagctagagtagttgacttaaggtgtg----ttgggttaaattgattaacagGGAAAGTGAATACGCAGCATGGACCCTTGTCAATGGATATGCACTTAACCACGTCACGATTTCTGTTCATCGGCTTAAATCTCATCTAAACAAAATCAAG
                                                                                                         |   |   ||||  |       | |||    | ||  |      |    | ||| |  |||  | ||    ||   ||   |||   | ||||||||||||||| || |||||||| ||||| ||||| |||||||| || ||   ||| |||||   ||||||  | | |||  || | |  |  ||||| 
gtacttgttatagtaccttgagtttttttactgaactttacaccgtttaacaaataaccgtttattaatccagtaatactttaaattgcctttttgtgctcatcctgagtggcatccctgagtatgctatttgcagttctgtactcctgtttctttgttcaaataacatttgctctttcttttcttttggacaccagGGAAAGTGAATATGCTGCATGGACTCTTGTTAATGGCTATGCACTAAATCATACCACAATTTCCACTCATCGCTTGATATCAGATATTAGAAGTATCAAT

upper sequence: AT1G07040.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G008607_T02 (Zea mays), 3'ss of exon 4
-------gtacatatgatcctaggtctctttgtttcttttgctagatcaagctagagtagttgacttaag-gtgtgttgggttaaat---tgattaacagGGAAAGTGAATACGCAGCATGGACCCTTGTCAATGGATATGCACTTAACCACGTCACGATTTCTGTTCATCGGCTTAAATCTCATCTAAACAAAATCAAG
        |   | | ||  |   |||  || | ||||||| |   | |   |    |  |||| ||  |    |  |   |   ||   ||   | ||||||||||||||| || |||||||| ||||| ||||| |||||||| || || | ||| ||| |    ||||| ||  ||||  || | |  |  || || 
tttgttcatttctttaatggtgtttctggttctgtcttttgtttttttatctttacctcattgatttttgcacttcctcactcttattcttggacaccagGGAAAGTGAATATGCTGCATGGACTCTTGTTAATGGCTATGCACTAAATCATGCCACAATTGCCACCCATCGCCTAGAATCAGATATCAGAAGTATTAAT

upper sequence: AT1G07040.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0026g01630.t01 (Vitis vinifera), 3'ss of exon 4
--------gtacatatgatcctaggtctctttgtttcttttgctagatcaagctagagtagttgacttaaggtgtgttgggttaaattg---attaacagGGAAAGTGAATACGCAGCATGGACCCTTGTCAATGGATATGCACTTAACCACGTCACGATTTCTGTTCATCGGCTTAAATCTCATCTAAACAAAATCAAG
         |  || |||   ||     ||| |||  | ||| | ||   |  | |      |     ||| | |      |||  ||    ||   ||||||||||||||| || || ||||||||||| ||||| |||||| | || || || || |||||   ||||| ||| ||||||||  | |  || ||  | 
taggctattttaatttgaaagtaatcaacttggttattgttgttggacttatgtgggacctctattccaagatcttactatttagtttatgaatacccagGGAAAGTGAATATGCTGCCTGGACCCTTGTAAATGGGTATGCAGTCAATCATGTTACCATTTCCACTCATCAGCTGAAATCTCACTTGAGAAATATTGAA

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|125230704|gb|EL244789.1|EL244789
EST:     ACTTTAACTTGGGAAAAGCCTCTATCTTCTGAGTTTGAGCAATTGGCTAG                         GGAAAGTGAATACGCAGCATGGACCCTTGT
genomic: ACTTTAACTTGGGAAAAGCCTCTATCTTCTGAGTTTGAGCAATTGGCTAGgtacatatga ... tgattaacagGGAAAGTGAATACGCAGCATGGACCCTTGT
EST: gi|86079974|gb|DR375731.1|DR375731
EST:     TCTGAGTTTGAGCAATTGGCTAG                         GGAAAGTGAATACGCAGCATGGACCYTTGTCAATGGATATGCACTTAACCA
genomic: TCTGAGTTTGAGCAATTGGCTAGgtacatatga ... tgattaacagGGAAAGTGAATACGCAGCATGGACCCTTGTCAATGGATATGCACTTAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagatcaagctagagtagttgacttaaggtgtgttgggttaaattgattaacagGGAAAGTGAATACGCAGCATGGACCCTTGTCAATGGATATGCACTTAACCACGTCACGATTTCTGTTCATCGGCTTAAATCTCATCTAAACAAAATCAAG
                                          aattgat  putative branch site (score: 4)
                                       ttaaattgattaaca  TA-rich tract