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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattctctgatgtagaaagctatgttttgtaacttttagtgggctgaactgtttcctctacttattttgcttgcaatatcaatttaaattattttaatctgtttttatcgcagTGCATGGGGAGCCATTGCTGGGAGTTATTAGAGTTTGCTATAACATTGCTCTAAACAG

Basic information

species Arabidopsis thaliana
transcript AT3G43300.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G43300.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 4
---gtaattctctgatgtagaaagctatgttttgtaacttttagtgggctgaactgtttcctctacttattttgcttgcaatatcaatttaaattattttaatctgtttttatcgcagTGCATGGGGAGCCATTGCTGGGAGTTATTAGAGTTTGCTATAACATTGCTCTAAACAG
   ||| ||||   ||||||| |  | | | |  |||  |  | ||   | | |||    |   ||  | ||    |    | |    ||    | ||||       ||  |  ||||| ||||| ||||||||||| || || |||||||| ||||||||||||||||| || ||
aaagtagttctgc-atgtagatatatttctatgttaaagtacaatg---taagctg----caaaacacaattcatcttttgtgtttgatt---ctgtttt-------ttggaatgcagTTCATGGAGAGCCATTGCTTGGGGTCATTAGAGTATGCTATAACATTGCTCTTAATAG

upper sequence: AT3G43300.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G167318_T01 (Zea mays), 3'ss of exon 4
gtaattctctgatgtagaaagctatgttttgtaactt--ttagtgggctgaactgtttcctctacttattttgcttgcaatatcaatttaaattattttaatctgttttt---atcgcagTGCATGGGGAGCCATTGCTGGGAGTTATTAGAGTTTGCTATAACATTGCTCTAAACAG------------------------------------------
               | | || | ||  | ||| ||   ||  |  | | || |       | || ||   |||  ||   ||  || |    | | | | |||||||||   |  ||||| ||||| ||||||||||| || || |||||||| ||||||||||||||||| || ||                                          
-------------caaaatagttctgcat-gtagctatattcctatgttaaagta------caacgtaagctgcaagctcaatacatcttttgtgtctgattctgttttttggaatgcagTTCATGGAGAGCCATTGCTTGGGGTCATTAGAGTATGCTATAACATTGCTCTTAATAGGTACCTGTTATATCGCTACCTTCTTGTTTGCAGTATGTTGCC
















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|124734542|gb|EH825944.1|EH825944
EST:     TTACAGCTGTTGCTTCAGGAAAGTTCAAAG                         TGCATGGGGAGCCATTGCTGGGAGTTATTAGAGTTTGCTATAACATTGCTC
genomic: TTACAGCTGTTGCTTCAGGAAAGTTCAAAGgtaattctct ... tttatcgcagTGCATGGGGAGCCATTGCTGGGAGTTATTAGAGTTTGCTATAACATTGCTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttattttgcttgcaatatcaatttaaattattttaatctgtttttatcgcagTGCATGGGGAGCCATTGCTGGGAGTTATTAGAGTTTGCTATAACATTGCTCTAAACAG
                                 ttttaat  putative branch site (score: 3)
                                       tctgttttt  CT-rich tract
            ttgcaatatcaattta  TA-rich tract