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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttcactctactttgaatgtaaaacttatgcagctatggttcttgtaaagaaaaagtttcttcatttaatggaacagGGAGATTGCGTTGGACTCTATTTTATTAACAGACCAGAGTGGTTGGTTGTGGATCATGCTTGTGCAGCATATTCATTTGTCTCTGTTCCTTTATATGATA

Basic information

species Arabidopsis thaliana
transcript AT5G27600.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G27600.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------------------------gtatgtttcactctactttgaatgta---aaacttatgcagctatggttcttgtaaagaaaaagtttcttcatttaa--tggaacagGGAGATTGCGTTGGACTCTATTTTATTAACAGACCAGAGTGGTTGGTTGTGGATCATGCTTGTGCAGCATATTCATTTGTCTCTGTTCCTTTATATGATA
                                                                      |||    |   ||       ||||   | |||||   ||      || || | ||       | | ||  || |   || | ||||| |  ||| ||||  | |||||||| |||||||| |||||| |  | || |||||||| ||||||||||||||||| || ||||| ||  | ||||| |
gtgagtcataatggtcgcaacaagtaccgtccttctttttttaactagtagcaggcagatcttgtcacacatggacaatgatataacatttgtatttacacttagagagtcccttttttttttaacttgctttattttttttaactctgaaccagGGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACA

upper sequence: AT5G27600.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 3'ss of exon 5
-----------gtatgtttcactc--tactttgaatgtaaaacttatgcagc------tatggttcttgtaaagaaaaagtttcttcatttaatggaacagGGAGATTGCGTTGGACTCTATTTTATTAACAGACCAGAGTGGTTGGTTGTGGATCATGCTTGTGCAGCATATTCATTTGTCTCTGTTCCTTTATATGATA
             || ||   ||   || | | ||   |||| || | ||||      |||   | || ||| |  |  |  |     | |  |||||||||| | |||| ||||||| ||||||||||||||||| |||||| || |||| || ||||| ||  |||| ||||||| | |||| |||||||||||||| |
ccttgttatggacatcttcagctgggtattataaaatgaaaagttgt-cagcccattttatatatattttaatgtgattgccttggtttcttgtggaacagGGGGCTTGCATTGGACTTTATTTTATTAACAGACCCGAGTGGCTGATTGTTGACCATGCCTGCTCAGCTTATTCATATATCTCAGTTCCTTTATATGACA
















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|116450759|gb|EG493351.1|EG493351
EST:     CTGAGCGACAAGCCATTGGTTCAGGACTCTTGTTTCATGGAGTTAACCAA                         GGAGATTGCGTTGGACTCTATTTTATTAACAGACCAGAGTGGTTGGTTGTG
genomic: CTGAGCGACAAGCCATTGGTTCAGGACTCTTGTTTCATGGAGTTAACCAAgtatgtttca ... aatggaacagGGAGATTGCGTTGGACTCTATTTTATTAACAGACCAGAGTGGTTGGTTGTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacttatgcagctatggttcttgtaaagaaaaagtttcttcatttaatggaacagGGAGATTGCGTTGGACTCTATTTTATTAACAGACCAGAGTGGTTGGTTGTGGATCATGCTTGTGCAGCATATTCATTTGTCTCTGTTCCTTTATATGATA
                                         atttaat  putative branch site (score: 4)
                       taaagaaaaagttt  TA-rich tract