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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcattctttttgtcaccaatagaaccaaatcttttttgatagttggatgttcaaaggtttctcatgcggaccttatttatgcagAACCGCACTTGCTGGTATAGTGACACTTTTGCATGCATGCCTTGACATGAAACCAATCATACTCGGGAAGTACCATTATGTGCTGTACTTCCTCGTTTTG

Basic information

species Arabidopsis thaliana
transcript AT2G20580.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20580.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os09g15750.1 (Oryza sativa), 3'ss of exon 22
gtaagttcattctttttgtcaccaatagaaccaaatcttttttgatagttggatgttcaaaggtttctcatgcggaccttatttatgcagAACCGCACTTGCTGGTATAGTGACACTTTTGCATGCATGCCTTGACATGAAACCAATCATACTCGGGAAGTACCATTATGTGCTGTACTTCCTCGTTTTG
|| |||   ||       |    |||       |||||| || ||       || ||| |||      |||      |||   | | ||| |  |||||||||||| | |||||  || ||||||| ||||||||||||||| | ||||| || ||||||||||||||  |||| ||  |||| |   | 
gtgagtaacttgcaaagttgttgaatctccttcaatcttattgga--accacattttctaagagagtccat-----tcttcacttttcagCATAGCACTTGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAAATCCATCATTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTA

upper sequence: AT2G20580.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os06g48640.2 (Oryza sativa), 3'ss of exon 22
gtaagttcattctttttgtcaccaatagaaccaaatcttttttgatagttggatgttcaaaggtttctcatgcg--gaccttatttatgcagAACCGCACTTGCTGGTATAGTGACACTTTTGCATGCATGCCTTGACATGAAACCAATCATACTCGGGAAGTACCATTATGTGCTGTACTTCCTCGTTTTG
|| |||   || |     |    |||       |||||| || ||       || ||| |||  |     | |   |  |||   | | ||| |  |||||||||||| | |||||  || ||||||| || |||||||||||| | ||||| || ||||||||||||||  |||| ||  ||||     | 
gtgagtaacttataaagttgttgaatctccttcaatcttattgga--accacattttctaagagtataagtccattgttcttcacttttcagCATAGCACTTGCTGGTCTTGTGACGGTTCTGCATGCCTGTCTTGACATGAAATCCATCATTCTGGGGAAGTACCATTACATGCTTTATATCCTTACCCTA
















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|116466338|gb|EG508930.1|EG508930
EST:     GGTCTCTTGACACTCAGCCCCTTCCACTCTGAACGGTTCTTGCTATCGCC                         AACCGCACTTGCTGGTATAGTGACACTTTTGCATGCATGCCTTGACATGAA
genomic: GGTCTCTTGACACTCAGCCCCTTCCACTCTGAACGGTTCTTGCTATCGCCgtaagttcat ... atttatgcagAACCGCACTTGCTGGTATAGTGACACTTTTGCATGCATGCCTTGACATGAA
EST: gi|86081058|gb|DR376815.1|DR376815
EST:     GGTCTCTTGACACTCAGCCCCTTCCACTCTGAACGGTTCTT-STATCGCC                         AACCGCACTTGCTGGTATAGTGACACTTTTGCATGCATGCCTTGACATGAA
genomic: GGTCTCTTGACACTCAGCCCCTTCCACTCTGAACGGTTCTTGCTATCGCCgtaagttcat ... atttatgcagAACCGCACTTGCTGGTATAGTGACACTTTTGCATGCATGCCTTGACATGAA
EST: gi|86050679|gb|DR346434.1|DR346434
EST:     GGTCTCTTGACACTCAGCCCCTTCCACTCTGAACGGTTCTTGCTATCGCC                         AACCGCACTTGCTGGTATAGTGACACTTTTGCATGCATGCCTTGACATGAA
genomic: GGTCTCTTGACACTCAGCCCCTTCCACTCTGAACGGTTCTTGCTATCGCCgtaagttcat ... atttatgcagAACCGCACTTGCTGGTATAGTGACACTTTTGCATGCATGCCTTGACATGAA
EST: gi|116466449|gb|EG509041.1|EG509041
EST:     GGTCTCTTGACACTCAGCCCCTTCCACTTTGAACGGTTCTTGCTATCGCC                         AACCGCACTTGCTGGTATAGTGACACTTTTGCATGCATGCCTTGACATGAA
genomic: GGTCTCTTGACACTCAGCCCCTTCCACTCTGAACGGTTCTTGCTATCGCCgtaagttcat ... atttatgcagAACCGCACTTGCTGGTATAGTGACACTTTTGCATGCATGCCTTGACATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttttgatagttggatgttcaaaggtttctcatgcggaccttatttatgcagAACCGCACTTGCTGGTATAGTGACACTTTTGCATGCATGCCTTGACATGAAACCAATCATACTCGGGAAGTACCATTATGTGCTGTACTTCCTCGTTTTG
    ttttgat  putative branch site (score: 4)
                                         ccttattt  putative PPT
                                           ttatttat  TA-rich tract