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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgtagattctttctttttttctttaatcaaattccatgttttatatgtatagagacacattggcccctatcacagtgaactaacttagaattctttgttccagGGAACTGGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGAGCCAGACGTTTCAAAACATGATGTGGATGCACAAATAGCTCTTAAACCTT

Basic information

species Arabidopsis thaliana
transcript AT5G51820.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os10g11140.1 (Oryza sativa), 3'ss of exon 20
------------------------------------------------------------------------gtatgttgtagattctttctttttttctt--taatcaaattccatgttttatatgt--atagagacacattggcccctatcaca-gtgaactaacttag---aattctttgttccagGGAACTGGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGAGCCAGACGTTTCAAAACATGATGTGGATGCACAAATAGCTCTTAAACCTT
                                                                        || || |  |  ||| |||| || ||  |  | |  |   |  || ||| | || |  |   | |  || ||        |||  ||     || ||||   | || | | ||  ||||||| || || |||||||| ||| | || ||||||||||| ||||| ||| | || |  ||||| |||||| ||||||||||||||||| | || ||||
gtacacagctatcactgatatttttttctcccttatcttgttgttggagttgctgcttctaggcgctcacttgtttgctcaaacttccttctcttcttaatgctgagaagcatgaatctttcacatattcactaaaagccactgattttgcccacttgttttacaatttagtatatttttctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAGTCTGATGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTT

upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 20
---------gtatgttgtagattctttctttttttctttaatcaaattccat--gttttatatgtatagagacacattggcccctatcacagtgaactaacttagaat---tctttgttccagGGAACTGGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGAGCCAGACGTTTCAAAACATGATGTGGATGCACAAATAGCTCTTAAACCTT
          | ||||      ||   ||| |    || ||  || ||  ||   | ||  |  | |||    | | |       ||  |  |    |  |||    |   ||||| || ||||||||||| || || || ||||| ||  || | ||||||||||| ||||| ||||| || || ||||||||||| ||||| ||||| ||  | ||||| |
gtatgtggcatttgtttgtttgtccaccttgtcgctttcaaagaagttgaatccatcttggaaatctaggcgtaaaattaaattcattgctatcttttttctttttctttttcttttttacagGGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAACCAGATGTCTCTAAACATGATGTTGATGCTCAAATTGCCTTAAAACCAT

upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 20
gtatgttgtagattctttctttttttctttaatcaaattccatgttttatatgtatagagacacattggcccctatcacagtgaactaacttagaattc--tttgttccagGGAACTGGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGAGCCAGACGTTTCAAAACATGATGTGGATGCACAAATAGCTCTTAAACCTT
|||||| | |  |  ||  || |   | ||   |   |   |    ||  ||  ||   |  | ||   | | ||  |   | |   |     |  ||   ||| || ||||| ||||| || || || || || ||  || | ||||||||||| ||||| ||||| || || ||||||||||| ||||| ||||| ||  | ||||| |
gtatgtggaatctgtttgtttgtccaccttgtccctttcaaagaagttgaatccatcttggaa-atctacgcataaaatt-taagtcagtgctgtttttatttttttacagGGTACTGGTTCTGCAGGGGCAACTGTTAGAGTGTACATTGAACAGTTTGAACCAGATGTCTCTAAACATGATGTTGATGCTCAAATTGCCTTAAAACCAT

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|125293991|gb|EL308076.1|EL308076
EST:     GGATGGATCCAGAATCATATTTCGTTTATCC                         GGAACTAGGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGA
genomic: GGATGGATCCAGAATCATATTTCGTTTATCCgtatgttgta ... tttgttccagGGAACT-GGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGA
EST: gi|125255042|gb|EL269127.1|EL269127
EST:     TTCACGGATGGATCCAGAATCATATTTCGTTTATCC                         GGAACTGGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGAG
genomic: TTCACGGATGGATCCAGAATCATATTTCGTTTATCCgtatgttgta ... tttgttccagGGAACTGGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGAG
EST: gi|86088359|gb|DR384118.1|DR384118
EST:     GTGTTCGGTTTGTGTTCACGGATGGATCCAGAATCATATTTCGTTTATCC                         GGAACTGGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGAG
genomic: GTGTTCGGTTTGTGTTCACGGATGGATCCAGAATCATATTTCGTTTATCCgtatgttgta ... tttgttccagGGAACTGGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagagacacattggcccctatcacagtgaactaacttagaattctttgttccagGGAACTGGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGAGCCAGACGTTTCAAAACATGATGTGGATGCACAAATAGCTCTTAAACCTT
                             aactaac  putative branch site (score: 1)
                                          ttctttgttcc  putative PPT
                                    ttagaatt  TA-rich tract