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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttaatgtttgaatatatcgtactttatatgtgctcatcacttagaaatagtttgcatagacccaagagtatggtaaagagatcacatttgaattaataaacgctgtttgatgaaatatattggatacttacctcttcagaaatgtttgttttatctgtgcttatattggttaaactttaaccttcatttcagACCAAGATTCTGTGAGACTATTGGCTGTTGAAGGGTGTGCAGCTCTTGGAAAGTTGTTGGAACCTCAGGATTGTGTTGCACGCATTTTACCTGTTATTGT

Basic information

species Arabidopsis thaliana
transcript AT1G25490.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
gtacttaatgtttgaatatatcgtactttatatgtgctcatcacttagaaatagtttgcatagacccaagagtatggtaaagagatcacatttgaattaataaacgctgtttgatgaaatatattggatacttacctcttcagaaatgtttgttttatctgtgcttatattggttaaactttaaccttcatttcagACCAAGATTCTGTGAGACTATTGGCTGTTGAAGGGTGTGCAGCTCTTGGAAAGTTGTTGGAACCTCAGGATTGTGTTGCACGCATTTTACCTGTTATTGT
                                                                                                  |  |||   ||  ||||  |     ||||    ||  || | ||         |  | |    ||| | ||    |    ||      ||  |  |||| |||||||| ||  |  | ||||| |||||||| ||||| |||||||| || ||||||||||| || |||||||| ||||  ||  | || ||||||||
------------------------------------------------------------------------------------------------ggagcaaatagtgcatgattgagccagttgggacatttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT

upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 3
gtacttaatgtttgaatatatcgtactttatatgtgctcatcacttagaaatagtttgcatagacccaagagtatggtaaagagatcacatttgaattaataaacgctgtttgatgaaatatattggatacttacctcttcagaaatgtttgttttatctgtgcttatattggttaaactttaaccttcatttcagACCAAGATTCTGTGAGACTATTGGCTGTTGAAGGGTGTGCAGCTCTTGGAAAGTTGTTGGAACCTCAGGATTGTGTTGCACGCATTTTACCTGTTATTGT
                                                                                                |   | || | |    |     |  |||| || | |||  ||      ||    |   |||  |  ||| | |          || |  ||| |  |||||||||||||| ||| |||||||||| ||||| || ||||| |||||||| ||||||||||| || || |||||||  ||||  ||| | || ||||||||
-----------------------------------------------------------------------------------------------ttgtttgaatgttacaaggcatcagttatttgaaa-ttagttcacagtcaaatcatacattacatcagctaagaagaaactgttttgactctttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT

upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 3
gtacttaatgtttgaatatatcgtactttatatgtgctcatcacttagaaatagtttgcatagacccaagagtatggtaaagagatcacatttgaattaataaac-gctgtttgatgaaatatattggatacttacctcttcagaaatgtttgttttatctgtgcttatattggttaaactttaaccttcatttcagACCAAGATTCTGTGAGACTATTGGCTGTTGAAGGGTGTGCAGCTCTTGGAAAGTTGTTGGAACCTCAGGATTGTGTTGCACGCATTTTACCTGTTATTGT
                                                                                   |||   |||||||| | |       ||||||     ||||| |     | |||   ||  | |    |  ||    || ||  || |   | |   |||||       ||||||| |||||||| ||| | || |||||||||||||| ||||| || ||||| || ||||||||||| || ||||| || |||| |||| | || || |||||
--------------------------------------------------------------------------------catgattgaatttgaatcattgggttagtgtttgc----atatagt-----catacgcatttgggaca--tcattaggactatgtctaaacctgctggtctttat------tttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGT

upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G122135_T04 (Zea mays), 3'ss of exon 3
gtacttaatgtttgaatatatcgtactttatatgtgctcatcacttagaaatagtttgcatagacccaagagtatggtaaagagatcacatttgaattaataaacgctgtttgatgaaatatattggatacttacctcttcagaaatgtttgttttatc--tgtgcttatattggttaaactttaaccttcattt-cagACCAAGATTCTGTGAGACTATTGGCTGTTGAAGGGTGTGCAGCTCTTGGAAAGTTGTTGGAACCTCAGGATTGTGTTGCACGCATTTTACCTGTTATTGT
                                                                                                 |||| |    ||  | ||  | | || ||  | | ||  |  ||| | |  ||||    |||  |  |  ||| |     |     |   ||| |||| |||| |||||||| ||| |  | |||||||||||||| ||||| |||||||| || |||||||| || || |||||||| || | |||| | || || |||||
------------------------------------------------------------------------------------------------ctaatcattattgaatcattgagt-tagtgtttgcata--tagtcatacacttttgggacatcattagggctatgtctaaaacgtcgtggtctttattttcagATCAAGATTCAGTGCGTTTGTTGGCTGTTGAAGGTTGTGCTGCTCTTGGTAAATTGTTGGAGCCACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGT

upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 3
gtacttaatgtttgaatatatcgtactttatatgtgctcatcacttagaaatagtttgcatagacccaagagtatggtaaagagatcacatttga-attaataaacgctgtttgatgaaatatattggatacttacctcttcagaaatgtttgttttatctgtgcttatattggttaaactttaaccttcatttcagACCAAGATTCTGTGAGACTATTGGCTGTTGAAGGGTGTGCAGCTCTTGGAAAGTTGTTGGAACCTCAGGATTGTGTTGCACGCATTTTACCTGTTATTGT
                                               | ||| |  | ||||   |      | || || |  ||     | ||  |||  |      ||  |  | | ||   |||  |  ||   |  | ||||     ||  |   || | ||  | |    |    | ||| |||     |||| ||||||||||| ||| | |||||||| || || ||||| |||||||| ||| ||||||| || || |||||||||||||  ||  | || ||||||||
-----------------------------------------------gtaattgaatacatatttcttgttctttg-tagatggaaagtgtctgtcatttttgtctattgcatatttacattggttgtgtgattgtgttgt-agaatctcctgaatgtactttcctcttttaatatgtgttgtaatcttggaa-cagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT

upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 3
gtacttaatgtttgaatatatcgtactttatatgtgctcatcacttagaaatagtttgcatagacccaagagtatggtaaagagatcacatttgaat-taataaacgctgtttgatgaaatatattggatacttacctcttcagaaatgtttgttttatctgtgcttatattggttaaactttaaccttcatttcagACCAAGATTCTGTGAGACTATTGGCTGTTGAAGGGTGTGCAGCTCTTGGAAAGTTGTTGGAACCTCAGGATTGTGTTGCACGCATTTTACCTGTTATTGT
                                          | ||  | | |  || | |   |     || |||| ||     |  ||||||  | | | | |   |   ||    | | | ||| | | |  |||       |||||    ||||    |  | ||||      || | ||| |||     |||| ||||||||||| ||| | |||||||| || || ||||| |||||||| ||| ||||||| || || |||||||||||||  ||  | || ||||||||
----------------------------------------gtaattgaatacatatttcttgttctttgtag-atggaaagtgtctgtcatttgtctgttacatat-ttacatgtgtgattgtgttgtagagtctcct------gaatgt--actttactcct-ttaatatgc----aattgtaatcttggaa-cagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT

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|86067631|gb|DR363388.1|DR363388
EST:     ACTATGTTCGATGATCTTACTAAAGATG                         ACCAAGATTCTGTGAGACTATTGGCTGTTGAAGGGTGTGCAGCTCTTGGAA
genomic: ACTATGTTCGATGATCTTACTAAAGATGgtacttaatg ... ttcatttcagACCAAGATTCTGTGAGACTATTGGCTGTTGAAGGGTGTGCAGCTCTTGGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaatgtttgttttatctgtgcttatattggttaaactttaaccttcatttcagACCAAGATTCTGTGAGACTATTGGCTGTTGAAGGGTGTGCAGCTCTTGGAAAGTTGTTGGAACCTCAGGATTGTGTTGCACGCATTTTACCTGTTATTGT
                                     ctttaac  putative branch site (score: 3)
                                           ccttcatttc  CT-rich tract
                       ttatattggttaaa  TA-rich tract