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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtctcgagactctcagtttgttgttaagcgtcttcttgttcatgtcaacaagatccatcatcgtgatctctatttggaatttgggctttaaacagATGTTACCGAGCCTTTGTTGATCGAGGTTGATCGGATTTACCATCTTGCTTGTCCTGCCTCTCCTATCTTCTACAAATACAACCCTGTTAAG

Basic information

species Arabidopsis thaliana
transcript AT5G59290.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 5
gtatggtctcgag-actctcagtttgttgttaagcgtcttcttgttcatgtcaacaagatccatcatcgtgatctctatttggaatttgggctttaaacagATGTTACCGAGCCTTTGTTGATCGAGGTTGATCGGATTTACCATCTTGCTTGTCCTGCCTCTCCTATCTTCTACAAATACAACCCTGTTAAG
 ||| || | | | ||      |    |||| | | ||   ||     |||    || | | || ||  ||||    |||   | ||||  |  |    |||||| || |||||||| |||||||||||||||| ||| ||||||||||| || |||||||||||||| |||||||||||||| || || |||
atattgtattgtgtacataacatactatgttcaacatcactttaaatctgtttgtaa-accaatgatgctgattctcattatcactttgatccctttgtagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG

upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 5
gta-tggtctcgagactctcagtttgttgttaagcgtcttcttgttcatgtcaacaagatccatcatc--gtgatctctatttggaatttgggctttaaacagATGTTACCGAGCCTTTGTTGATCGAGGTTGATCGGATTTACCATCTTGCTTGTCCTGCCTCTCCTATCTTCTACAAATACAACCCTGTTAAG
||| || |   |      |  ||   |  |  |   |  ||   ||||  | ||     |   | | |   ||||    |||   | | |    |||    |||||| || |||||||| |||||||||||||||| ||| ||||||||||| || |||||||||||||| |||||||||||||| || || |||
gtaatgatgatgctgtattgtgtacataatgtactatgctcagcttcactttaaatctgtttgtaaaccaatgatgctgattctcattatcactttt---tagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG

upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 4
-gtatggtctcgagactctcagtttgttgttaagcgtcttcttgttc----atgtcaacaagatccatcatcgtgatctctatttggaatttgggctttaaacagATGTTACCGAGCCTTTGTTGATCGAGGTTGATCGGATTTACCATCTTGCTTGTCCTGCCTCTCCTATCTTCTACAAATACAACCCTGTTAAG
   ||    |  |   |   | |  | ||   ||  |||    |||     ||||     |  |  || |   ||   | || ||    |||   |  | ||||||||| || ||||  |||||||| ||||||||||  || || |||||||| || ||||| ||||| ||||||||||||||||||||||| |||
aacataacatgaatgattcta-tcaggtgcagagtttctctgcgtttttagatgtgttttaatttaattaaaatg-catgtacttttctttt---ccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG

upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 3
gtatggtctcgagactctcagtttgttgttaagcgtcttcttgttcatgtcaacaagatcca---tcatcgtgatctctat-ttggaatttgggctttaaacagATGTTACCGAGCCTTTGTTGATCGAGGTTGATCGGATTTACCATCTTGCTTGTCCTGCCTCTCCTATCTTCTACAAATACAACCCTGTTAAG
  |   |  |  || |     | |  |||  |  || ||  |||   | |  |   | |  |   | ||    ||   |||  |   ||||   |  | ||||||||| || ||||  |||||||| ||||||||||  || || |||||||| || || || ||||| || |||||||||||||||||||| |||
--aacatgacatgaatgatgctatcatgtgcatagtttttctgtgtttttagatgcgttgtaatttaattaaaatgcatatacttttatttt--ccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAG

upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 4
-gtatggtctcgagactctcagtttgt--tgttaagcgtcttcttgttcatgtcaacaagatccatcatcgtgatctctatttggaatttgggctttaaacagATGTTACCGAGCCTTTGTTGATCGAGGTTGATCGGATTTACCATCTTGCTTGTCCTGCCTCTCCTATCTTCTACAAATACAACCCTGTTAAG
 ||     ||          ||| | |  |||| ||    || ||    || | ||    ||  || ||  ||||    |||   |   ||  |  |    |||||| || || ||||||  ||| |||||||||| ||| ||||||||||| || ||||| |||||||| ||||||||||| || || || |||
agttataccttagtgtatatagtatatcgtgttcagaaggtttttaaatatctgaa---aattgatgatactgatacacattatcatcatgatccctttgtagATGTCACTGAACCTTTGACGATTGAGGTTGATCAGATCTACCATCTTGCGTGCCCTGCATCTCCTATTTTCTACAAATATAATCCCGTGAAG

upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 4
-gtatggtctcgagactctcagtttgt--tgttaagcgtcttcttgttcatgtcaacaagatccatcatcgtgatctctatttggaatttgggctttaaacagATGTTACCGAGCCTTTGTTGATCGAGGTTGATCGGATTTACCATCTTGCTTGTCCTGCCTCTCCTATCTTCTACAAATACAACCCTGTTAAG
 ||     ||          ||| | |  |||| ||  | |  ||    ||||| | ||| |  || ||   |||    |||   | | ||  |  |    |||||| || || ||||||  ||| |||||||||| ||| ||||||||||| || || || |||||||| ||||||||||| || ||||| |||
agtgataccttagtgtatatagtatatcatgttcagaatgtctttaa--atgtctaaaag-ttaatgatacggatacacattatcattatgatccctttgtagATGTCACTGAACCTTTGACGATTGAGGTTGATCAGATCTACCATCTTGCATGCCCCGCATCTCCTATTTTCTACAAATATAATCCTGTGAAG

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|86047698|gb|DR343453.1|DR343453
EST:     AAACCTCAAGAAGTGGATCGGTCACCCCAGGTTTGAACTTATTCGTCACG                         ATGTTACCGAGCCTTTGTTGATCGAGGTTGATCGGATTTACCATCTTGCTT
genomic: AAACCTCAAGAAGTGGATCGGTCACCCCAGGTTTGAACTTATTCGTCACGgtatggtctc ... ctttaaacagATGTTACCGAGCCTTTGTTGATCGAGGTTGATCGGATTTACCATCTTGCTT
EST: gi|124832184|gb|EH916623.1|EH916623
EST:     GGTCACCCCAGGTTTGAACTTATTCGTCACG                         ATGTTTACCGAGCCTTTGTTGATCGAGGTTGATCGGATTTACCATCTTGCT
genomic: GGTCACCCCAGGTTTGAACTTATTCGTCACGgtatggtctc ... ctttaaacagATG-TTACCGAGCCTTTGTTGATCGAGGTTGATCGGATTTACCATCTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtcaacaagatccatcatcgtgatctctatttggaatttgggctttaaacagATGTTACCGAGCCTTTGTTGATCGAGGTTGATCGGATTTACCATCTTGCTTGTCCTGCCTCTCCTATCTTCTACAAATACAACCCTGTTAAG
                                              tttaaaca  TA-rich tract