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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaatctttacttgcacccatgtaccttgatttttacatgtagattgttctggtttgtttcattccttatctctgagtattgattatttgctacatatttttcagGTCTTTGCAACAGCTTCATATGATGACCATAAAAATATTGTACTCCTGGCGTTTGAAATTATCGAGAAGATTTTGCGGGAGTACTTTCCCTACATTACTG

Basic information

species Oryza sativa
transcript LOC_Os03g14260.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14260.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 8
gtatggaatctttacttgcacccatgtaccttgatttttacatgtagattgttctggtttgtttcattccttatctctgagtattgattatttgctacatatttttcagGTCTTTGCAACAGCTTCATATGATGACCATAAAAATATTGTACTCCTGGCGTTTGAAATTATCGAGAAGATTTTGCGGGAGTACTTTCCCTACATTACTG
|||||  | ||| |||      |||||||| | | | |||  |  |||    ||||     ||    |  | |   ||||  || ||||    | |  | || |||||||||||||| ||||| ||||||||||| || ||||||||||||||  |||| ||||||||||| || |||||||||||||| |||||||| ||||||||||
gtatgacaccttcact------catgtaccataactcttatctaaagacc--tctgcaacattcttgttttcagtcctgaacatggattgccggtt-tacatctttcagGTCTTTGCGACAGCGTCATATGATGATCACAAAAATATTGTACTATTGGCCTTTGAAATTATAGAAAAGATTTTGCGGGAATACTTTCCATACATTACTG

upper sequence: LOC_Os03g14260.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 9
gtatggaatctttacttgcacccatgtaccttgatttttacatgtagattgttctggtttgtttcattccttatctctgagtattgattatttgctacatatttttcagGTCTTTGCAACAGCTTCATATGATGACCATAAAAATATTGTACTCCTGGCGTTTGAAATTATCGAGAAGATTTTGCGGGAGTACTTTCCCTACATTACTG
||| |   |  | |  | |     | ||    ||  || |  |   |  | |  | |||  |||  || ||   ||||   || || | ||       ||    ||||||| ||  |||||||  | ||||||||||| ||||| ||||||||| |  | ||||||||||| ||||||||| | || || |||||||| ||||| ||||
gta-gagctgataaactcctattgtctatagagagcttcaattaatgcatatgtttgttcattt--tttctctcctctacttactgctcatagatctgat----ttcagGTATTCACAACAGCAGCTTATGATGACCACAAAAACATTGTACTCTTATCTTTTGAAATTATGGAGAAGATTATTCGAGATTACTTTCCATACATCACTG

upper sequence: LOC_Os03g14260.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 8
gtatggaatctttacttgcacccatgtaccttgatttttacatgtagattgttctggtttgtttcattccttatctctgagtattgattatttgctacatatttttcagGTCTTTGCAACAGCTTCATATGATGACCATAAAAATATTGTACTCCTGGCGTTTGAAATTATCGAGAAGATTTTGCGGGAGTACTTTCCCTACATTACTG
||| |   |  | |  | |     | ||    ||  || |  |   | |  |  | ||   |||  |||     ||||   ||||| | ||   |   ||    ||||||| ||  || ||||  | ||||||||||| ||||| ||||||||| |||| ||||||||||| ||||||||| | || || |||||||| ||||| ||||
gta-gagctgataaactcctattgtctatagagagcttcaattaatgctaatgtttgtggatttttttctcctcctctacttattgctcatagacctgat----ttcagGTATTCACAGCAGCAGCTTATGATGACCACAAAAACATTGTACTCTTGGCTTTTGAAATTATGGAGAAGATTATTCGAGATTACTTTCCATACATCACTG

upper sequence: LOC_Os03g14260.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA18G45360.1 (Glycine max), 3'ss of exon 10
gtatggaatctttacttgcacccatgtaccttgatttttacatgtagattgttctggtttgtttcattccttatctctgagtattgattatttgct-----acatatttttcagGTCTTTGCAACAGCTTCATATGATGACCATAAAAATATTGTACTCCTGGCGTTTGAAATTATCGAGAAGATTTTGCGGGAGTACTTTCCCTACATTACTG
||| ||    ||||  | |      |  | |  ||||   |||| | | |||| | || ||    | |  || | ||    | |  | |  |||||     ||||| ||  ||||  ||  |||||||  ||||||||||||| ||||| ||||||||| |||| ||||||||||| ||||||||| | || || ||||||||  |||| ||||
gtagggctaatttatgttccatagagggcttcaattt--gcatggaaaatgtttttgtctgccgaagtttttctttcattatttctactcattgcttgtggacataattc-cagGCATTCACAACAGCAGCATATGATGACCACAAAAACATTGTACTCTTGGCTTTTGAAATTATGGAGAAGATTATTCGAGATTACTTTCCTCACATCACTG

upper sequence: LOC_Os03g14260.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA18G45340.1 (Glycine max), 3'ss of exon 8
gtatggaatctttacttgcacccatgtaccttgatttttacatgtagattgttctggtttgtttcattccttatctctgagtattgattatttgctacatatttttcagGTCTTTGCAACAGCTTCATATGATGACCATAAAAATATTGTACTCCTGGCGTTTGAAATTATCGAGAAGATTTTGCGGGAGTACTTTCCCTACATTACTG
|||  |    |  |||   |    | ||    ||  || |  |   |    |  | |||  |||  || ||   ||||   || || | ||   |   ||    ||||||| ||  |||||||  | ||||||||||| ||||| ||||||||| | || ||||||||||| ||||||||| | || || |||||||| ||||| ||||
gtaaagctgataaactcctatt-gtctatagagagattcaattaatgcaaatgtttgttcattt--tttctctcctctacttactgctcatagacctgat----ttcagGTATTCACAACAGCAGCTTATGATGACCACAAAAACATTGTACTCTTAGCTTTTGAAATTATGGAGAAGATTATTCGAGATTACTTTCCATACATCACTG

upper sequence: LOC_Os03g14260.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 8
gtatggaatctttacttgcacccatgtaccttgatttttacatgtagattgttctggtttgtttcattccttatctc----tgagtattgattatttgctacatatttttcagGTCTTTGCAACAGCTTCATATGATGACCATAAAAATATTGTACTCCTGGCGTTTGAAATTATCGAGAAGATTTTGCGGGAGTACTTTCCCTACATTACTG
||| ||    |||   | |      |  | |  ||||   |||| | | |||| | || || |  | |  || | ||    |   || | |||  |||     |   || ||||| ||  |||||||  ||||||||||||| ||||| |||||||||||||| ||||||||||| ||||||||| | || || |||||||| | ||| ||||
gtagggctaatttctgttccgtagagggcttcaattt--gcatggaaaatgtttttgtctgctgaagtttttctttcattatttctactcattgcttgtggacttaattccagGTATTCACAACAGCGGCATATGATGACCACAAAAACATTGTACTCCTGGCTTTTGAAATTATGGAGAAGATTATTCGAGATTACTTTCCATGCATCACTG

upper sequence: LOC_Os03g14260.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------------gtatggaatctttacttgcacccatgtaccttgatttttacatgtagattgttc--tggtttgtttcattccttatctctgagtattgattatttgct---acatatttttcagGTCTTTGCAACAGCTTCATATGATGACCATAAAAATATTGTACTCCTGGCGTTTGAAATTATCGAGAAGATTTTGCGGGAGTACTTTCCCTACATTACTG
                                 ||  |||| |  |  ||      || |  ||  || ||  || |   ||  ||  || |||  ||   |   |  || ||   |  |||||||       | || |||||||||||||  |||||||  | |||||||| |||||||| || ||||||||||| |||||||| || ||||||||| |||| || ||||| |||||||||||||
gtattgaaatctgtccaatctgtagttttctattaaagaatatgcaagtgagggagtg-attttagttcttcaatttgatttcatcattgattttatttggtgaatggctatgttaacagattattaatgtgaatatttttttcagGTCTTCACAACAGCAGCTTATGATGATCATAAAAACATAGTACTCCTGGCCTTTGAAATAATTGAGAAGATTGTGCGAGACTACTTCCCCTACATTACTG

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|29682831|gb|CB679106.1|CB679106
EST:     TCTTGGCACGTGTTAGTCATGTGAAATCAGGGTGGAAGAGTATGTTTATG                         GTCTTTGCAACAGCTTCATATGATGACCATAAAAATATTGTACTCCTGGCG
genomic: TCTTGGCACGTGTTAGTCATGTGAAATCAGGGTGGAAGAGTATGTTTATGgtatggaatc ... tatttttcagGTCTTTGCAACAGCTTCATATGATGACCATAAAAATATTGTACTCCTGGCG
EST: gi|29628227|gb|CB633238.1|CB633238
EST:     TCTTGGCACGTGTTAGTCATGTGAAATCAGGGTGGAAGAGTATGTTTATG                         GTCTTTGCAACAGCATCATATGATGACCATAAAAATATTGTACTCCTGGCG
genomic: TCTTGGCACGTGTTAGTCATGTGAAATCAGGGTGGAAGAGTATGTTTATGgtatggaatc ... tatttttcagGTCTTTGCAACAGCTTCATATGATGACCATAAAAATATTGTACTCCTGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtttgtttcattccttatctctgagtattgattatttgctacatatttttcagGTCTTTGCAACAGCTTCATATGATGACCATAAAAATATTGTACTCCTGGCGTTTGAAATTATCGAGAAGATTTTGCGGGAGTACTTTCCCTACATTACTG
                           tattgat  putative branch site (score: 3)
                                             tatttttc  putative PPT
                         agtattgattattt  TA-rich tract