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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcaactaaccgtttgagtgatggcatttgtttcctgttgtggttgagatgtgcttattgttcttcctgatagagaaacaactaacctcatcaaatagttgagacgcgcgtactgcttattgacaacaggaaacaactaacctcatcaaatgggctgcagGTATCAAGAGATTTTGACTGATCCAAGCTATGCTGGTCAATTTGTCCTCATGACCAACCCACATATTGGAAACACTGGTGTTAATCCTG

Basic information

species Oryza sativa
transcript LOC_Os02g47850.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47850.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G029573_T01 (Zea mays), 3'ss of exon 3
gtaaatcaactaaccgtttgagtgatggcatttgtttcctgttgtggttgagatgtgcttattgttcttcctgatagagaaacaactaacctcatcaaatagttgagacgcgcgtactgcttattgacaacaggaaacaactaacctcatcaaatgggctgcagGTATCAAGAGATTTTGACTGATCCAAGCTATGCTGGTCAATTTGTCCTCATGACCAACCCACATATTGGAAACACTGGTGTTAATCCTG
                                               |||| |  ||    ||||   | | | ||     |  | ||    || || | | |  ||    |  ||    || ||    ||| |  |||  |              || ||||| ||||| ||||||||||| |||||||| ||||||||||| |||||||| |||||||| || |||||||| |||||||| ||||||||||
----------------------------------------------attga-acatgac--ttgtcgatgcagttatgttgatgatta--tgcaccata-attctaggtaggactaagaattgttacttacatggcacatttgt------------ggttgcagCTATCAGGAGATTTTGACCGATCCAAGTTATGCTGGTCAGTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTG

upper sequence: LOC_Os02g47850.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G147450_T03 (Zea mays), 3'ss of exon 4
gtaaatcaactaaccgtttgagtgatggcatttgtttcctgttgtggttgagatgtgcttattgttcttcctgatagagaaacaactaacctcatcaaatagttgagacgcgcgtactgcttattgacaacaggaaaca--actaacctcat-caaatg-ggctgcagGTATCAAGAGATTTTGACTGATCCAAGCTATGCTGGTCAATTTGTCCTCATGACCAACCCACATATTGGAAACACTGGTGTTAATCCTG
                                                                  |||   || |     |  | ||   |  || ||| |||||       |  |   |   || ||  | |||     ||  |  |    ||  || || ||||| ||||| ||||||||||| ||||||||||||||||||||||||||||| |||||||| || |||||||                     
-----------------------------------------------------------------acttgtcga-atgttgatgatta-tgttgtcgaat-gttgatgattatgcgccattctatgtcactaagaattgttacctatgtggcacatttgtggttgcagCTATCAGGAGATTTTGACAGATCCAAGCTATGCTGGTCAATTTGTCCTGATGACCAATCCCCATATTG---------------------

upper sequence: LOC_Os02g47850.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G147450_T02 (Zea mays), 3'ss of exon 2
gtaaatcaactaaccgtttgagtgatggcatttgtttcctgttgtggttgagatgtgcttattgttcttcctgatagagaaacaactaacctcatcaaatagttgagacgcgcgtactgcttattgacaacaggaaaca--actaacctcat-caaatg-ggctgcagGTATCAAGAGATTTTGACTGATCCAAGCTATGCTGGTCAATTTGTCCTCATGACCAACCCACATATTGGAAACACTGGTGTTAATCCTG
                                                                  |||   || |     |  | ||   |  || ||| |||||       |  |   |   || ||  | |||     ||  |  |    ||  || || ||||| ||||| ||||||||||| ||||||||||||||||||||||||||||| |||||||| || |||||||| |||||||| ||||||||||
-----------------------------------------------------------------acttgtcga-atgttgatgatta-tgttgtcgaat-gttgatgattatgcgccattctatgtcactaagaattgttacctatgtggcacatttgtggttgcagCTATCAGGAGATTTTGACAGATCCAAGCTATGCTGGTCAATTTGTCCTGATGACCAATCCCCATATTGGTAACACTGGCGTTAATCCTG

upper sequence: LOC_Os02g47850.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G15510.3 (Glycine max), 3'ss of exon 2
gtaaatcaactaaccgtttgagtgatggcatttgtttcctgttgtggttgagatgtgcttattgttcttcctgatagagaaacaactaacctcatcaaatagttgagacgcgcgtactgcttattgacaacaggaaacaactaacctcatcaaatgggctgcagGTATCAAGAGATTTTGACTGATCCAAGCTATGCTGGTCAATTTGTCCTCATGACCAACCCACATATTGGAAACACTGGTGTTAATCCTG
                              |  |  | || |     ||| |||| |     |||||||  |              |   ||       ||  ||||  |   ||  |  || |||                    |       ||     |||||||||||| |||||||| ||||| || |||||||| || ||||| |||||||| || ||||||||||| ||||||||  | |||  ||
-----------------------------gtgaggatactatgaatcttgggatgcg-----tgttctttttt---------tggttttgcttgcatgctaaatgagtggttggttttctttgttgtg-----------------ttgtgtgtgtgattctcagGTATCAAGAAATTTTGACAGATCCTAGTTATGCTGGCCAGTTTGTGCTCATGACAAATCCACATATTGGGAACACTGGCATAAATTTTG

upper sequence: LOC_Os02g47850.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G32190.1 (Glycine max), 3'ss of exon 2
gtaaatcaactaaccgtttgagtgatggcatttgtttcctgttgtggttgagatgtgcttattgttcttcctgatagagaaacaactaacctcatcaaatagttgagacgcgcgtactgcttattgacaacaggaaacaactaacctcatcaaatgggctgcagGTATCAAGAGATTTTGACTGATCCAAGCTATGCTGGTCAATTTGTCCTCATGACCAACCCACATATTGGAAACACTGGTGTTAATCCTG
                                                |||||||  || | | |   |    |  |  |  ||   || || | |  || | |    ||   ||     || || |              |||    |||   |   ||||||||||||||| ||| | || ||||| || ||||||||||| ||||| || ||||| || ||||||||||| ||||||||||| |||  ||
-----------------------------------------------gtgagatgaactaactttatatataaaccggcattcattcaatctgagc--atggatataccg-atgtttcatttgtttat------------ttaataatatctgttaa-ctgcagGTATCAAGAAATTCTAACAGATCCTAGTTATGCTGGTCAGTTTGTACTGATGACAAATCCACATATTGGTAACACTGGTGTAAATTTTG

upper sequence: LOC_Os02g47850.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G39390.1 (Glycine max), 3'ss of exon 2
gtaaatcaactaaccgtttgagtgatggcatttgtttcctgttgtggttgagatgtgcttattgttcttcctgatagagaaacaactaacctcatcaaatagttgagacgcgcgtactgcttat-tgacaacaggaaacaactaacctcatcaaatgggctgcagGTATCAAGAGATTTTGACTGATCCAAGCTATGCTGGTCAATTTGTCCTCATGACCAACCCACATATTGGAAACACTGGTGTTAATCCTG
                                                 | || |    |||   ||||       | ||      |  | |  |||     |||   |  || | |||  ||| || |             |    |       ||     |||||||||||| |||||||||||||| || |||||||| || ||||| |||||||| |||||||||||||| || |||||  | |||  ||
-------------------------------------------------gtgaggaaactatgaatctt-------gggatgtgtgtttctttttcatggctttg---cttgcatgctgaatatgtggctggttttctttgttgtgttgtgtgtgtgattatcagGTATCAAGAAATTTTGACTGATCCTAGTTATGCTGGCCAGTTTGTGCTCATGACAAACCCACATATTGGGAATACTGGCATAAATTTTG

upper sequence: LOC_Os02g47850.3 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G27740.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaatcaactaaccgtttgagtgatggcatttgtttcctgttgtggttgagatgtgcttattgttcttcctgatagagaaacaactaacctcatcaaatagttgagacgcgcgtactgcttattgacaacaggaaacaactaacctcatcaaatgggctgcagGTATCAAGAGATTTTGACTGATCCAAGCTATGCTGGTCAATTTGTCCTCATGACCAACCCACATATTGGAAACACTGGTGTTAATCCTG
                                                      ||   | ||||||||  ||||      | | |  ||||||  | || |||||     || |||||  | ||        ||      |    |       |||     ||||||||||| ||||| |||||||| || |||||||| || ||||| || ||||| |||||||| ||||| || |||||||| |||||||
------------------------------------------------------gtatgttttgttctt--tgatttcattatatc--acctcaa-agattgttgattttagcttactgaatctta-------gattttgtttgtttt------tgga----agGTATCAAGAAATTTTAACTGATCCTAGTTATGCTGGGCAGTTTGTGCTAATGACAAACCCACAAATTGGTAATACTGGTGTCAATCCTG

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|58656843|gb|CK045523.1|CK045523
EST:     GCTTCAGGAACACAAGTTGGTGAAGTGGTATTTAATACATCTTTGACAGG                         GTATCAAGAGATTTTGACTGATCCAAGCTATGCTGGTCAATTTGTCCTCAT
genomic: GCTTCAGGAACACAAGTTGGTGAAGTGGTATTTAATACATCTTTGACAGGgtaaatcaac ... tgggctgcagGTATCAAGAGATTTTGACTGATCCAAGCTATGCTGGTCAATTTGTCCTCAT
EST: gi|58690939|gb|CK079626.1|CK079626
EST:     GCTTCAGGAACACAAGTTGGTGAAGTGGTATTTAATACATCTTTGACAGG                         GTATCAAGAGATTTTGACTGATCCAAGCTATGCTGGTCAATTTGTCCTCAT
genomic: GCTTCAGGAACACAAGTTGGTGAAGTGGTATTTAATACATCTTTGACAGGgtaaatcaac ... tgggctgcagGTATCAAGAGATTTTGACTGATCCAAGCTATGCTGGTCAATTTGTCCTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgcgtactgcttattgacaacaggaaacaactaacctcatcaaatgggctgcagGTATCAAGAGATTTTGACTGATCCAAGCTATGCTGGTCAATTTGTCCTCATGACCAACCCACATATTGGAAACACTGGTGTTAATCCTG
                             aactaac  putative branch site (score: 1)
           ttattga  TA-rich tract