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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttactttgatccctcatttgcattgtctttctgtaatagttaataaaagctaatggcttatcctcttctaacttgttgttatgggctggattgcagGGGTTTGATAACCTTAGAAGTCAGAGTGTTGCCCCTCCACAATGGACAATGCGCAACATTGATGACAG

Basic information

species Oryza sativa
transcript LOC_Os03g42750.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G099056_T01 (Zea mays), 3'ss of exon 3
gtacttactttgatccctcatttgcattgtctttc-tgtaatagttaataaaagctaatggcttatcctcttctaacttgtt--gttatggg-ctggattgcagGGGTTTGATAACCTTAGAAGTCAGAGTGTTGCCCCTCCACAATGGACAATGCGCAACATTGATGACAG
|||  |||||||||| ||  || ||| ||  | |  || | ||  | |  | | |    |   |||||  | ||||||  ||  ||| |  | | ||| ||||||| |||||||||||||| ||||||||||||||||| ||||||||||| ||||| ||||||||||||||
gtatgtactttgatctct--ttcgcaatgcttctggtggagtatctgaagagaacatcggttatatccattactaactctttatgttttatgtccggactgcagGGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAG

upper sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 3
gtacttactttgatccctcatttgcattgtctttctgtaatagttaataaaagctaatggcttatcctcttctaacttgttgttatgggc-tggattgcagGGGTTTGATAACCTTAGAAGTCAGAGTGTTGCCCCTCCACAATGGACAATGCGCAACATTGATGACAG
             |   |   | | |  |         |  | | ||  |   |        || | | ||   | ||| || |       |   ||  |||||||||||||||||||||| |||||||| || |||||||| ||||||||||||||  | ||||||||
------------gtaagtttctggaacagaagcaaatcaggattcaaccatttcctgctatgtagcttgtttctatttgctgatgaatatgtatcttatagGGGTTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCACAGTGGACAATGCGCAATGTCGATGACAG

upper sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G36540.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------------gtactta-ctttgatccctcatttgcattgtctttctgtaatagttaataaaagctaatggcttatcctcttctaacttgttgtta--tgggctgga-----------ttgcagGGGTTTGATAACCTTAGAAGTCAGAGTGTTGCCCCTCCACAATGGACAATGCGCAACATTGATGACAG
                                                            ||  ||  | | ||  |   ||  | |    | | |  |   | ||  |  |   |  |   | ||    | | ||    ||| |   |||||||             |||||||| ||||||||||||||||| |||||||| || ||||| |||||||| |||||||| || ||||||||
gtaaagttccatgatggaagagatctttattttcttctagttctagaagacattttctcagtttttggcatagaagcaatatgagaagcaccctaccattccattttttggagtttgttttttgatgtcttcccaatcatttgcttgttgggctgatgcatgtgtatcttgcagGGATTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCTCAATGGACCATGCGCAATATCGATGACAG

upper sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------------gtacttactttgatccctcatttgcattgtctttctgtaatagttaataaaagctaatggcttatcctcttctaacttgttgttatgggctggattgcagGGGTTTGATAACCTTAGAAGTCAGAGTGTTGCCCCTCCACAATGGACAATGCGCAACATTGATGACAG
                                                                                  | | ||    | ||   |||      | ||| | |  |  ||  ||     |         |    |  |    || ||  ||| | |   |||||||| ||||||||||||||||| |||||||| || ||||| |||||||| |||||||| |||||||| ||
gtaaagttccatgatagaagagatctttatgttctagttctagacatgttctcagtttctggcactgaagcaatatgcgaagcatcctaccgttccctgttttggagttttttttttttttttttgtatgtcttcccaatcatttgcttgttgggctgatgc-atgcg-tatcttgcagGGATTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCTCAATGGACCATGCGCAATATTGATGATAG

upper sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G47560.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacttactttgatccctcatttgcattgtctttctgtaatagttaataaaa-gctaatggcttatcctcttctaact--tgttgtt-atgggctggattgcagGGGTTTGATAACCTTAGAAGTCAGAGTGTTGCCCCTCCACAATGGACAATGCGCAACATTGATGACAG
     |  |   |   ||  |  |  || |  ||   ||||   ||| | |  | | |    ||  | | |||  |||  | ||| | |||    |  ||  ||||||||||||| || || ||||| |||||||| |||||||| ||||| |||||||||| |||||||||
----ctgatgcaaagtcttttaggggttttacttaaataatttgtaaaacactgttcaatattttccatgttcccactgcttttgctgatgcaaagtcttttagGGGTTTGATAATCTCAGGAGTCAAAGTGTTGCTCCTCCACAGTGGACCATGCGCAACACTGATGACAG

upper sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G47550.2 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------------gtacttacttt----gatccctcatttgcattgtctttctgtaatagttaataaaagct-aatggctt--atcctcttctaacttgttgttatgggctggattgcagGGGTTTGATAACCTTAGAAGTCAGAGTGTTGCCCCTCCACAATGGACAATGCGCAACATTGATGACAG
                                                   | |  |  | |    ||      | ||| | | |  || |||||| || ||  |  | | |||   ||  ||         |||| |  | |||    |  ||  ||||||||||||| || || ||||| |||||||| |||||||| ||||| |||||||||| |||||||||
gtaagattttaatgaagcttacagtacctaagattttaagaagaaatgcatgcatctggtgtaagagactttgtaattgtaat-tgattgtgtaattgtaaaatactgttcaatattttctatgtatcctctacttttgctgatgcaaagtcttttagGGGTTTGATAATCTCAGGAGTCAAAGTGTTGCTCCTCCACAGTGGACCATGCGCAACACTGATGACAG

upper sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 3
--gtacttactttgatccctcatttgcattgtctttctgtaatagttaataaaagctaatggcttatcctcttctaacttgttgtt-atgggctggattgcagGGGTTTGATAACCTTAGAAGTCAGAGTGTTGCCCCTCCACAATGGACAATGCGCAACATTGATGACAG
    | | | ||  ||   ||   ||    | || |         ||  |     ||     | ||| || ||     ||| |||| || |  ||   |  |||| |||||||| || ||||| |||||||| || || || || |||||||||||||| |||||||||||
gcaaaatgaattcaatttttc--ctgttgaggctctaaacttagatttgtggtttctc-catcatattcttttaccctttgctgttgattgaatgtcatatagGGATTTGATAATCTCAGAAGCCAGAGTGTCGCTCCACCTCAGTGGACAATGCGCAATATTGATGACAG

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|88372502|gb|CI610825.1|CI610825
EST:     CAAAGGTTGAGGTTATTTCGAATGATCCTAGTGGTTGCACGTTTGTATTG                         GGGTTTGATAACCTTAGAAGTCAGAGTGTTGCCCCTCCACAATGGACAATG
genomic: CAAAGGTTGAGGTTATTTCGAATGATCCTAGTGGTTGCACGTTTGTATTGgtacttactt ... tggattgcagGGGTTTGATAACCTTAGAAGTCAGAGTGTTGCCCCTCCACAATGGACAATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataaaagctaatggcttatcctcttctaacttgttgttatgggctggattgcagGGGTTTGATAACCTTAGAAGTCAGAGTGTTGCCCCTCCACAATGGACAATGCGCAACATTGATGACAG
                        ttctaac  putative branch site (score: 1)
                                  ttgttat  TA-rich tract