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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatattgagatttgcaactgtgtgttgtaaccatgtgcagttttgggcacttattaacgaggctctgcttggctgtctgcagTTATCTGGCACCAGAATACGCACAGAGTGGACAAATAACAGAGAAAGCTGATGTATACTCTTTTGGGGTTGTGTTAGTTGAACTTGTCACTGGGCGCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g41870.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G480607_T04 (Zea mays), 3'ss of exon 6
gtaaatattgagatttgcaactgtgtgttgtaaccatgtgcagtt-----ttgggcacttattaacga-ggctctgcttggctgtctgcagTTATCTGGCACCAGAATACGCACAGAGTGGACAAATAACAGAGAAAGCTGATGTATACTCTTTTGGGGTTGTGTTAGTTGAACTTGTCACTGGGCGCAAG
||   | || | | |      ||  | || | | |||  ||| ||     || |    |   ||||||  ||| |  |   |||||||||| |||||||| || ||||| ||||||||||| |||||||||||||| ||||||||||||||||| |||||||||||||| ||||||||||||||||| |||
gtgggttttaatactattctatgaatattttcatcataggcaattaaacttttgagtttagctaacgacagctttatt--actgtctgcagCTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGATGTATACTCTTTCGGGGTTGTGTTAGTGGAACTTGTCACTGGGCGGAAG

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G13690.1 (Arabidopsis thaliana), 3'ss of exon 7
-----gtaaatattgagatttgcaactgtgtgttgtaaccatgtgcagttttgggcacttattaacgaggctctgcttggctg-tctgcagTTATCTGGCACCAGAATACGCACAGAGTGGACAAATAACAGAGAAAGCTGATGTATACTCTTTTGGGGTTGTGTTAGTTGAACTTGTCACTGGGCGCAAG
       |  || | |   |  ||  |   |  || |||  |   || |||  | |  ||  |||  ||    ||||||| || | ||||| ||||| || || ||||| || || || || ||||| ||||| ||||||||||| ||||| || ||||||||  ||||||| || |||||||| ||||| 
gtgagacacctactaaagctatcattttgctcctgaaac--ttaacaattt--gtctgttgctaa-aagaaattgcttggttggtgtgcagCTATCTAGCTCCCGAATATGCTCAAAGCGGGCAAATCACAGAAAAAGCTGATGTCTACTCGTTCGGGGTTGTTCTAGTTGAGCTAGTCACTGGCCGCAAA

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G55200.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaatattgagatttgcaactgtgtgttgtaaccatgtgcagttttgggca-cttattaacgaggctctgcttggctgtctgcagTTATCTGGCACCAGAATACGCACAGAGTGGACAAATAACAGAGAAAGCTGATGTATACTCTTTTGGGGTTGTGTTAGTTGAACTTGTCACTGGGCGCAAG
     ||   | ||||  ||||        | | |||   || | | | | |  || | ||| |   ||||  |  ||   |  || ||| | || ||||| || || || ||||||||||| ||||||||||| ||||| ||||| || |||||||| ||  | |||||  |||| || || || 
----gtaacaaaatttataacta-----aatcatcattctcactctagagtaatttctcaactactttctgtgtttcttgttttagCTATTTAGCTCCAGAGTATGCTCAAAGTGGACAAATCACAGAGAAAGCCGATGTTTACTCGTTCGGGGTTGTATTGATCGAACTAATCACGGGTCGTAAA

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv09s0002g02420.t01 (Vitis vinifera), 3'ss of exon 6
gtaaatattgagatttgcaactgtgtgttgtaaccatgtgcagttttgggcacttatt------aacgag--gctctgcttggctgtctgcagTTATCTGGCACCAGAATACGCACAGAGTGGACAAATAACAGAGAAAGCTGATGTATACTCTTTTGGGGTTGTGTTAGTTGAACTTGTCACTGGGCGCAAG
|||| || |||   |  || || | || | ||||  |      |||    |  ||||       || |||    ||||||      | || || ||| |||| |||||||| || || || || ||||| ||||| || ||||||||||| |||||||||||||| || || || |||||||| || || || 
gtaactactgaa--tgacagct-tttgctttaacttta-atgctttcacactgttatagtatcaaatgagctattctgctccttgttatgtagGTATTTGGCTCCAGAATATGCTCAAAGCGGCCAAATCACAGAAAAGGCTGATGTATATTCTTTTGGGGTTGTCTTGGTGGAGCTTGTCACAGGACGAAAA

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv11s0016g02430.t01 (Vitis vinifera), 3'ss of exon 6
gtaaatattgagatttgcaactgtgtgttgtaaccatgtgcagttttgggcacttattaacgaggctctg---cttggctgtctgcagTTATCTGGCACCAGAATACGCACAGAGTGGACAAATAACAGAGAAAGCTGATGTATACTCTTTTGGGGTTGTGTTAGTTGAACTTGTCACTGGGCGCAAG
||||| |   ||      | || |  | |   | ||     || |      | |    |   |  |  |    |||   | | | ||| || ||| | |||||||| || || ||||| ||||| ||||| ||||||||||||||||| ||||| || ||||| || || ||  | || || || || 
gtaaacaagaaggac--aagcttttggcttccatcaatactagctaaaaataatggcaagtcaaaccattaatcttacttttgtacagGTACCTGTCTCCAGAATATGCTCAAAGTGGCCAAATCACAGAAAAAGCTGATGTATACTCCTTTGGAGTAGTGTTGGTGGAGCTCATTACAGGACGGAAA

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ12405 (Selaginella moellendorffii), 3'ss of exon 6
gtaaatattgagatttgcaactgtgtgttgtaaccatgtgcagttttgggcacttattaacgaggctctgcttggctgtctgcagTTATCTGGCACCAGAATACGCACAGAGTGGACAAATAACAGAGAAAGCTGATGTATACTCTTTTGGGGTTGTGTTAGTTGAACTTGTCACTGGGCGCAAG
                | |||| | || |||     | | |  ||     || |  ||   ||  ||      ||    ||| || ||  ||||||| || ||  | || |  |||||||| ||||||||||| ||||| |||||||||||  | ||| |  | || ||||| | ||| || |||
----------------gtaactct-tgctgtgttttttttcc-ttgccttcattctttggtgacact------gg--agctgtagGTACTTGGCACCTGAGTATACTCAAACAGGACAAATCACAGAGAAAGCCGATGTTTACTCTTTTGGCATCGTGCTCCTGGAGCTTGTAAGTGGTCGGAAG

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|25798254|gb|CA754215.1|CA754215
EST:     CAACCTGATGGTGACATGGGTGTTGACACGAGAGTAATTGGAACATTCGG                         TTATCTGGCACCAGAATACGCACAGAGTGGACAAATAACAGAGAAAGCTGA
genomic: CAACCTGATGGTGACATGGGTGTTGACACGAGAGTAATTGGAACATTCGGgtaaatattg ... ctgtctgcagTTATCTGGCACCAGAATACGCACAGAGTGGACAAATAACAGAGAAAGCTGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaccatgtgcagttttgggcacttattaacgaggctctgcttggctgtctgcagTTATCTGGCACCAGAATACGCACAGAGTGGACAAATAACAGAGAAAGCTGATGTATACTCTTTTGGGGTTGTGTTAGTTGAACTTGTCACTGGGCGCAAG
                        tattaac  putative branch site (score: 1)
                     acttattaa  TA-rich tract