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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatgaaataattcatttaaattcatctttttcctgaactgcgctggtgtacattttatggttttatccctcttgccactgggtgaataggacaa...

Basic information

species Oryza sativa
transcript LOC_Os07g08880.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g08880.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G097726_T02 (Zea mays), 5'ss of exon 3
GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatg-aaataattcatttaaattcatctttttcctgaactgcgctggtgtacattttatggttttatccctcttgccactgggtgaataggacaa
||| |||||||| ||||||||||||||||| |||||||||||||||||||| |||||||| ||||| ||||||| | |  | || |  |||        |   ||||  |  || ||  |    | | |||    | |  || | |     || | | |   |       
GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcattatagatgaagcatgctggcctaatatttttttatacagcatttacctccttttctctggtgcattctttaattcaattgattgctttattg-

upper sequence: LOC_Os07g08880.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA04G01140.1 (Glycine max), 5'ss of exon 3
GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatgaaataattcatttaaattcatctttttcctgaactgcgctggtgtacattttatggttttatccctcttgccactgg-gtgaataggacaa--
||  || || ||||||||||| ||||| ||||||||||| ||| ||||||||||||  ||| |||| |||| |||  ||||    |    | | ||| ||||||    |   | | |   |      || | | |||||||   ||| | | ||||  ||   ||  |    
GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTGgtaagt--tgaatatgtaaggtgatattaatctttaatttattccgtgtctgc-cctgttgttttgttttatgtttctggactctggtatgttcagttctgta

upper sequence: LOC_Os07g08880.2 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S56_182V6.1 (Physcomitrella patens), 5'ss of exon 3
GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatgaaataattcatttaaattcatctttttcctgaactgc-gctggtgtacattttatggttttatccctcttgccactgggtgaataggacaa---
 |  ||||||||||| ||||||||||||||||| ||| | ||| | ||||||||    |||   || ||||  ||    | ||   || |||  || ||  |      || | |   |  |  ||   ||||||     |||    ||    | | |     |      |   
TTATTGCAAGTGTGAAATGCCATACAATCCTGACGACTTGATGGTTCAATGTGAAATCTGCAAAGACTGgttggt--ctatattcctcctttctatgcaagtgca--gtggattattgtagaagttgtttttatctcagtattttcctgaatattcgcaaggtgaacttaccc

upper sequence: LOC_Os07g08880.2 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S384_37V6.1 (Physcomitrella patens), 5'ss of exon 3
GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatgaaataattcatttaaattcatctttttcctgaactgcgctggtgtacattttatggttttatccc--tcttgccactgggtgaataggacaa
||  ||||||||||||||||||||||| |||||  || | ||| |  ||||  |    |||   || |||||||   ||   |  |  | |     |||||  |    ||   ||| | |     || |  |   |  |  | |   ||       | | |  |    |  
GTATTGCAAGTGTGAGATGCCATACAACCCTGACCACGTGATGCTGGAATGCAACAGTTGCAAAGACTGgtgag-gttgctgtgctctaatattgctcatcagtgaagtgc-ttgctcagtcagtcagtaaagactcgtgcctcgacctaagtctcgtgcgcttgaagctt

upper sequence: LOC_Os07g08880.2 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S298_65V6.1 (Physcomitrella patens), 5'ss of exon 3
GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatgaaataattcatttaaattcatc------tttttcctgaactgcgctggtgtacattttatggttttatccctcttgccactgggtgaataggacaa
 |  |||||||| |||||||| ||||||||||||||| | ||| | ||||||||    |||   || ||||  |   |    |  |   || || | |  |        |||| |    |  ||  |  ||  |   |  |     |   |||||  | || |    | | ||  
TTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTGgtaggcc-tatgcttctctgttcaactgcgacaaagtgcatttctttgtatttgcccggatatttgcaagaggacggtt--tcttg--agtgaggagcttgcacc-

upper sequence: LOC_Os07g08880.2 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ17782 (Selaginella moellendorffii), 5'ss of exon 3
GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatgaaataattcatttaaattcatctttttcctgaactgcgctggtgtacattttatggttttatccctcttgccactgggtgaataggacaa
||  |||||||||||||||||||||||||| || ||  | ||| | || || |||   |||   ||||||| |||  |    | || ||    |    |  |||      || | | ||  | | | | |   |                                   
GTATTGCAAGTGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTGgtaagtcctc--ttcatccaaacgagcaaagttttgatgcaaaatac-ctcctttgcgtctccag-----------------------------------

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|218504563|gb|FG952376.1|FG952376
EST:     CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG                         GTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCNNNNNNNCTAGA
genomic: CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatg ... tgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGA
EST: gi|3462559|gb|AF074797.1|AF074797
EST:     CATACAATCCTGATGACCTTATGATCCAATGTTGAGGAATGCTCTGATTG                         GTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCNAAAAAACTANA
genomic: CATACAATCCTGATGACCTTATGATCCAATGT-GAGGAATGCTCTGATTGgtgagtaatg ... tgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGA
EST: gi|86261244|gb|CI014311.1|CI014311
EST:     CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG                         GTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCNNNNNNNCTAGA
genomic: CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatg ... tgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGA
EST: gi|218497932|gb|FG957265.1|FG957265
EST:     CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG                         GTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAA-CTAGA
genomic: CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatg ... tgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGA
EST: gi|88201730|gb|CI202085.1|CI202085
EST:     CATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG                         GTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCNNNNNNNCTAGA
genomic: CATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatg ... tgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGA
EST: gi|86498011|gb|CI140644.1|CI140644
EST:     CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG                         GTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCNNNNNNNCTAGA
genomic: CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatg ... tgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGA
EST: gi|29686487|gb|CB682762.1|CB682762
EST:     CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG                         GTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCNNNNNNNCTAGA
genomic: CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatg ... tgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGA
EST: gi|88964512|gb|CI055208.1|CI055208
EST:     GAGGAATGCTCTGATTG                         GTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCCAAAAAACTAGA
genomic: GAGGAATGCTCTGATTGgtgagtaatg ... tgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGA
EST: gi|38471848|gb|CF955979.1|CF955979
EST:     CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG                         GTTTCACCCTTTTTGCAT
genomic: CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatg ... tgctttccagGTTTCACCCTTCTTGCAT