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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgctcctccgcctcgtctcctcctccgcctcgagatctgatgaggggtttcgcatgctaccgcgtggttgtgcgcagGTGCTGTACTGGCTCTCCGGCCTCACGTGCAACGACGAGAACTTCGTCACCAAGGCCGGCGCGCAGCGCGCCGCCGCCGCCCACGGCATCGCCCTCGTCG

Basic information

species Oryza sativa
transcript LOC_Os01g71300.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g71300.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G046558_T01 (Zea mays), 3'ss of exon 1
gtaagtgctcctccgcctcgtctcc---tcctccgcctcga-gatctgatgaggggtttcgcatgctaccgcgtggttg-tgcgcagGTGCTGTACTGGCTCTCCGGCCTCACGTGCAACGACGAGAACTTCGTCACCAAGGCCGGCGCGCAGCGCGCCGCCGCCGCCCACGGCATCGCCCTCGTCG
|| ||||| || |||||   |||||   ||||||  |||   |  || ||  | |   |  | || |  |   ||| || |  ||||||||||||||||||||| || ||||| |||| ||||||||| ||| |||  ||| ||||||| |||||||||||||| |||||||||||||||||||| |
gtgagtgcgccgccgccctttctccctatcctccttctctctgggctaatatgtg--ctgacgtggtgtcctatggatgctttgcagGTGCTGTACTGGCTCTCGGGTCTCACCTGCACCGACGAGAATTTCATCATAAAGTCCGGCGCCCAGCGCGCCGCCGCTGCCCACGGCATCGCCCTCGTGG

upper sequence: LOC_Os01g71300.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G155334_T01 (Zea mays), 3'ss of exon 1
gtaagtgctcctccgcctcgtctcc---tcctccgcctcgagatctgatgaggggtttcg-catgctaccgcgtggttgtgc-gcagGTGCTGTACTGGCTCTCCGGCCTCACGTGCAACGACGAGAACTTCGTCACCAAGGCCGGCGCGCAGCGCGCCGCCGCCGCCCACGGCATCGCCCTCGTCG----------
|| ||||| |  || ||    ||||   ||||||  | |    || | | |   |    | |  | |  |   ||| ||  | ||||||||||||||||||||| |||||||| || | ||||||||| ||| |||  ||||          |||||||||||||||| ||||||||||||| |||           
gtgagtgcgcagccaccctcgctccctatcctccctccctctctcggctaatatgcgctgacgcggtgtcttatggatgctctgcagGTGCTGTACTGGCTCTCGGGCCTCACCTGTACCGACGAGAATTTCATCATGAAGG----------GCGCGCCGCCGCCGCCAACGGCATCGCCCTTGTCACGCCTGACAC

upper sequence: LOC_Os01g71300.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G108369_T01 (Zea mays), 3'ss of exon 1
gtaagtgctcctccgcctcgtctcc---tcctccgcctcga-gatctgatgaggggtttcgcatgctaccgcgtggttg-tgcgcagGTGCTGTACTGGCTCTCCGGCCTCACGTGCAACGACGAGAACTTCGTCACCAAGGCCGGCGCGCAGCGCGCCGCCGCCGCCCACGGCATCGCCCTCGTCG
|| ||||| ||  ||||   |||||   ||||||  |||   |  || ||  | |   |  | || |  |   ||| || |  ||||||||||||||||||||| || ||||| |||| ||||||||| ||| |||  ||| || |||| |||||||||||||| ||||||| |||||||||||| |
gtgagtgcgccgtcgccctttctccctatcctccttctctctgggctaatatgtg--ctgacgtggtgtccaatggatgctttgcagGTGCTGTACTGGCTCTCGGGTCTCACCTGCACCGACGAGAATTTCATCATAAAGTCCAGCGCCCAGCGCGCCGCCGCTGCCCACGACATCGCCCTCGTGG

upper sequence: LOC_Os01g71300.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G33350.1 (Glycine max), 3'ss of exon 1
gtaagtgctcctccgcctcgtctcctcctccgcctcga---gatctgatgaggggtttcgcatgct-----accgcgtggttgtgc------------gcagGTGCTGTACTGGCTCTCCGGCCTCACGTGCAACGACGAGAACTTCGTCACCAAGGCCGGCGCGCAGCGCGCCGCCGCCGCCCACGGCATCGCCCTCGTCG
|| ||| |  |||    |   | | |    |    | |    | || ||   |   |||      |     |||  |   ||||||              ||||||||||||  ||||| |||||||| |||| ||||||||||||| |   |||| | || || ||||| |||||  ||||| | ||  | ||| | || |
gtgagtccctctctcaatttccccatttctcattccaatttaacctaattttgcacttcctcgattgattgacccggctattgtgctttgaatgaataatagGTGCTGTACTTTCTCTCTGGCCTCACTTGCACCGACGAGAACTTCATATTCAAGTCGGGTGCTCAGCGTGCCGCTTCCGCCGAGGGTGTTGCCTTGGTTG

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|33793279|gb|CF322520.1|CF322520
EST:     GGCATCCGACCTCCCC                         GTGCTGTACTGGCTCTCCGGCCTCACGTGCAACGACGAGAACTTCGTCACC
genomic: GGCATCCGACCTCCCCgtaagtgctc ... ttgtgcgcagGTGCTGTACTGGCTCTCCGGCCTCACGTGCAACGACGAGAACTTCGTCACC
EST: gi|58591479|gb|CF989787.1|CF989787
EST:     CCATGACCTTCTCCGTCTTCCTCCCGCCGTCGCCGGCATCCGACCGGGCC                         GTGCTGTACTGGCTCTCCGGCCTCACGTGCAACGACGAGAACTTCGTCACC
genomic: CCATGACCTTCTCCGTCTTCCTCCCGCCGTCGCCGGCATCCGACCTCCCCgtaagtgctc ... ttgtgcgcagGTGCTGTACTGGCTCTCCGGCCTCACGTGCAACGACGAGAACTTCGTCACC
EST: gi|58604050|gb|CK014578.1|CK014578
EST:     CCATGACCTTCTCCGTCTTCCTCCCGCCGTCGCCGGCATTCGACCTCCCC                         GTGCTGTACTGGCTCTCCGGCCTCACGTGCAACGACGAGAACTTCGTCACC
genomic: CCATGACCTTCTCCGTCTTCCTCCCGCCGTCGCCGGCATCCGACCTCCCCgtaagtgctc ... ttgtgcgcagGTGCTGTACTGGCTCTCCGGCCTCACGTGCAACGACGAGAACTTCGTCACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccgcctcgagatctgatgaggggtttcgcatgctaccgcgtggttgtgcgcagGTGCTGTACTGGCTCTCCGGCCTCACGTGCAACGACGAGAACTTCGTCACCAAGGCCGGCGCGCAGCGCGCCGCCGCCGCCCACGGCATCGCCCTCGTCG
            atctgat  putative branch site (score: 4)