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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagaataattgcttgacctagttcatattcagtccacaaatttggcaatttatattcctgtgagcattccattatttactgtagaatatatctacttatgaagctaacctttttctcatgccctttttagGTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGGGAGACTGGTTACAGAATAACCTCAATAGCAGCAACAAATGACCAGGCTG

Basic information

species Oryza sativa
transcript LOC_Os07g07560.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G110085_T01 (Zea mays), 3'ss of exon 10
gttagaataattgctt-gacc------tagttcatattcagtccacaaatttggcaa---tttatattcctgtgagcattccattatttactgtagaatatatctacttatgaagctaacctttttctcatgcccttt-ttagGTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGGGAGACTGGTTACAGAATAACCTCAATAGCAGCAACAAATGACCAGGCTG
||||| || ||||||| ||||       |||   | |   ||   |     | || |    | | | |||| |||  |||   | |  |  ||    | | || ||   | | |  || ||    | ||    |   | | |||||||||| ||||||||||| || || || ||||||||| | ||||| |||||||  || ||||| ||||| || || || || || || ||||| |  |
gttaggatgattgctttgaccgcgcagcagtatctgtgttgtgggctcgccttgccagcgctcacactcctctga--attgtgtcaactgatgcctga-acatttaacaaggcatttagcccccctttcccaactactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAAGGCATCTACCGGCGCTGGGAGAGCGGCTACAGGATAACTTCCATGGCGGCCACCAACGACCAAGTCG

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 15
gttagaataattgcttgacctagttcatattcagtccacaaatttggcaatttatattcctgtgagcattccattatttactgtagaatatatctacttatgaagc----taacctttttctcatgccctttttagGTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGGGAGACTGGTTACAGAATAACCTCAATAGCAGCAACAAATGACCAGGCTG
||||| || |||||||   |        | |   ||        ||     | | | |||| |||  |||   | |  |  ||    | | || || |||  ||||    || || | ||  |   |   | | |||||||||| ||||||||||| || || || || |||||||| ||||| |||||||  || ||||| ||||| || |  ||||| || || ||||| || |
gttaggatgattgctttgaccgcgcagcagt--atctgtg---ctgtgggctcacactcctctga--attgtgtcaactgatgcctga-acatttatttaacaagccatttacccctctttcccaactactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGGGAGAGCGGCTACAGGATAACTTCCACGGCAGCCACCAACGACCAAGCCG

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 15
gttagaataattgcttgacc---tagttcatattcagtccacaaatttggcaatttatattcctgtgagcattccattatttactgtagaatatatctacttatgaagctaacctttttctcatgccctttttagGTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGGGAGACTGGTTACAGAATAACCTCAATAGCAGCAACAAATGACCAGGCTG
||||| || |||||||||||    ||    |||| |  |       |||   |   |||||||| |||  |||  |  |   ||||  |  |   | |  | |  || | |           |  |  || | |||||||||| ||||| ||||| || || || |||||||| |||||||||||||||| ||||||||| ||||| || | ||| || || |||||||| ||||
gttaggatgattgcttgaccacgcaggcattatttatgctgtgtccttgcgtaaccatattcctctga--attgtacca---actgaggcctgagtat-ttaaccaaacaacaacaacaaaaaaactgttgtcagGTTGTAGAGTTGGACTTCCTGTACCCTAGCGAAGGCATTCATCGGCGATGGGAGAGTGGTTACAGGATAACTTCCACAGCGGCCACCAATGACCAAGCTG

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G480263_T01 (Zea mays), 3'ss of exon 11
gttagaataattgctt-gacc------tagttcatattcagtccacaaatttggcaa---tttatattcctgtgagcattccattatttactgtagaatatatctacttatgaagctaacctttttctcatgcccttt-ttagGTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGGGAGACTGGTTACAGAATAACCTCAATAGCAGCAACAAATGACCAGGCTG
||||| || ||||||| ||||       |||   | |   ||   |     | || |    | | | |||| |||  |||   | |  |  |||   | | || ||   | | |  || ||    | ||    |   | | |||||||||| ||||||||||| || || || ||||||||||| || || |||||||  || ||||| ||||| || |  || || || ||  |||| || |
gttaggatgattgctttgaccgcgtagcagtatctgtgttgtgggctcgccttgccagcgctcacactcctctga--attatgtcaactgatgtctga-acatttaacaaggcatttagcccccctttcccaactactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAAGGCATCCACCGACGCTGGGAGAGCGGCTACAGGATAACTTCCACGGCGGCCACCAACAACCAAGCCG

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|22304710|gb|BQ905932.1|BQ905932
EST:     AATTCGCTGGGGTGTAGTTTATGTCAAGGAACTCAGGTTACTCTGAACAG                         CTTGTAGAATTGGATTTCCTATATCCAAGGTGAAGGCATCCATCGGCGATG
genomic: AA-TCGCTGGGGTGTAG-TTATGTCAAGGAACTCAGGTTACTCTGAACAGgttagaataa ... ccctttttagGTTGTAGAATTGGATTTCCTATATCCAA-GTGAAGGCATCCATCGGCGATG
EST: gi|88966779|gb|CI366002.1|CI366002
EST:     GAACTCAGG-TACTCTGAACAG                         G-TGTAGAATTGGATTTCCTATATCCAAATGAAGGCATCCATCGGCGATGG
genomic: GAACTCAGGTTACTCTGAACAGgttagaataa ... ccctttttagGTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGG
EST: gi|218490208|gb|FG966190.1|FG966190
EST:     GAAATCGCTGGGGTGTAGTTATGTCAAGGAACTCAGGTTACTCTGAACAG                         GTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGG
genomic: GAAATCGCTGGGGTGTAGTTATGTCAAGGAACTCAGGTTACTCTGAACAGgttagaataa ... ccctttttagGTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGG
EST: gi|86866762|gb|CI343562.1|CI343562
EST:     GAAATCGCTGGGGTGTAGTTATGTCAAGGAACTCAGGTTACTCTGAACAG                         GTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGG
genomic: GAAATCGCTGGGGTGTAGTTATGTCAAGGAACTCAGGTTACTCTGAACAGgttagaataa ... ccctttttagGTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactgtagaatatatctacttatgaagctaacctttttctcatgccctttttagGTTGTAGAATTGGATTTCCTATATCCAAGTGAAGGCATCCATCGGCGATGGGAGACTGGTTACAGAATAACCTCAATAGCAGCAACAAATGACCAGGCTG
                          agctaac  putative branch site (score: 2)
                                cctttttctcatgccc  CT-rich tract
         aatatatctacttat  TA-rich tract