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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggttggttccattgagtagtattcagttactgttttactcgtcttttttcacttaattgtagactccgtctgaaaaatgtagttccctgacagattagattggtttgcattgcagACAAGCATTCAGAGATGAGCTTGATGTGCTACAACTAATACGGCATCCGAATGTCGTGCAATTTTTAGGTGCTGTAACACAAAGCAGCCCAATGATGATT

Basic information

species Oryza sativa
transcript LOC_Os01g54480.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54480.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G045366_T01 (Zea mays), 3'ss of exon 4
gtgggttggttccattgagtagtattcagttactgttttactcgtcttttttcacttaattgtagactccgtctgaaaaatgtagttccctgacagattagattggtttgcattgcagACAAGCATTCAGAGATGAGCTTGATGTGCTACAACTAATACGGCATCCGAATGTCGTGCAATTTTTAGGTGCTGTAACACAAAGCAGCCCAATGATGATT
               || ||||| | || ||      || || |||| | ||  ||| ||| ||  || |            || |  ||||| || || |||      || || ||| || ||||||||||| |||||||||||||| ||||| ||||| ||||| ||||| ||||||||||| || ||||| ||||||||||  ||||||||||||
--------------gtgggtagtttccacttg-----tttctggtctatgttggctttattttacccttc------------tattatcctgatagtttggat------gccttacagGCAGGCATTCAGAGACGAGCTTGATGTGCTGCAACTTATACGTCATCCAAATGTTGTGCAATTTTTGGGCGCTGTGACACAAAGCAATCCAATGATGATT

upper sequence: LOC_Os01g54480.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G29520.1 (Glycine max), 3'ss of exon 4
gtgggttggttccattgagtagtattcagttactgttttactcgtcttttttcacttaattgtagactccgtctgaaaaatgtagttccctgacagattagattggtttgcattgcagACAAGCATTCAGAGATGAGCTTGATGTGCTACAACTAATACGGCATCCGAATGTCGTGCAATTTTTAGGTGCTGTAACACAAAGCAGCCCAATGATGATT
               |||||     |||   | |||   |||    || || || ||   | || |||   ||   | |||         | | | | | ||||        |  |||  | || |||||||||||||||| | || | ||   ||| |||||||| |||||||| |||||| | |||||||| || || || || ||||||||||||
--------------gtgagtttctctcaaccattgtgcaacta---ttattacagtttgctatatactt--tcatgataat---------taatatacttgatt------tttcacagGAAGGCTTTCAGAGATGAGCTTGCTCTGTTCCAGAAAATCCGGCATCCAAATGTCGTCCAATTTCTGGGTGCTGTGACCCAGAGTAGTCCAATGATGATT

upper sequence: LOC_Os01g54480.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G45770.1 (Glycine max), 3'ss of exon 4
gtgggttggttccattgagtagtattcagttactgttttactcgtcttttttcacttaattgtagactccgtctgaaaaatgtagttccctgacagattagattg-gtttgcattgcagACAAGCATTCAGAGATGAGCTTGATGTGCTACAACTAATACGGCATCCGAATGTCGTGCAATTTTTAGGTGCTGTAACACAAAGCAGCCCAATGATGATT
||||||||||    ||  | |      || |   |||| | || | |   ||   ||| |     | ||    |    | | |  |   |       || | | |  | ||  |  |||| | |||||    |||||||||    ||||  |   |||| | ||||| ||||| || || ||||| |||||||||||||||||||  || |||||||||
gtgggttggtctacttatgca------agctgtcgtttcattcatgtcaattggattattca---attcttaattgttattctcatattcgattttgtttgttggcatctgtttatcagAAAGGCATTTCATGATGAGCTTACATTGCTTGAGAAAATAAGACATCCAAATGTAGTCCAGTTTTTGGGTGCTGTAACACAAAGCACACCGATGATGATT

upper sequence: LOC_Os01g54480.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA14G03040.1 (Glycine max), 3'ss of exon 4
gtgggttggttccattgagtagtattcagttactgttttactcgtcttttttcacttaattgtagactccgtctgaaaaatgtagttccctgacagattagatt----ggtttgcattg--cagACAAGCATTCAGAGATGAGCTTGATGTGCTACAACTAATACGGCATCCGAATGTCGTGCAATTTTTAGGTGCTGTAACACAAAGCAGCCCAATGATGATT
||||||||||    ||  | | |       |  ||||| | || | |   || ||| ||||| | | || ||    ||  | || |  | |    ||||   ||    ||| |   ||   |||| | |||||     ||||||||    | ||  |   |||| ||||||| ||||| || || ||||| |||||||||||||||||||  ||||||||||||
gtgggttggtctacttatgcaat------ctgttgtttcattcatgtcaatt-actcaattggatattcagttctcaatttttattctcatcgtggattttgtttcttggtgtatgtttatcagAAAGGCATTTCATTATGAGCTTACATTACTTGAGAAAATAAGGCATCCAAATGTAGTCCAGTTTTTGGGTGCTGTAACACAAAGCACACCAATGATGATT

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|117235877|gb|CT847833.1|CT847833
EST:     GTTGCTGTTAAGAAGCTTGATGACGATCTAATTATGGACGAGAACAAAGT                         ACAAGCATTCAGAGATGAGCTTGATGTGCTACAACTAATACGGCATCCGAA
genomic: GTTGCTGTTAAGAAGCTTGATGACGATCTAATTATGGACGAGAACAAAGTgtgggttggt ... tgcattgcagACAAGCATTCAGAGATGAGCTTGATGTGCTACAACTAATACGGCATCCGAA
EST: gi|29678487|gb|CB674762.1|CB674762
EST:     GTTGCTGTTAAGAAGCTTGATGACGATCTAATTATGGACGAGAACAAAGT                         ACAAGCATTCAGAGATGAGCTTGATGTGCTACAACTAATACGGCATCCGAA
genomic: GTTGCTGTTAAGAAGCTTGATGACGATCTAATTATGGACGAGAACAAAGTgtgggttggt ... tgcattgcagACAAGCATTCAGAGATGAGCTTGATGTGCTACAACTAATACGGCATCCGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agactccgtctgaaaaatgtagttccctgacagattagattggtttgcattgcagACAAGCATTCAGAGATGAGCTTGATGTGCTACAACTAATACGGCATCCGAATGTCGTGCAATTTTTAGGTGCTGTAACACAAAGCAGCCCAATGATGATT
                        ccctgac  putative branch site (score: 3)
            aaaaatgta  TA-rich tract