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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgaacataatttcgcggttagagtttcaagctctagttaccaagtttaccatattttctttaacagtaatcctatctgttttccctccttgtgcttagGTCAAGGAATTGTGGAAAGCCCATATGAGGCACCAGGATCCTACAGAGACTTTGAACAAGGACATAATATCTCACTTTGTTCTCCGTCTTGTCTACTGCA

Basic information

species Oryza sativa
transcript LOC_Os07g22400.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g22400.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G130351_T01 (Zea mays), 3'ss of exon 2
-----cttgaacataatttcgcggttagagtttcaagctctagttaccaagtttaccatattttctttaacagtaatcctatctgttttccctccttgtgctt-agGTCAAGGAATTGTGGAAAGCCCATATGAGGCACCAGGATCCTACAGAGACTTTGAACAAGGACATAATATCTCACTTTGTTCTCCGTCTTGTCTACTGCA
     || || | || ||  |   ||||  || ||       |  | |    | |    ||||| |||  ||   ||   ||   || | |     ||  ||| ||||||| |||||||||||  | || ||| |||||||||||||  ||||||||||||| ||||| |||||||| |||||||| |||||||||||||||||||
gaaccctagaccctagttatgtacttagcattgcagcactctggcatcggtctaa----attttgttt--caaatataaaatgccttattctattctgcacttcagGTCAATGAATTGTGGAAGACACACATGGGGCACCAGGATCCAGCAGAGACTTTGAATAAGGATATAATATCACACTTTGTGCTCCGTCTTGTCTACTGCA

upper sequence: LOC_Os07g22400.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G044317_T04 (Zea mays), 3'ss of exon 2
cttgaacataatttcgcggttagagtttcaagctcta----gttaccaagtttaccatattttctttaacagtaatcctatctgttttccctccttgtgcttagGTCAAGGAATTGTGGAAAGCCCATATGAGGCACCAGGATCCTACAGAGACTTTGAACAAGGACATAATATCTCACTTTGTTCTCCGTCTTGTCTACTGCA
       |   ||| ||      ||||     |||||     ||      ||   |  | |||  ||   | ||    | ||| | |||  | ||     | ||||||  |||||||||||  | || |||||||||||||||||  |||||| |||||||||||| |||||||| |||||||| |||||||| ||||||||||
---atggaaggttttgcaaccctagttatggactctatcgcattctggcattgctctaacttttgttttaaatagaaatgtct-tgttctgttctgcacttcagGTCAGTGAATTGTGGAAGACACACATGAGGCACCAGGATCCAGCAGAGAATTTGAACAAGGATATAATATCGCACTTTGTGCTCCGTCTAGTCTACTGCA
















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|58665435|gb|CK054121.1|CK054121
EST:     TCGCCGACGGGCTCTCGCGAGGGAAGAGACCGGAGGAAATGGAGAAATTG                         GTCAAGGAATTGTGGAAAGCCCATATGAGGCACCAGGATCCTACAGAGACT
genomic: TCGCCGACGGGCTCTCGCGAGGGAAGAGACCGGAGGAAATGGAGAAATTGgtgagccgtc ... ttgtgcttagGTCAAGGAATTGTGGAAAGCCCATATGAGGCACCAGGATCCTACAGAGACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttaccatattttctttaacagtaatcctatctgttttccctccttgtgcttagGTCAAGGAATTGTGGAAAGCCCATATGAGGCACCAGGATCCTACAGAGACTTTGAACAAGGACATAATATCTCACTTTGTTCTCCGTCTTGTCTACTGCA
              ctttaac  putative branch site (score: 3)
                          tcctatctgttttccc  putative PPT
       atattttctttaaca  TA-rich tract