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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaccccagccaattaacatggctagtatgaaatattgtgaactgtgaaacacccaaatttttcagtcttaaatttatcctttttgtcatttctatgtagGTTTGGCCCCTTGATATAGAGATGAAGTTCCTGGAGCCATTTGGACGGGAACTACATTCCATGAAAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g56890.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56890.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G127453_T03 (Zea mays), 3'ss of exon 2
---aaaccccagccaattaacatggctagtatgaaatattgtgaactgtgaaacacccaaatttttcagtcttaaatttatcc-tttttgtcatttctatgtagGTTTGGCCCCTTGATATAGAGATGAAGTTCCTGGAGCCATTTGGACGGGAACTACATTCCATGAAAAAG
     |           |||  |||| |   |   |        | ||||||  |    |  ||    || | ||| ||| |  || || ||  || |||| |||| |||||| |||||||||| ||||||||||| |||||||||||||||||||||||||| |||||||| 
cattgatgattatttgataatttggccatctttggaagcaagtcaatgtgaattatatgatctt----gtttaaaacttaacaattcttttcccttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA

upper sequence: LOC_Os01g56890.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G132978_T01 (Zea mays), 3'ss of exon 2
------aaaccccagccaattaacatggctagtatgaaatattgtgaactgtgaaacacccaaatttttcagtcttaaatttatcctttttgtcatttctatgtagGTTTGGCCCCTTGATATAGAGATGAAGTTCCTGGAGCCATTTGGACGGGAACTACATTCCATGAAAAAG
      | || | |     | |   ||   | ||| | ||||| ||     |     |    |  |||| |     ||| ||| | ||||   |  || | || |||||||||||||||||||||| ||||||||||| |||||||||||||||||  ||||||| |||||||| 
ggcttcatactctatgttgt-acgttgatgattattagatattttgg-tcatattttatttgatctttttaa----aaacttaccattttccccccttgtgtgcagGTTTGGCCCCTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAGTTACATTCAATGAAAAAA

upper sequence: LOC_Os01g56890.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G127453_T02 (Zea mays), 3'ss of exon 2
---aaaccccagccaattaacatggctagtatgaaatattgtgaactgtgaaacacccaaatttttcagtcttaaatttatcc-tttttgtcatttctatgtagGTTTGGCCCCTTGATATAGAGATGAAGTTCCTGGAGCCATTTGGACGGGAACTACATTCCATGAAAAAG-------------------------------
     |           |||  |||| |   |   |        | ||||||  |    |  ||    || | ||| ||| |  || || ||  || |||| |||| |||||| |||||||||| ||||||||||| |||||||||||||||||||||||||| ||||||||                                
cattgatgattatttgataatttggccatctttggaagcaagtcaatgtgaattatatgatctt----gtttaaaacttaacaattcttttcccttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAAGTGAGTCTTTAGCATTAGACTTGTTTACATG

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|33799632|gb|CF325677.1|CF325677
EST:     AGTGCATCGTGCCCGGGCAGCAGGCGCCGCTGCGGCTGCTGGGCCTCAAG                         GTTTGGCCCCTTGATATAGAGATGAAGTTCCTGGAGCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGGCAGCAGGCGCCGCTGCGGCTGCTGGGCCTCAAGgtacgaaccg ... ttctatgtagGTTTGGCCCCTTGATATAGAGATGAAGTTCCTGGAGCCATTTGGACGGGAA
EST: gi|58592272|gb|CF990580.1|CF990580
EST:     AGTGCATCGTGCCCGGGCAGCAGGCGCCGCTGCGGCTGCTGGGCCTCAAG                         GTTTGGCCCCTTGATATAGAGATGAAGTTCCTGGAGCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGGCAGCAGGCGCCGCTGCGGCTGCTGGGCCTCAAGgtacgaaccg ... ttctatgtagGTTTGGCCCCTTGATATAGAGATGAAGTTCCTGGAGCCATTTGGACGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaacacccaaatttttcagtcttaaatttatcctttttgtcatttctatgtagGTTTGGCCCCTTGATATAGAGATGAAGTTCCTGGAGCCATTTGGACGGGAACTACATTCCATGAAAAAG
                            tttatcctttttgtca  CT-rich tract
          aaatttttcagtctta  TA-rich tract