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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaacatgcccgcttgctcgatcgtcaattcctacttccccgtatttccgttcgttcggtttgcgctgaatcggccagtgacagtgagtgtgaatcgatggatgttgaattcgacgaccttgctgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCGCCGCTCGACGACGACGCCGGCGCCGCCGTCATCGCGCACGCCTTCCGCC

Basic information

species Oryza sativa
transcript LOC_Os01g43090.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43090.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G024315_T01 (Zea mays), 3'ss of exon 1
-----gtgaacatgcc--cgcttgctcgatcgtcaatt--cctacttccccgtatttccgttcgttcggtttgcgctgaatcggccagtgacagtgagtg---tgaatcgatggatgttgaattcgacgaccttgc-tgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCGCCGCTCGACGACGACGCCGGCGCCGCCGTCATCGCGCACGCCTTCCGCC
      |  |  | ||  || | ||     |   ||||  | |  | |  ||    | | | || || ||    |     ||| || ||| |  ||| ||    || |||   |||  ||| | | |   || | | ||||||||||||||||||||||||||||||||||||| ||||||||||||||||| ||||| |||||||| ||||||  |||||||||||||||||| ||| |||
gtctcttttatctcccaacgttcgcctctccccgaattatcttgttgcggcggccgtgcctccgctctgtcgttgtccggtcgcccggtg-ctttgattgaatcgactcggccgat--tgattccaatttccatccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCCCCGCTGGACGACGAGGCCGGCATCGCCGTCATCGCGCACGCTTTCAGCC
















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|15072292|gb|D40458.2|D40458
EST:     CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
genomic: CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAGgtgaacatgc ... cttgctgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
EST: gi|88421693|gb|CI586662.1|CI586662
EST:     CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
genomic: CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAGgtgaacatgc ... cttgctgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
EST: gi|58689204|gb|CK077891.1|CK077891
EST:     GCCTCGAGT-AAGCTCGGCACCCGGGGCCTAGAG                         GTGT-CAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
genomic: GCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAGgtgaacatgc ... cttgctgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
EST: gi|88447787|gb|CI576983.1|CI576983
EST:     CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
genomic: CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAGgtgaacatgc ... cttgctgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
EST: gi|29638513|gb|CB643522.1|CB643522
EST:     CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
genomic: CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAGgtgaacatgc ... cttgctgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
EST: gi|88353692|gb|CI633083.1|CI633083
EST:     CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
genomic: CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAGgtgaacatgc ... cttgctgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
EST: gi|88313245|gb|CI594875.1|CI594875
EST:     CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
genomic: CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAGgtgaacatgc ... cttgctgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
EST: gi|88301464|gb|CI597157.1|CI597157
EST:     CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
genomic: CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAGgtgaacatgc ... cttgctgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
EST: gi|88410056|gb|CI573295.1|CI573295
EST:     CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
genomic: CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAGgtgaacatgc ... cttgctgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
EST: gi|25798009|gb|CA753970.1|CA753970
EST:     CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
genomic: CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAGgtgaacatgc ... cttgctgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
EST: gi|88370552|gb|CI590130.1|CI590130
EST:     CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAATTCG
genomic: CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAGgtgaacatgc ... cttgctgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
EST: gi|29682107|gb|CB678382.1|CB678382
EST:     CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
genomic: CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAGgtgaacatgc ... cttgctgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
EST: gi|88359539|gb|CI621070.1|CI621070
EST:     CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG
genomic: CTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAGgtgaacatgc ... cttgctgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 74 (downstream exon)
Score: 43

TCACTCTCACTCCCCCTGCGACCGCCGCCGAGAGGCCATGGCGGAGCAAGCTCCACTGGCGCCGATGCCTCGAGTCAAGCTCGGCACCCGGGGCCTAGAGgtgaacatgc ... cttgctgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCGCCGCTCGACGACGACGCCGGCGCCGCCGTCATCGCGCACGCCTTCCGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccagtgacagtgagtgtgaatcgatggatgttgaattcgacgaccttgctgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCGCCGCTCGACGACGACGCCGGCGCCGCCGTCATCGCGCACGCCTTCCGCC
                                            ccttgct  CT-rich tract
                               ttgaatt  TA-rich tract