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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCACGGCGGTGCGGTGACCGGAGGTCGGAGAGAAGTTCGGTGGTGGGCGACAACAGGAATGGATACGTCGAGACTGACCCAACTGGTCGCTATGGCCGGgtaatttatttacttcttcttcttgcaatctgaacttgctcactttcttattccaaagagaaatttgacttgtttcctttcaaagttcaatattatcatg...

Basic information

species Oryza sativa
transcript LOC_Os12g02250.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g02250.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G032619_T01 (Zea mays), 5'ss of exon 2
TGCACGGCGGTGCGGTGAC--CGGAGGTCGGAGAGA-AGTTCGGTGGTGGGCGACAACAGGAATGGATACGTCGAGACTGACCCAACTGGTCGCTATGGCCGGgta---atttatt-tacttcttcttcttgcaatctgaacttgctcactttcttattccaaagagaaatttgacttgtttcctttcaaagttcaatattatcatg
   |||||||||||| | |  | |  |||||   || ||  ||| || ||| ||||||   || |||||||||||||||||||| || ||||||||||| ||||||   |   |   |    |||| ||||    |      |||||  || | |  | |||       ||| ||  |         ||   | ||  ||  || | 
---ACGGCGGTGCGGCGGCGTCCGGCGTCGGCTGGATAGGGCGGCGGCGGGAGACAACGCCAACGGATACGTCGAGACTGACCCCACCGGTCGCTATGGACGGgtacgcacgcagcatgtcccttcctcttcttcttcttctttgctttctct-tcctgccatttgctgattggatatacacgtacgca---tgcagcatgttcttc
















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|88723325|gb|CI746835.1|CI746835
EST:     ACAACAGGAATGGATACGTCGAGACTGACCCAACTGGTCGCTATGGCCGG                         TTGTCGGAGGTGCTGGGGAAGGGTGCGATGAAGACGGTGTACCGAGGGTTC
genomic: ACAACAGGAATGGATACGTCGAGACTGACCCAACTGGTCGCTATGGCCGGgtaatttatt ... atgtgtgcagTTGTCGGAGGTGCTGGGGAAGGGTGCGATGAAGACGGTGTACCGAGGGTTC
EST: gi|88419624|gb|CI686842.1|CI686842
EST:     ACAACAGGAATGGATACGTCGAGACTGACCCAACTGGTCGCTATGGCCGG                         TTGTCGGAGGTGCTGGGGAAGGGTGCGATGAAGACGGTGTACCGAGGGTTC
genomic: ACAACAGGAATGGATACGTCGAGACTGACCCAACTGGTCGCTATGGCCGGgtaatttatt ... atgtgtgcagTTGTCGGAGGTGCTGGGGAAGGGTGCGATGAAGACGGTGTACCGAGGGTTC
EST: gi|88730740|gb|CI754353.1|CI754353
EST:     ACAACAGGAATGGATACGTNGAGACTGACCCAACTGGTCGCTATGGCCGG                         TTGTCGGAGGTGCTGGGGAAGGGTGCGATGAACACGGTGTACCGAGGGTTC
genomic: ACAACAGGAATGGATACGTCGAGACTGACCCAACTGGTCGCTATGGCCGGgtaatttatt ... atgtgtgcagTTGTCGGAGGTGCTGGGGAAGGGTGCGATGAAGACGGTGTACCGAGGGTTC
EST: gi|88425298|gb|CI564815.1|CI564815
EST:     ACAACAGGAATGGATACGTCGAGACTGACCCAAGTGGTCGCTATGGCCGG                         TTGTCGGAGGTGCTGGGGAAGGGTGCGATGAACACCGTGTAACGAGGGTTA
genomic: ACAACAGGAATGGATACGTCGAGACTGACCCAACTGGTCGCTATGGCCGGgtaatttatt ... atgtgtgcagTTGTCGGAGGTGCTGGGGAAGGGTGCGATGAAGACGGTGTACCGAGGGTTC
EST: gi|88449954|gb|CI572085.1|CI572085
EST:     ACAACAGGAATGGATACGTCGAGACTGACCCAACTGGTCGCTATGGCCGG                         TTGTCGGAGGTGCTGGGGAAGGGTGCGATGAAGACGGTGTACCGAGGGTTC
genomic: ACAACAGGAATGGATACGTCGAGACTGACCCAACTGGTCGCTATGGCCGGgtaatttatt ... atgtgtgcagTTGTCGGAGGTGCTGGGGAAGGGTGCGATGAAGACGGTGTACCGAGGGTTC
EST: gi|88369410|gb|CI580432.1|CI580432
EST:     ACAACAGGAATGGATACGTCGAGACTGACCCAACTGGTCGCTATGGCCGG                         TTGTCGGAGGTGCTGGGGAAGGGTGCGATGAAGACGGTGTACCGAGGGTTC
genomic: ACAACAGGAATGGATACGTCGAGACTGACCCAACTGGTCGCTATGGCCGGgtaatttatt ... atgtgtgcagTTGTCGGAGGTGCTGGGGAAGGGTGCGATGAAGACGGTGTACCGAGGGTTC

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: 57 (upstream exon), 73 (downstream exon)
Score: 35

TGCACGGCGGTGCGGTGACCGGAGGTCGGAGAGAAGTTCGGTGGTGGGCGACAACAGGAATGGATACGTCGAGACTGACCCAACTGGTCGCTATGGCCGGgtaatttatt ... atgtgtgcagTTGTCGGAGGTGCTGGGGAAGGGTGCGATGAAGACGGTGTACCGAGGGTTCGACGAGCTGCGGGGGGTGGAGGTGGCGTGGAACCAGGCCACCATCTCCG




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