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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATGgtaagtttagtttccatgcattccatctaatttcatgaaaaatatattttttacaaaaggtactcgatccattctcttctctagagcag

Basic information

species Oryza sativa
transcript LOC_Os12g03860.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03860.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G877788_T03 (Zea mays), 5'ss of exon 2
CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATGgtaagttta---gtttccatgc-----attccatctaatttcatgaaaa-----atatatttttt-------------acaaaaggtactcgatccattctctt-ctctagagcag-----------------
||||||||||| | ||| ||||||||||||| ||||||||||||||  |    || | | |||     ||||  |||  |    |||||       |  ||||| |              |||  |    ||  ||  || |||| |||   |                     
CTCTGCCAATCACGTCCCTGTTCCCCTTCCTCTACTTCATGgtaagcctgcctgtctgcctgcctgccattctttctgttgctctgaaatcatccgtgcattttctttctttttatttggcaagggactttccttctcttttctttctcctaatttatagtggtgaccaaacag
















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|87008889|gb|CI304832.1|CI304832
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATG                         ATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATGgtaagtttag ... tctagagcagATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|33795182|gb|CF323464.1|CF323464
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATG                         AGCAGATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATGgtaagtttag ... tctagagcagA-----TAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCT
EST: gi|88571513|gb|CI662886.1|CI662886
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATG                         ATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATGgtaagtttag ... tctagagcagATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|88372054|gb|CI641689.1|CI641689
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATG                         ATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATGgtaagtttag ... tctagagcagATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|88694564|gb|CI738602.1|CI738602
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATG                         ATAAGAGACTTGCATGTCGCTCGGACAGAGGAAGATATCGGAT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATGgtaagtttag ... tctagagcagATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGAT
EST: gi|33692622|gb|CF320861.1|CF320861
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATG                         ATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATGgtaagtttag ... tctagagcagATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|33677540|gb|CF305779.1|CF305779
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATG                         ATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATGgtaagtttag ... tctagagcagATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|88342532|gb|CI637108.1|CI637108
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATG                         ATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATGgtaagtttag ... tctagagcagATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT

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: 44 (upstream exon), 75 (downstream exon)
Score: 7

CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATGgtaagtttag ... tctagagcagATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG




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