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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCGgttatgctcaattctcatctccttcatgcaaaacgttgggatattttcctcgtcctgttatctgtgtgcaaaaaattgacagttctctgcatttccttag

Basic information

species Oryza sativa
transcript LOC_Os04g45190.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g45190.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G155543_T01 (Zea mays), 5'ss of exon 3
GTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCGgttatgct-------caattctcatctccttcatgcaaaacgt-tgggatattttcctcgtcctgttatctgt-gtgcaaaaaattgacagttctctgcatttccttag
|| ||||| || ||||| ||||||||||| ||| |||| ||||| ||||| ||||| || |||||||||||||||||||| ||| || |        |||  |||| |||||||   | ||     |  || ||   | ||  |  | |  || |  | ||||    |||| |  || |||| || || ||
GTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATCGTGCCACCTCGGTCCACCAGCGATGTCATTGgtaattccaacagaccaacactcacctccttccctccaagttcatttgacatgggcgtccccaagattactatcattcaaatgcctgac-gccctttgcaatttctcag

upper sequence: LOC_Os04g45190.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G155543_T04 (Zea mays), 5'ss of exon 2
------------------GTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCGgttatgct-------caattctcatctccttcatgcaaaacgt-tgggatattttcctcgtcctgttatctgt-gtgcaaaaaattgacagttctctgcatttccttag
                  || ||||| || ||||| ||||||||||| ||| |||| ||||| ||||| ||||| || |||||||||||||||||||| ||| || |        |||  |||| |||||||   | ||     |  || ||   | ||  |  | |  || |  | ||||    |||| |  || |||| || || ||
TGATTTTGAGTCCGACAGGTTAAGACGACGAGCCCGAAGAAGTACTGTGTCCGGCCCAACAGCGGCATCGTGCCACCTCGGTCCACCAGCGATGTCATTGgtaattccaacagaccaacactcacctccttccctccaagttcatttgacatgggcgtccccaagattactatcattcaaatgcctgac-gccctttgcaatttctcag
















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|163928274|gb|EG714654.1|EG714654
EST:     CAGTCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCG                         TAACAATGCAAGCCCAACGGGAGGCAC
genomic: CAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCGgttatgctca ... atttccttagTAACAATGCAAGCCCAACGGGAGGCAC
EST: gi|428790|gb|D24946.1|D24946
EST:     CAGGNCGAACAGTGGCATTGTGCCGCCACGGTNCACCAGCGATGTCATCG                         TAACAATGCAAG
genomic: CAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCGgttatgctca ... atttccttagTAACAATGCAAG
EST: gi|27547307|gb|CA765509.2|CA765509
EST:     CAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCG                         TAACAATGCAAGCCCAACGGGAGGCACCAGCAGACATGCAGTGCAAAGACA
genomic: CAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCGgttatgctca ... atttccttagTAACAATGCAAGCCCAACGGGAGGCACCAGCAGACATGCAGTGCAAAGACA
EST: gi|88317555|gb|CI672132.1|CI672132
EST:     CAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCG                         TAANAATGCAAGCCCAACGGGAGGCACCAGCAGACATGCAGTGCAAAGACA
genomic: CAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCGgttatgctca ... atttccttagTAACAATGCAAGCCCAACGGGAGGCACCAGCAGACATGCAGTGCAAAGACA
EST: gi|88330878|gb|CI636890.1|CI636890
EST:     CAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCG                         TAACAATGCAAGCCCAACGGGAGGCACCAGCAGACATGCAGTGCAAAGACA
genomic: CAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCGgttatgctca ... atttccttagTAACAATGCAAGCCCAACGGGAGGCACCAGCAGACATGCAGTGCAAAGACA
EST: gi|117238779|gb|CT842528.1|CT842528
EST:     CAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCG                         TAACAATGCAAGCCCAACGGGAGGCACCAGCAGACATGCAGTGCAAAGACA
genomic: CAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCGgttatgctca ... atttccttagTAACAATGCAAGCCCAACGGGAGGCACCAGCAGACATGCAGTGCAAAGACA
EST: gi|58606663|gb|CK034696.1|CK034696
EST:     CAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCG                         TAACAATGCAAGCCCAACGGGAGGCACCAGCAGACATGCAGTGCAAAGACA
genomic: CAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCGgttatgctca ... atttccttagTAACAATGCAAGCCCAACGGGAGGCACCAGCAGACATGCAGTGCAAAGACA
EST: gi|163929427|gb|EG713396.1|EG713396
EST:     CAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCG                         TAACAATGCAAGCCCAACGGGAGGCACCAGCAGACATGCAGTGCAAAGACA
genomic: CAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCGgttatgctca ... atttccttagTAACAATGCAAGCCCAACGGGAGGCACCAGCAGACATGCAGTGCAAAGACA

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: 48 (upstream exon), 42 (downstream exon)
Score: 22

GTCAAGACAACTAGCCCAAAGAAGTACTGCGTCAGGCCGAACAGTGGCATTGTGCCGCCACGGTCCACCAGCGATGTCATCGgttatgctca ... atttccttagTAACAATGCAAGCCCAACGGGAGGCACCAGCAGACATGCAGTGCAAAGACAAGTTTCTAGTGCAGAGCGTTGTGGTGACTGAAGGCACAACAACCAAGGA




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