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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTAAGCAGGAATTTCCCAGAAAAGGAATCCCCCCTGCTCCACCGAAGCATGCCTTTTCAAGAATAAATTCAAGCAGGGTGCTTCTAGAAGAGgttagccgttatgtatattgattaatttttgctttgttcgatgtcaaatactacattcagttgtgcttagcctttttgaccggtggttcttgaaatgttttgtttgcag

Basic information

species Oryza sativa
transcript LOC_Os06g43560.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g43560.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G093065_T01 (Zea mays), 5'ss of exon 4
CTTAAGCAGGAATTTCCCAGAAAAGGAATCCCCCCTGCTCCACCGAAGCATGCCTTTTCAAGAATAAATTCAAGCAGGGTGCTTCTAGAAGAGgttagccgtt------------atgtatattgattaatttttgctttgttcg--atgtcaaata------ctacattcagttgtg--------cttagcctttttgaccggtggttcttgaaatgttttgtttgcag
||||||   |  |||||||||||||   ||||  | ||||| ||||||||||| || | ||||||||||||||||||| |||||||||||||||| |   ||             |||||  ||  ||| |||   |  | |||    |||||| |        ||| |  ||  ||         | |   ||  ||  | | |   |||  || |||| || ||||||
CTTAAGAGCGCGTTTCCCAGAAAAGATGTCCCATCGGCTCCTCCGAAGCATGCTTTCTTAAGAATAAATTCAAGCAGGTTGCTTCTAGAAGAGgtaaaatgtatcttaaaactcaatgtacttttgttagtttccccccttttccctgtgtcaattggatgctttacgtcaagcagtatactatttcgtgttctgcttctcggatttgtctcaaattgttatggttgcag

upper sequence: LOC_Os06g43560.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G131070_T01 (Zea mays), 5'ss of exon 4
CTTAAGCAGGAATTTCCCAGAAAAGGAATCCCCCCTGCTCCACCGAAGCATGCCTTTTCAAGAATAAATTCAAGCAGGGTGCTTCTAGAAGAGgttagccgt-------------------tatgtatattgattaatttttgctttgttcgatgtcaa------------------atactacattcagttgtgcttagcctttttgaccggtggttcttgaaatgttttgtttgcag
||||||   | ||||||||||||||    |||  | ||||| ||||||||||| || | ||||||||||||||||||| |||||||||||||||| |    |                   | |||  |||  |||||||   |||    | |||||||                  ||| || | ||  ||||  |  || | || |||  ||    ||  || | || || ||||||
CTTAAGAGCGCATTTCCCAGAAAAGATGCCCCGTCGGCTCCTCCGAAGCATGCTTTCTTAAGAATAAATTCAAGCAGGTTGCTTCTAGAAGAGgtaaaatatattttaaaactcaatgtactttgttaattacttaatttcctcttctccctatgtcaactggatgctttacgtgaaatagtatactcttttgtattctgcttcttggacttgt----ctcaaactattatgattgcag
















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|58606206|gb|CK034239.1|CK034239
EST:     CGAAGCATGCCTTTTCAAGAATAAATTCAAGCAGGGTGCTTCTAGAAGAG                         AGAAGGAACGCTTGGGAGGAGTGGATGCAAAAGCTACTTTCTGACATTGAG
genomic: CGAAGCATGCCTTTTCAAGAATAAATTCAAGCAGGGTGCTTCTAGAAGAGgttagccgtt ... ttgtttgcagAGAAGGAACGCTTTGGAGGAGTGGATGCAAAAGCTACTTTCTGACATTGAG
EST: gi|29636297|gb|CB641306.1|CB641306
EST:     CGAAGCATGCCTTTTCAAGAATAAATTCAAGCAGGGTGCTTCTAGAAGAG                         AGAAGGAACGCTTTGGAGGAGTGGATGCAAAAGCTACTTTCTGACATTGAG
genomic: CGAAGCATGCCTTTTCAAGAATAAATTCAAGCAGGGTGCTTCTAGAAGAGgttagccgtt ... ttgtttgcagAGAAGGAACGCTTTGGAGGAGTGGATGCAAAAGCTACTTTCTGACATTGAG
EST: gi|29636296|gb|CB641305.1|CB641305
EST:     CGAA-CATGCCTTTCCAAGAATAAATTCAAGCAGGGTGCTTCTAGAAGAG                         AGAAGGAACGCTTTGGAGGAGTGGATGCAAAAGCTACTTTCTGACATTGAG
genomic: CGAAGCATGCCTTTTCAAGAATAAATTCAAGCAGGGTGCTTCTAGAAGAGgttagccgtt ... ttgtttgcagAGAAGGAACGCTTTGGAGGAGTGGATGCAAAAGCTACTTTCTGACATTGAG
EST: gi|12405104|gb|AU166705.1|AU166705
EST:     CGAAGCATGCCTTTTCAAGAATAAATTCAAGCAGGGTGCTTCTAGAAGAG                         AGAAGGAACGCTTTGGAGGAGTGGATGCAAAAGCTACTTTCTGACATTGAG
genomic: CGAAGCATGCCTTTTCAAGAATAAATTCAAGCAGGGTGCTTCTAGAAGAGgttagccgtt ... ttgtttgcagAGAAGGAACGCTTTGGAGGAGTGGATGCAAAAGCTACTTTCTGACATTGAG
EST: gi|29625298|gb|CB630309.1|CB630309
EST:     CGAAGCATGCCTTTTCAAGAATAAATTCAAGCAGGGTGCTTCTAGAAGAG                         AGAAGGAACGCTTTGGAGGAGTGGATGCAAAAGCTACTTTCTGACATTGAG
genomic: CGAAGCATGCCTTTTCAAGAATAAATTCAAGCAGGGTGCTTCTAGAAGAGgttagccgtt ... ttgtttgcagAGAAGGAACGCTTTGGAGGAGTGGATGCAAAAGCTACTTTCTGACATTGAG

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: 71 (upstream exon), 52 (downstream exon)
Score: 13

CTTAAGCAGGAATTTCCCAGAAAAGGAATCCCCCCTGCTCCACCGAAGCATGCCTTTTCAAGAATAAATTCAAGCAGGGTGCTTCTAGAAGAGgttagccgtt ... ttgtttgcagAGAAGGAACGCTTTGGAGGAGTGGATGCAAAAGCTACTTTCTGACATTGAGTTGTCGAGAAGTGCACCTGTTGCTGCTTTTCTTGAGCTGGAAGCTGCTG




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