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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCGATCTCTTGATGGAGTTAGGAGCTGGGATAGAGTTAGCTACGGCAGCTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAGgtttgacctagcggtttactgtgacgagtcctaacattaatatggcttgtttgataaagttactgtaatgaaccctttttgtacctgcaaatgtactgaagattgttctacttgatgaaattgttacattcag

Basic information

species Oryza sativa
transcript LOC_Os05g34650.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g34650.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G833124_T01 (Zea mays), 5'ss of exon 5
TGGCGATCTCTTGATGGAGTTAGGAGCTGGGATAGAGTTAGCTACGGCAGCTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAGgtttgacctagcggtttactgtgacgagtcctaa--cattaatatggcttgtttgataaagttactgtaatgaaccctttttgtacctgcaaatgtactgaagattgttctacttgatgaaattgttacattcag
||| |||||||||||||||||||||||||||||||| |||||||| ||||||||||| || ||||||||||| ||||| ||||| |||||||||||||||||||| ||||  | |||  ||  ||  |    |     ||  ||| |  ||||   |||  ||  |    ||    | ||    |   |   ||| | || |   |  | |  |||||| | ||  | |  ||||
TGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAATTAGCTACTGCAGCTTTCCCACAGCTTTTCCTACCAATGGCATGCATAGCAAATGTTGTTAAGgtttgtcctactgatttgttgcaacttgcaacaggttcttgctatagtatgtt-actaatatttttaacttg----ccttgcaaaatgggtgatgaaatgtattctact-tgtttgatgcattttctcctatcag
















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|428047|gb|D24195.1|D24195
EST:     CTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAG                         AATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACAAGGCA
genomic: CTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAGgtttgaccta ... ttacattcagAATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACAAGGCA
EST: gi|38475296|gb|CF959429.1|CF959429
EST:     CTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAG                         AATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACAAGGCA
genomic: CTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAGgtttgaccta ... ttacattcagAATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACAAGGCA
EST: gi|428912|gb|D25068.1|D25068
EST:     CTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAG                         AATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACAAGGCA
genomic: CTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAGgtttgaccta ... ttacattcagAATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACAAGGCA
EST: gi|58666538|gb|CK055224.1|CK055224
EST:     CTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAG                         AATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACAAGGCA
genomic: CTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAGgtttgaccta ... ttacattcagAATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACAAGGCA
EST: gi|58684548|gb|CK073235.1|CK073235
EST:     CTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAG                         AATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACAAGGCA
genomic: CTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAGgtttgaccta ... ttacattcagAATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACAAGGCA
EST: gi|58686301|gb|CK074988.1|CK074988
EST:     CTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAG                         AATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACA
genomic: CTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAGgtttgaccta ... ttacattcagAATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACA
EST: gi|218493919|gb|FG945282.1|FG945282
EST:     CTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAG                         AATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACAAGGCA
genomic: CTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAGgtttgaccta ... ttacattcagAATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACAAGGCA
EST: gi|29645586|gb|CB650593.1|CB650593
EST:     CTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAG                         AATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACAAGGCA
genomic: CTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAGgtttgaccta ... ttacattcagAATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACAAGGCA
EST: gi|58674742|gb|CK063429.1|CK063429
EST:     CTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAG                         AATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACAAGGCA
genomic: CTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAGgtttgaccta ... ttacattcagAATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACAAGGCA

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: 65 (upstream exon), 72 (downstream exon)
Score: 50

TGGCGATCTCTTGATGGAGTTAGGAGCTGGGATAGAGTTAGCTACGGCAGCTTTCCCTCAACTTTTCCTACCTATGGCTTGCATCGCAAATGTTGTTAAGgtttgaccta ... ttacattcagAATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACAAGGCATATGCAAAAGGAGAAAATATTGGAGATGTCACTGCCAAAGGAGAAAGTG




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