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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGGAATATCTAGTCTTAAAGTTGTgtaagtacaattcctggtgctgagtgcttggctgcaaacaatcttgaatgtgataaattttacccccttgttctttcag

Basic information

species Oryza sativa
transcript LOC_Os01g59440.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59440.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G815009_T01 (Zea mays), 5'ss of exon 4
GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGGAATATCTAGTCTTAAAGTTGTgtaagta-----caattcctggtgctgagtgcttgg----ctgcaaac-aatcttgaatgtgataaattttacccccttgttctttcag
|||||||||||||||||  ||||||||||| ||||||||||||||  | |||||||||||||| |||||||||||||||     ||||| |   || | ||   |       || || |  | |  | ||| ||| || | |  || ||||| ||||||||
GCGGCTCAATGGCAATCATTTGACTGGGCCGATCCCAAGGGAACTTTCTGGAATATCTAGTCTCAAAGTTGTgtaagtaaatatcaatttcaaatgtttagcattctattctctccagattagtgctcaatttgacaa-tctacccaccttgctctttcag

upper sequence: LOC_Os01g59440.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G121820_T01 (Zea mays), 5'ss of exon 4
GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGGAATATCTAGTCTTAAAGTTGTgtaagtacaattc-----ctggtgctgagtgcttggctg----caaac-aatcttgaatgtgataaattttacccccttgttctttcag
||| |||||||||||||  ||||||||||| |||||||||||||| || |||||||||||||| |||||||||| ||||||  ||     |   || | ||   |    |     || || |||  | ||| | | || | |  || |||| || ||||||
GCGTCTCAATGGCAATCATTTGACTGGGCCCATCCCAAGGGAACTCGCTGGAATATCTAGTCTCAAAGTTGTgtgagtacacgtcagcctcaaatgtttagaattctattctttccacactaatactcaattttacaa-tctacccaccttattatttcag
















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|2317317|gb|C22371.1|C22371
EST:     ACTGGGCCAATCCCAAGGGAACTGGCCGGAATATCTAGGCTTAAAGTTGT                         TGATGTTTCAAGCAATGATCTGTGTGGAACAATTCCTTACATCAGGGACCA
genomic: ACTGGGCCAATCCCAAGGGAACTGGCCGGAATATCTAGTCTTAAAGTTGTgtaagtacaa ... gttctttcagTGATGTTTCAAGCAATGATCTGTGTGGAACAATTCCT-ACATCAGG-ACCA
EST: gi|27577115|gb|CA999809.1|CA999809
EST:     ACTGGGCCAATCCCAAGGGAACTGGCCGGAATATCTAGTCTTAAAGTTGT                         TGATGTTTCAAGCAATGATCTGTGTGGAACAATTCCTACATCAGGACCATT
genomic: ACTGGGCCAATCCCAAGGGAACTGGCCGGAATATCTAGTCTTAAAGTTGTgtaagtacaa ... gttctttcagTGATGTTTCAAGCAATGATCTGTGTGGAACAATTCCTACATCAGGACCATT

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: 70 (upstream exon), 72 (downstream exon)
Score: 178

GCGGCTCAATGGCAATCGCTTGACTGGGCCAATCCCAAGGGAACTGGCCGGAATATCTAGTCTTAAAGTTGTgtaagtacaa ... gttctttcagTGATGTTTCAAGCAATGATCTGTGTGGAACAATTCCTACATCAGGACCATTTGAGCACATTCCCCTAAGCAAGTAAGTTTGACTGCCTTTGTGATACTAT




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