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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATCAAGATCTTAGCAAATGCTGATGGAGTACGGTTGCTGCGCACATTGGAAAATCGTTCATTTGATGCTTCTCGGAGTGCGTCTGAGACTGTAACAAAGgtaagttcttgtgaccatttaaaattacaactaaatatttttgcaagcttgacccaatagatccatcttggtgcag

Basic information

species Oryza sativa
transcript LOC_Os03g14980.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G550865_T02 (Zea mays), 5'ss of exon 3
TATCAAGATCTTAGCAAATGCTGATGGAGTACGGTTGCTGCGCACATTGGAAAATCGTTCATTTGATGCTTCTCGGAGTGCGTCTGAGACTGTAACAAAGgtaagttcttgtgaccatttaaaattacaactaaatatttttgcaagcttgacccaatagatccatcttggtgcag
 ||||||||||||||||||||||||||| | ||||||||||||||  ||||||||||||| |||||||||||||| | ||| |||||| ||||||||||||| | | ||||| ||||   |||| | |    ||  || | ||||||| | | | |||  |||| | ||  |||||
CATCAAGATCTTAGCAAATGCTGATGGACTTCGGTTGCTGCGCACGCTGGAAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAGgtta-tgcttgtaaccac--aaaaattctgagaagaatatctgcaagcatcatctaatcaatccttgtttatgcag

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G030422_T02 (Zea mays), 5'ss of exon 17
TATCAAGATCTTAGCAAATGCTGATGGAGTACGGTTGCTGCGCACATTGGAAAATCGTTCATTTGATGCTTCTCGGAGTGCGTCTGAGACTGTAACAAAGgtaagttcttgtgaccatttaaaattacaactaaatatttttgcaagcttgacccaatagatccatcttggtgcag
|||||||||||||||||||||||||||| | ||||||||||||||| ||||||||||||| |||||||||||||| | ||| |||||| ||||||||||||||| | || || ||||   ||||||    ||||  || | ||||||| |||   ||| ||||| | ||  |||||
TATCAAGATCTTAGCAAATGCTGATGGACTTCGGTTGCTGCGCACACTGGAAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAGgtaattactggtaaccac--aaaatt----ctaagaatatctgcaagcatgatgtaatcgatccttgtttatgcag
















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|58659010|gb|CK047690.1|CK047690
EST:     TGAGACTGTAACAAAG                         -CCCTAATGAATCCATTGACTGCTGCTGCTGCTGCGGCGGCGTCAGCTGC-
genomic: TGAGACTGTAACAAAGgtaagttctt ... cttggtgcagCCCCTAATGAATCCATTGACTGCTGCTGCTGCTGCGGCGGCGTCAGCTGCT
EST: gi|29671653|gb|CB667928.1|CB667928
EST:     AAAATCGTTCATTTGATGCTTCTCGGAGTGCGTCTGAGACTGTAACAAAA                         CCCCTAATGAATCCATTGACTGCTGCTGCTGCTGC
genomic: AAAATCGTTCATTTGATGCTTCTCGGAGTGCGTCTGAGACTGTAACAAAGgtaagttctt ... cttggtgcagCCCCTAATGAATCCATTGACTGCTGCTGCTGCTGC
EST: gi|44675806|gb|CR289240.1|CR289240
EST:     AAATCGTTCATTTGATGCTTCTCAGGAGTGCGTCTGAGACTGTAACAAAG                         CCCCTAATTGA-TCCATTTGACTGCTGCT
genomic: AAATCGTTCATTTGATGCTTCTC-GGAGTGCGTCTGAGACTGTAACAAAGgtaagttctt ... cttggtgcagCCCCTAAT-GAATCCATT-GACTGCTGCT

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), 67 (downstream exon)
Score: 88

TATCAAGATCTTAGCAAATGCTGATGGAGTACGGTTGCTGCGCACATTGGAAAATCGTTCATTTGATGCTTCTCGGAGTGCGTCTGAGACTGTAACAAAGgtaagttctt ... cttggtgcagCCCCTAATGAATCCATTGACTGCTGCTGCTGCTGCGGCGGCGTCAGCTGCTGCTGCCGGGACTAGTTCAGGAAATGCTGCTCCACCGGCAATAACTGCAC




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