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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACTTGGGAAGAACTGGATGCAGGAGAGATGACCTTGAATCCCTTGCATACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAGgttaattttgattgattttatgacttttttgttgctacatgcactaatttcgttttgtaattcatgaatgaacttag

Basic information

species Oryza sativa
transcript LOC_Os01g10150.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10150.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G045259_T02 (Zea mays), 5'ss of exon 9
CCACTTGGGAAGAACTGGATGCAGGAGAGATGACCTTGAATCCCTTGCATACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAGgttaattttgattgattttatgacttttttgttgctacatgcactaatttcgttttgtaattcatgaatgaacttag------------------------------
||||||||||||||||||  | ||||||||||| ||||||||||| |||||||| |||||||| ||||||||||||||||| ||||||||||||| ||| |||| | | | ||||| || ||      || ||  |||    |||  |||  | || | ||| |   |   ||  |                               
CCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTCCGTGGCCGCCTCCCTTGGCAAGGATACCAAgttagtgtag-ttgatgttctgctcacctttttcttactcctactctttttttgtttttatttaaatactcacaaattttttatctgttattcttcaatcaatttag

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA04G09080.1 (Glycine max), 5'ss of exon 9
CCACTTGGGAAGAACTGGATGCAGGAGAGATGACCTTGAATCCCTTGCATACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAGgttaattttgattgattttatgacttttttgttgcta-catgcactaatttcgtt-ttgtaattcatgaatgaacttag
|||  | || ||||| ||  |||||||||||||| | ||||| ||||| ||||| ||| | || ||||| ||||| || || ||||||||||||| |||||||| | ||  || |  |  | | |||  |  |  |   |      ||| |  || || | |||  |   |      ||
CCATCTTGGTAGAACAGGTAGCAGGAGAGATGACTTGGAATCTCTTGCTTACACTCTTGTCTTTCTTCTTCGTGGTCGGCTACCTTGGCAAGGATACCAGgttattattccttcaaatagtcattttagtactaatggtaaatgaaaatatgattcttatgatttttt--ttgttacag

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA06G09190.1 (Glycine max), 5'ss of exon 9
CCACTTGGGAAGAACTGGATGCAGGAGAGATGACCTTGAATCCCTTGCATACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAGgttaattttgattgattttatgacttttttgttgctacatgcactaatttcgttttgtaattcatgaatgaacttag-----
 ||  | ||  |||| ||  |||||||||||||| | ||||| ||||| ||||| ||| | || ||||| ||||| || || |||||||||||||  ||||||| | ||| || |    ||     ||||  | |||  || |  |||     | ||    | |||||     ||       
TCATCTTGGTCGAACAGGTAGCAGGAGAGATGACTTGGAATCTCTTGCTTACACTCTTGTCTTTCTTCTTCGTGGTCGGCTACCTTGGCAAGGATATCAGgttattattgtttca---aatagtcattttagtactaattgta--aatgaaaatatgactcttatgaaactttttgttacag

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 9
CCACTTGGGAAGAACTGGATGCAGGAGAGATGACCTTGAATCCCTTGCATACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAGgttaattttgattgattttatgac----ttttttgttgctacatgcactaatttcgttttgtaattcatgaatgaacttag------------------------------------------------
 || ||||| ||||||||  | |||||||||||  | ||||| ||||| ||||| ||||||||||| |||||||| || || ||||||||||| |  ||||||   |    | ||  ||  ||     ||| ||  | ||        | |  |     |  ||||  |   |   |||                                                  
TCATTTGGGGAGAACTGGCAGTAGGAGAGATGATTTGGAATCTCTTGCTTACACTCTTATTTTCCTCCTCCGTGGTCGTCTACCTTGGCAAGGTTATCAGgttggctccattcgaagttccgataaaatttgttccttctcttcaatttgaagttccgataaaatttgttccttgtcttcctttcaagtttttgacttgatttttttgttcttaaaatcccatatatag

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 5'ss of exon 9
CCACTTGGGAAGAACTGGATGCAGGAGAGATGACCTTGAATCCCTTGCATACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAGgttaattttgattgattttatgacttttttgttgctacatgcactaatttcgttttgtaattcatgaatgaacttag
 ||| | ||||| |||||| |||| ||||||||  | ||||| ||||| ||||| || ||||| ||||||||||| || |||||||||||||| | ||||||| |   |     |  |||       |||  |  ||  ||      |      || | |  ||  |      ||||
TCACCTTGGAAGGACTGGAAGCAGAAGAGATGATTTGGAATCTCTTGCTTACACCCTCATTTTTCTTCTCCGTGGACGGCTGCCTTGGCAAGGTTACCAGgttgacagtttccaaacttaaataggattttcttttatgtgattctgtacatcattctgaaccaacagcttctttag

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|58696276|gb|CK084963.1|CK084963
EST:     CACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGTGCAAGGATTCCAG                         TGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCA
genomic: CACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTG-GCAAGGATTCCAGgttaattttg ... atgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCA
EST: gi|88573975|gb|CI665744.1|CI665744
EST:     ACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAG                         GGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTC
genomic: ACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAGgttaattttg ... atgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTC
EST: gi|29645031|gb|CB650038.1|CB650038
EST:     ACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAG                         GGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCA
genomic: ACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAGgttaattttg ... atgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCA
EST: gi|29670785|gb|CB667060.1|CB667060
EST:     ACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAG                         GGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCA
genomic: ACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAGgttaattttg ... atgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCA