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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACCGGCCAGCAACCCCACCAGATGGCGAGGACGAATTTACTGATGATGATGGTACTGTTTACAAGTGGGATCGTGTCCTGAGGGCATGGGTTCCTCAAgtgagtgcttccaacctcctgttcttaggttcatttactcatgacttttgtttttggtagttctgattttgcctgagatattaattagatattgtgtttt...

Basic information

species Oryza sativa
transcript LOC_Os04g41910.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41910.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G074351_T01 (Zea mays), 5'ss of exon 3
TGACCGGCCAGCAACCCCACCAGATGGCGAGGACGAATTTACTGATGATGATGGTACTGTTTACAAGTGGGATCGTGTCCTGAGGGCATGGGTTCCTCAAgtgagtgcttccaacctcctgttcttaggttcatttactcatgacttttgtttttggtagttc-tgattttgcctgagatattaattagatattgtgtttt
||| ||||||||||||||||| || || |||   |||||||||||||||||||| ||  ||||||| ||||| |||    |||||||||||||||||||||||||| || |  | ||    ||   | |   |  ||   |       |  ||       ||  |    |  | |   |      |||| | |   ||   
TGAGCGGCCAGCAACCCCACCGGACGGAGAGTCAGAATTTACTGATGATGATGGCACCATTTACAAATGGGACCGTACTTTGAGGGCATGGGTTCCTCAAgtgagtactgcttatctgtccttgccatggctagctaaatacactgcctagttccatccattaattgactgactttccaccaagcttaggtctctagtac-

upper sequence: LOC_Os04g41910.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G171660_T03 (Zea mays), 5'ss of exon 3
TGACCGGCCAGCAACCCCACCAGATGGCGAGGACGAATTTACTGATGATGATGGTACTGTTTACAAGTGGGATCGTGTCCTGAGGGCATGGGTTCCTCAAgtgagtgcttccaacctcctgttcttaggttcatttactcatgacttttgtttttggtagtt--ctgattttgcctgagatattaattagatattgtgtttt
||| |||||||||||||| || ||||| ||||| |||||||||||||||||||| ||  ||||||| ||||| |||    |||||||||||||||||||||||||| || | || ||    ||   | |   |  ||   |       |  ||     |||    |||||     |     ||| | |  ||   || |   
TGAGCGGCCAGCAACCCCCCCTGATGGAGAGGAAGAATTTACTGATGATGATGGCACCATTTACAAATGGGACCGTACTTTGAGGGCATGGGTTCCTCAAgtgagtactgctaatctgtctttgccatgactagctaaatacactgcctagttccaccagtcgattgattgactttccaccattgaattcatga-gtctcc-

upper sequence: LOC_Os04g41910.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA20G36110.1 (Glycine max), 5'ss of exon 4
TGACCGGCCAGCAACCCCACCAGATGGCGAGGACGAATTTACTGATGATGATGGTACTGTTTACAAGTGGGATCGTGTCCTGAGGGCATGGGTTCCTCAAgtgagtgcttccaacctcctgttcttaggttcatttactcatgacttttgtttttggtagttctgattttgcctgagatattaattag-atattgtgtttt
|||  | ||  | || ||||| || || || || | |||||||||||||||||| ||||| || ||||||||| |    || || || |||||||| || ||  |||| |   |  |   | | |||   ||||   |     | |||| ||  |   |    |  | | ||| | ||| ||  ||   ||||| || || 
TGAGAGACCTTCGACGCCACCTGAGGGTGAAGAAGGATTTACTGATGATGATGGAACTGTATATAAGTGGGATAGGAGTCTTAGAGCTTGGGTTCCCCAGgtccgtgcattacatgtgtcgctattattatcatcatcatcatattttttttaatctcatactttgtgtggccagtgatgttctttgttatattatgatt-

upper sequence: LOC_Os04g41910.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA10G31450.1 (Glycine max), 5'ss of exon 5
TGACCGGCCAGCAACCCCACCAGATGGCGAGGACGAATTTACTGATGATGATGGTACTGTTTACAAGTGGGATCGTGTCCTGAGGGCATGGGTTCCTCAAgtg-agtgcttcca-acctcctgttcttaggttcatttactcatgacttttgtttttggtagttctgattttgcctgagatattaattagatattg-tgtttt
|||  | ||  | || ||||| || || || || |||||||||||||||||||| ||||| || ||||||||| |    || ||||| |||||||| || ||   |||||  ||    |   | | |||   | |||   | || |   |  |  |   ||  | || |||   || | |  ||   | |  | || |||| |
TGAGAGACCTTCGACACCACCTGAGGGTGAAGAAGAATTTACTGATGATGATGGAACTGTATATAAGTGGGATAGGAATCTTAGGGCTTGGGTTCCCCAGgtttggtgctgacatgtgtatcgctattattattatt--attattatcatcatcat-aatatatttgttttactctcatactttgtgtggccagtgatgttct

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|29636733|gb|CB641742.1|CB641742
EST:     ATGGTACTGTTTACAAGTGGGATCGTGTCCTGAGGGCATGGGTTCCTCAA                         GATGACCTAGAAGGCAAAAATGACAACTATGAAGTTGAAGACATGACTTTT
genomic: ATGGTACTGTTTACAAGTGGGATCGTGTCCTGAGGGCATGGGTTCCTCAAgtgagtgctt ... tctttcgcagGATGACCTAGAAGGCAAAAATGACAACTATGAAGTTGAAGACATGACTTTT
EST: gi|29676260|gb|CB672535.1|CB672535
EST:     ATGGTACTGTTTACAAGTGGGATCGTGTCCTGAGGGCATGGGTTCCTCAA                         GATGACCTAGAAGGCAAAAATGACAACTATGAAGTTGAAGACATGACTTTT
genomic: ATGGTACTGTTTACAAGTGGGATCGTGTCCTGAGGGCATGGGTTCCTCAAgtgagtgctt ... tctttcgcagGATGACCTAGAAGGCAAAAATGACAACTATGAAGTTGAAGACATGACTTTT