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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgccaagtcgtcgtagatttattatactatgtgtagtatttccttaaccatgcaatgcttctaagttctaaccgtgtatcattttttaaatattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAA

Basic information

species Oryza sativa
transcript LOC_Os03g49420.2
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G033619_T02 (Zea mays), 3'ss of exon 16
ctgccaagtcgtcgtagatttattatactatgtgtagtatttccttaacc-atgcaatgcttctaagttcta--accgtgtatcattttttaaatattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAA--------
  | ||| || |  |  | |  | ||| | |   |  ||| || ||||   |||  ||| | | ||||| |   ||| | ||||| ||     || | |||||||  ||||||| |||||||||||  | || ||||||||||| ||||| ||||||||| | || |||||||| || |||  |||||||||| |        
tcggcaattcat-attaactgctaatagtcttgttgctatatcattaatttatgagatg-tacaaagttttgtgaccatatatcacttggctcat-tgaacagGTAATTCCTGCCTGGTTAAGTTGCCTTCCGATAAAAAATGATTTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCAGTAAGTAA

upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 16
ctgccaagtcgtcgtagatttattatactatgtgtagtatttccttaacc-atgcaatgcttctaagttcta--accgtgtatcattttttaaatattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAA
  | ||| || |  |  | |  | ||| | |   |  ||| || ||||   |||  ||| | | ||||| |   ||| | ||||| ||     || | |||||||  ||||||| |||||||||||  | || ||||||||||| ||||| ||||||||| | || |||||||| || |||  |||||||||| |
tcggcaattcat-attaactgctaatagtcttgttgctatatcattaatttatgagatg-tacaaagttttgtgaccatatatcacttggctcat-tgaacagGTAATTCCTGCCTGGTTAAGTTGCCTTCCGATAAAAAATGATTTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCA

upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 17
ctgccaagtcgtcgtagatttattat--actatgtgtagtatttccttaaccatgcaatgcttctaagttctaacc-gtgtatcattttttaaatattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAA
     | |  | | |  ||   | ||   |||    |  | ||| ||     ||  ||   |  |    | |   | || |   ||| | |     || ||||||||||||||| ||||| ||||| |||||||||||   ||| || |||||||||||  | |||||||| ||||| ||| | ||| |||| | 
---agaggaagccatgtatacgtcattagctagtcttgttcttttctaccatatttaactttgttggcctttcctctgtcttaaattgtgtggtatttgacagGTTGTTCCTGCCTGGTTGAGTTGCTTGCCAATAAAGGGTGATTTGATCGAGGCCAAAGTTGTTCATGACCAACTTTGTTCAATGGTTGAAAT

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|29681491|gb|CB677766.1|CB677766
EST:     CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAG                         GTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
genomic: CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttaca ... atattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
EST: gi|29679232|gb|CB675507.1|CB675507
EST:     CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAG                         GTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
genomic: CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttaca ... atattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
EST: gi|29629241|gb|CB634252.1|CB634252
EST:     CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAG                         GTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
genomic: CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttaca ... atattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
EST: gi|27576974|gb|CA999668.1|CA999668
EST:     CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAG                         GTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
genomic: CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttaca ... atattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
EST: gi|29629841|gb|CB634850.1|CB634850
EST:     CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAG                         GTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
genomic: CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttaca ... atattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaccatgcaatgcttctaagttctaaccgtgtatcattttttaaatattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAA
                     ttctaac  putative branch site (score: 1)
                              tgtatcattttttaaa  TA-rich tract