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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcactacattgcatgatgacatgataattaaaatattttctctcttattcttagtttttcccattccctaacatcataacgtgtgtcctgtttggcagGTTAGGAGATTTTTTCACTCCCACTTCAAGGTTGATAGAGACCTTCAATCGTCAGTTGTTGTTTATTCACAGAAGAGTGTATTGTGATCACTGTGGCAGA

Basic information

species Oryza sativa
transcript LOC_Os01g39810.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39810.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G164175_T01 (Zea mays), 3'ss of exon 9
-tagcactacattgcatgatgacatgataattaaaatattttctctcttattcttagtttttcccattccctaacatcataacgtgtgtcctgtttggcagGTTAGGAGATTTTTTCACTCCCACTTCAAGGTTGATAGAGACCTTCAATCGTCAGTTGTTGTTTATTCACAGAAGAGTGTATTGTGATC-ACTGTGGCAGA
   ||   |    |   ||  ||| || ||| |  |||   | | |  | ||| ||    |     ||        | |||||   |||  || ||||||| | ||||| ||||| ||||| || ||||||||||| ||||||||||| ||| | ||||| |||||||||| || || |||  | ||||  | |   |  | 
catgcttgattcagagggagcacacgacaataatgataggatttgttgt-ttcataacagtagtagttaaactcattaataacaattgttatggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCGGCTGTTGTGGTTTATTCACGGAGGAATGTGCTCTGATTTAGTACTGATG-

upper sequence: LOC_Os01g39810.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G000937_T02 (Zea mays), 3'ss of exon 10
ta-gcactacattgcatgatgacatgataattaaaatat--tttctctcttattcttagtttttcccattccctaacatcataacgtgtgtcctgtttggcagGTTAGGAGATTTTTTCACTCCCACTTCAAGGTTGATAGAGACCTTCAATCGTCAGTTGTTGTTTATTCACAGAAGAGTGTATTGTGATC-ACTGTGGCAGA
|| | |  |    |   ||  |||||  ||| |  |||   ||| |   ||  |   |||    | ||  | |     | ||||    |||  || ||||||| | ||||| ||||| ||||| || |||||| |||| ||||||||||| ||| | ||||| |||||||||  || |  |||  | ||||  | |   |  | 
tatgtatgattcagagggagtacatgtcaataatgataggatttattgtttcataacagtaaaactcaaactcattggtaataat---tgttatggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGATTGACAGAGACCTTCAGTCGGCTGTTGTGGTTTATTCATGGAGGGATGTGCTATGATTTAGTACTGATG-

upper sequence: LOC_Os01g39810.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G103473_T01 (Zea mays), 3'ss of exon 3
tagcactacattgcatgatg-acatgataattaaaatat--tttctctcttattcttagtttttcccattccctaacatcataacgtgtgtcctgtttggcagGTTAGGAGATTTTTTCACTCCCACTTCAAGGTTGATAGAGACCTTCAATCGTCAGTTGTTGTTTATTCACAGAAGAGTGTATTGTGATC-ACTGTGGCAGA
||    |   |   | |  | |||||  ||| |  |||   ||| |   ||  |   |||  | | ||  | |     | ||||    |||  || ||||||| | ||||||||||| ||||| || ||||||||||||||||||||||| ||| | ||||| |||||||||| || |  |||  | ||||  | |   |  | 
tatgtttgattcagagggagtacatgtcaataatgataggatttattgtttcataacagtaatactcaaactcattggtaataat---tgttatggttggcagATGAGGAGATTTTTCCACTCACATTTCAAGGTTGATAGAGACCTTCAGTCGGCTGTTGTGGTTTATTCACGGAGGGATGTGCTATGATTTAGTACTGATG-

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|86427881|gb|CI072978.1|CI072978
EST:     AATCTGAAGAAAGGCATGTCAAGTTGCTTCTGCGCAATTCATTTCAAGAG                         GTTAGGAGATTTTTTCACTCCCACTTCAAGGTTGATAGAGACCTTCAATCG
genomic: AATCTGAAGAAAGGCATGTCAAGTTGCTTCTGCGCAATTCATTTCAAGAGgtaaaacact ... tgtttggcagGTTAGGAGATTTTTTCACTCCCACTTCAAGGTTGATAGAGACCTTCAATCG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttattcttagtttttcccattccctaacatcataacgtgtgtcctgtttggcagGTTAGGAGATTTTTTCACTCCCACTTCAAGGTTGATAGAGACCTTCAATCGTCAGTTGTTGTTTATTCACAGAAGAGTGTATTGTGATCACTGTGGCAGA
                              tcataac  putative branch site (score: 2)
                                          tcctgttt  putative PPT
       ttagttttt  TA-rich tract