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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctttcgtcatgcagagtattatggtagaaaggttttattgtattagcagcattcacatacttacagtgtaacagaataactgtactttttctcgccagGCACTTGATACATTTAATACTGCAATTGTATCTCCAATCTATTATGTAATGTTCACAACACTAACAATACTTGCAAGCGTCATAATGTTCAAG

Basic information

species Oryza sativa
transcript LOC_Os05g43790.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g43790.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G120175_T03 (Zea mays), 3'ss of exon 6
ttctttcgtcatgcagagtattatggtag-----aaaggttttattgtattagcagcattcacatacttacagtgtaacagaataactgtactttttctcgccagGCACTTGATACATTTAATACTGCAATTGTATCTCCAATCTATTATGTAATGTTCACAACACTAACAATACTTGCAAGCGTCATAATGTTCAAG
      ||   || || || |||    ||     | |  | |||   || | |   |  |       |||  | ||||   | |   | |  |||||   |  |||||||||| || || || || ||||||||||||||||| |||||||||||||||||||| || ||||||||||| ||||||||||||||||||
--acaacgcactgaagtgtgttactagagttaccacaaatattaagctactggttcctgttctgc-tttatggagtaa-gtagtggtttttttttttgctgt-agGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG

upper sequence: LOC_Os05g43790.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA14G03790.1 (Glycine max), 3'ss of exon 6
----------ttctttcgtcatgcagagtattatggtagaaaggttttattgtattagcagcattcacatacttacagtgtaacagaataactgtactttttctcgccagGCACTTGATACATTTAATACTGCAATTGTATCTCCAATCTATTATGTAATGTTCACAACACTAACAATACTTGCAAGCGTCATAATGTTCAAG
          |||     |  | | | | |||||  || |||| | ||||   ||  | |   ||     | |||   |  |     || | || | | ||||     |||| ||||| || || || || |||||||||||||| || || ||||| |||||||||||||| |||||||| || || || |||||||| |||
ttctagagaattcagattttct-ctgtgcattata-tacaaagttcttat---atatgaaattttggatcaattattcttcactgacatgattgcaatatttc-----agGCTCTTGACACCTTCAACACAGCAATTGTATCTCCTATATACTATGTCATGTTCACAACACTTACAATACTAGCCAGTGTAATAATGTTTAAG

upper sequence: LOC_Os05g43790.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA02G44980.2 (Glycine max), 3'ss of exon 5
ttctttcgtcatgcagagtattatggtagaaaggttttat-tgtatta------gcagcattcacatacttacagtgtaacagaataactgtactttttct-cgccagGCACTTGATACATTTAATACTGCAATTGTATCTCCAATCTATTATGTAATGTTCACAACACTAACAATACTTGCAAGCGTCATAATGTTCAAG
       |   | | | |||||||  || |||| | |||| | ||| |      | | || | || || ||||  |  |     || | |||| | |   |    ||||| ||||| || || || || |||||||||||||| || || ||||| |||||||||||||| |||||||| || || || |||||||| |||
------agattttctgtgtattata-tacaaagttcttatatatatgaaattttggatcaattac-taattactcttcactgacatgattgtattgtaattatttcagGCTCTTGACACCTTCAACACAGCAATTGTATCTCCTATATACTATGTCATGTTCACAACACTTACAATACTAGCCAGTGTAATAATGTTTAAG

upper sequence: LOC_Os05g43790.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv06s0009g03650.t01 (Vitis vinifera), 3'ss of exon 6
-ttctttcgtcatgcagagtattatggtagaaaggttttattgtattagcagcattcacatacttacagtgtaacagaataactgtactttttctcgccagGCACTTGATACATTTAATACTGCAATTGTATCTCCAATCTATTATGTAATGTTCACAACACTAACAATACTTGCAAGCGTCATAATGTTCAAG
 |||||     |||       | |   | ||  | |  || || |  |  |   |||  ||    |   | |      | |||  |  | |       ||||| |||||||| || || |||||| |||| || || || |||||||| ||||||||| |||| ||||| ||||| || || ||||||||||||
attcttaaaggatgtttcacttgaatatggattgatgctactggac-ataaattttctgatcaaaagttttttctctcacaacatttttctgatgtttcagGCTCTTGATACTTTCAACACTGCAGTTGTGTCCCCCATATATTATGTCATGTTCACATCACTTACAATCCTTGCTAGTGTGATAATGTTCAAG

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|218503663|gb|FG954349.1|FG954349
EST:     TGCTTATAGTGGCCACTTGTGTGCTAACACAGATGAATTACTTGAACAAG                         GCACTTGATACATTTAATACTGCAATTGTATCTCCAATCTATTATGTAATG
genomic: TGCTTATAGTGGCCACTTGTGTGCTAACACAGATGAATTACTTGAACAAGgtctgtttgt ... ttctcgccagGCACTTGATACATTTAATACTGCAATTGTATCTCCAATCTATTATGTAATG
EST: gi|33662767|gb|CF293734.1|CF293734
EST:     TGCTTATAGTGGCCACTTGTGTGCTAACACAGATGAATTACTTGAACAAG                         GCACTTGATACATTTAATACTGCAATTGTATCTCCAATCTATTATGTAATG
genomic: TGCTTATAGTGGCCACTTGTGTGCTAACACAGATGAATTACTTGAACAAGgtctgtttgt ... ttctcgccagGCACTTGATACATTTAATACTGCAATTGTATCTCCAATCTATTATGTAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcagcattcacatacttacagtgtaacagaataactgtactttttctcgccagGCACTTGATACATTTAATACTGCAATTGTATCTCCAATCTATTATGTAATGTTCACAACACTAACAATACTTGCAAGCGTCATAATGTTCAAG
                                    ctgtactttttctc  CT-rich tract
                                       tacttttt  TA-rich tract