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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatattgtatatgtggtctgtaacttgtattaccagaaaattacttgaagctctttatattcagttttggttgctcaactaattcatgccttttacagGCTTTTAAATCCAAGTACATTTGCTGGTTGGTTTGGTCGATCATTGTATCAT

Basic information

species Oryza sativa
transcript LOC_Os11g25980.2
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g25980.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G479163_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------------ttcatattgtatatgtg-gtctgtaacttgtattaccaga-aaattacttgaagct---ctttatattcagttttggttgctcaactaattcatgccttttacagGCTTTTAAATCCAAGTACATTTGCTGGTTGGTTTGGTCGATCATTGTATCAT
                                                | || || |   | |  | | ||| | |   || | ||| |||||   |   | |   ||||  ||||  |||  |||  | ||||| || |     |||  |||||| | ||||||||||| |||||||||||||||||||||||||||||||||
gtaaactatacccttgcatgttgctgttaagggtcggtatctcttttgtgattttattcttatctgccagtatccta-gttcctagataaattttattttgttaaacttttaattccttttaagtt--ttaactatttgaatatctttgtagGCTTCTCAATCCAAGTACCTTTGCTGGTTGGTTTGGTCGATCATTGTATCAT

upper sequence: LOC_Os11g25980.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA12G33340.1 (Glycine max), 3'ss of exon 22
ttcatattgtatatgtggtctgtaacttgtattaccagaaaattacttgaa---gctctttatattcagtt--ttggt---tgctcaactaatt-catgcctttta-cagGCTTTTAAATCCAAGTACATTTGCTGGTTGGTTTGGTCGATCATTGTATCAT
         || |  |    |  |||    |     | |||| |  || |    || ||  |||  || ||  ||||       | || ||| | ||    ||  | ||||||| ||||||| |||||||||||||| |||||||| |||||  | |  |||
---------ta-acctttcattaaaccaaaaaaggaaaaaaaatgtttaactttgcactgaatagccacttcattggcaagcagtaaattaactacaaatattgaaacagGCTTCTAAATCCTAGTACATTTGCTGGATGGTTTGGGCGATCTCTCTTCCAT

upper sequence: LOC_Os11g25980.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA13G37090.1 (Glycine max), 3'ss of exon 22
ttcatattgtatatgtggtctgtaacttgtattaccagaaaattacttgaagctctttatattcagttttggttgctcaactaattcatgccttttacagGCTTTTAAATCCAAGTACATTTGCTGGTTGGTTTGGTCGATCATTGTATCAT
                 || ||||| || |  | | |  |   |       ||| |||| || |  |    ||     || ||    |    |   |||||||| ||||||| |||||||||||||| |||||||| |||||  | |  |||
-----------------gtttgtaa-ttatgctgctattagcctt------gctgtttaaatgccataa-agtcatctaatta--caaatattggaacagGCTTCTAAATCCTAGTACATTTGCTGGATGGTTTGGGCGATCTCTCTTCCAT

upper sequence: LOC_Os11g25980.2 (Oryza sativa), 3'ss of exon 22
lower sequence: AT5G44240.1 (Arabidopsis thaliana), 3'ss of exon 21
-ttcatattgtatatgtggtctgtaacttgtattaccagaaaattacttgaagctctttatattcagttttggttgctcaactaattcatgccttt-tacagGCTTTTAAATCCAAGTACATTTGCTGGTTGGTTTGGTCGATCATTGTATCAT
 |     |  |  ||   ||||  | || || | || | |     | |  |   |   ||  || |    |  ||| | |  | |||  |  |    | ||||||| | |||||||| |||||||| ||||||||||| |||||  | |  || 
gtatgcttgattaatagtgtctaaatctggtttcactatatctgaagtcaactgttcatacgtttatgcatatttgttaatttcatttttctcacgattcagGCTTCTGAATCCAAGCACATTTGCGGGTTGGTTTGGCCGATCCCTTTTCCAC

upper sequence: LOC_Os11g25980.2 (Oryza sativa), 3'ss of exon 22
lower sequence: EFJ13671 (Selaginella moellendorffii), 3'ss of exon 20
ttcatattgtatatgtggtctgtaacttgtattaccagaaaattacttgaagctctttatattcagttttggttgctcaactaattcatgccttttacagGCTTTTAAATCCAAGTACATTTGCTGGTTGGTTTGGTCGATCATTGTATCAT
                                                 |||    |   | |  | | |  ||| |||| ||| |  |   ||   ||||||||||||||| || ||||||||||| |||||||| ||  || | | ||| 
-----------------------------------------------gtaaggcagtggcagt-ggctctcattg-tcaa-taacttgtagttt---cagGCTTTTAAATCCCAGCACATTTGCTGGCTGGTTTGGCCGGGCACTTTTTCAC

upper sequence: LOC_Os11g25980.2 (Oryza sativa), 3'ss of exon 22
lower sequence: EFJ28965 (Selaginella moellendorffii), 3'ss of exon 20
ttcatattgtatatgtggtctgtaacttgtattaccagaaaattacttgaagctctttatattcagttttggttgctcaactaattcatgccttttacagGCTTTTAAATCCAAGTACATTTGCTGGTTGGTTTGGTCGATCATTGTATCAT
                                                | |   | ||       | | |  ||| |||| ||| |  |   ||   ||||||||||||||| || ||||||||||| |||||||| ||  || | | ||| 
------------------------------------------------gtaaggcattggcggtggctctcattg-tcaa-taacttgtagttt---cagGCTTTTAAATCCCAGCACATTTGCTGGCTGGTTTGGCCGGGCACTTTTTCAC

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|163929268|gb|EG711029.1|EG711029
EST:     AAGACAGTGATGCAAAATCCAGAGATATTGCTCTACTGCCAGGCTGGAAG                         GCTTTTAAATCCAAGTACATTTGCTGGTTGGTTTGGTCGATCATTGTATCA
genomic: AAGACAGTGATGCAAAATCCAGAGATATTGCTCTACTGCCAGGCTGGAAGgtaatttaca ... ccttttacagGCTTTTAAATCCAAGTACATTTGCTGGTTGGTTTGGTCGATCATTGTATCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgaagctctttatattcagttttggttgctcaactaattcatgccttttacagGCTTTTAAATCCAAGTACATTTGCTGGTTGGTTTGGTCGATCATTGTATCAT
                                 aactaat  putative branch site (score: 2)
                                           tgcctttt  putative PPT
          tttatattcagtttt  TA-rich tract