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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaagtgttaagatgatgagcatctgtacatcatagagacatactccttgattcttgaaatttatgtccagtcatctgtatcctctcttctgcagGGAGTGTGGACTAGCTCACAAGACAATAATTTTTGTCCTAGAAGAGTTTGACCTCTTTGCTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g49010.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g49010.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G876520_T04 (Zea mays), 3'ss of exon 1
------gtaagtgaagtgttaagatgatgagcatctgtacatcatagagacatactccttgattcttgaaatttatgtccagtcat-ctgtatcctctcttctgcagGGAGTGTGGACTAGCTCACAAGACAATAATTTTTGTCCTAGAAGAGTTTGACCTCTTTGCTCAG
       | |||||| |  |   || ||| | || ||||     | ||| |||| || ||  ||| | |   || | | || |  |  | ||| |||||||||| |||||||| ||||||||||||||||||||| | ||| | |||||||| || |||||||||||||||
gtgagctttagtgaaataatgccataatgggtat-tgta-----ttgagccatagtctttagttcataattcttttattcatttctgttttatactctcttctgtagGGAGTGCGGACTAGCTCACAAGACAATACTATTTATTCTAGAAGAATTCGACCTCTTTGCTCAG

upper sequence: LOC_Os01g49010.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G25850.1 (Glycine max), 3'ss of exon 7
gtaagtgaagtgttaagatgatgagcatctgtacatcatagagacatactccttgattcttgaaatttatgtccagtcatctgtatcctctcttctgcagGGAGTGTGGACTAGCTCACAAGACAATAATTTTTGTCCTAGAAGAGTTTGACCTCTTTGCTCAG
                     |||| |     |  | || |    | |       ||  ||  || || |    |  ||| | |   || | || |  ||||| |||||| |||| || || ||||||||||||||  | || ||||||||||| |||||||||
--------------------gtgagtaa--aaattttattggttgaaaaaggaaaataatttgaagttcta---aagcatttattatcttttttttctagGGAATGTGGATTAGCACATAAAACAATAATTTTTGTTTTGGATGAGTTTGACCTGTTTGCTCAG

upper sequence: LOC_Os01g49010.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv01s0011g04400.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------------gtaagtgaagtgttaagatgatgagcatctgta-catcatagagacatactccttgattcttgaaatttatgtccagtcatctgtatcctctcttctgcagGGAGTGTGGACTAGCTCACAAGACAATAATTTTTGTCCTAGAAGAGTTTGACCTCTTTGCTCAG---------------------
                                                |   ||  | | |    | ||||| ||| | |    |||| || |  |  |  ||   | |     || |||     || | | | |  |||||| | ||||||||||||| |||||||||||||||| ||||||||  | || ||||||||| ||||  |||||                     
gtgagtgtacacatttggtaggtgattgtgtcctccgtcagtgctgaggcttgttcattttgctaaagatgaccatttttggtttcatggaaaagttgttattctctttct---ttcatgaattttcttatttgtgatctcttgt-cagGGAGTGTGGATTAGCTCACAAGACAATCATTTTTGTATTGGATGAGTTTGACTTCTTCACTCAGGCAAGATTACCTCTCTCTCAT

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|218491615|gb|FG954647.1|FG954647
EST:     GCTTCTTCAGATGACAACACGGAATTCATGATTGACATGTTACG                         GGAGTGTGGACTAGCTCACAAGACAATAATTTTTGTCCTAGAAGAGTTTGA
genomic: GCTTCTTCAGATGACAACACGGAATTCATGATTGACATGTTACGgtaagtgaag ... tcttctgcagGGAGTGTGGACTAGCTCACAAGACAATAATTTTTGTCCTAGAAGAGTTTGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactccttgattcttgaaatttatgtccagtcatctgtatcctctcttctgcagGGAGTGTGGACTAGCTCACAAGACAATAATTTTTGTCCTAGAAGAGTTTGACCTCTTTGCTCAG
     ccttgat  putative branch site (score: 5)
                                  tctgtatcctctcttc  putative PPT
          attcttgaaatttat  TA-rich tract