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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcttgttgcttaccatgaagttgggcatgcaatttgtgggtaagagataatctgcatatttgctaactgtgcttttgtttattacttgcatatcaaaattccgtgcaactattcatatctggaaatgtattctttgtagaactttgacgcctggccacgaccctgtccaaaagGTTACTTTGATCCCGAGGGGTCAAGCTCGTGGTCTCACATGGTTCATTCCAATGGACGACCCAACGCTCATCTCCAGGCAACAACTGTTCGCCAGAATTG

Basic information

species Oryza sativa
transcript LOC_Os06g45820.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45820.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G087598_T02 (Zea mays), 3'ss of exon 2
gtcttgttgcttaccatgaagttgggcatgcaatttgtgggtaagagataatctgcatatttgctaactgtgcttttgtttattacttgcatatcaaaattccgtgcaactattcatatc-tggaaatgtattctttgtagaactttgacgcctggccacgaccctgtccaaaagGTTACTTTGATCCCGAGGGGTCAAGCTCGTGGTCTCACATGGTTCATTCCAATGGACGACCCAACGCTCATCTCCAGGCAACAACTGTTCGCCAGAATTG
                                  || ||  | |    |   |||| | ||||       |    ||| | |  | || ||| ||||| ||   | ||   |||  |    |||||||    |||||| |||||||||||||||||||| || ||||||||||||||||| ||  | || |||||||||||||||||||| |||||||| || || ||||| ||||||||                                   
---------------------------------cttttgatttat---tggactgcctttttgtatgtcttttccttggtaacca-ttccatgtcaaatttatct-cattgatttgtggagtggaaat---ctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA----------------------------------

upper sequence: LOC_Os06g45820.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G110408_T01 (Zea mays), 3'ss of exon 3
gtcttgttgcttaccatgaagttgggcatgcaatttgtgggtaagagataatctgcatatttgctaactgtgcttttgtttattacttgcatatcaaaattccgtgcaact--attcatatctggaaatgtattctttgtagaactttgacgcctggccacgaccctgtccaaaagGTTACTTTGATCCCGAGGGGTCAAGCTCGTGGTCTCACATGGTTCATTCCAATGGACGACCCAACGCTCATCTCCAGGCAACAACTGTTCGCCAGAATTG
                                  || || || |    |    ||| | ||||    |  |    ||| | |  | || |||  |||| ||      ||    |||||| | ||||||     |||||| ||||||||||| |||||||| || ||||||||||||||||| || ||||| |||||||||||||||||||| |||||||| || || ||||| ||||||||                                   
----------------------------------ttttgagttat---tggagtgcct-tttgtacgcgatttccttggtaacca-ttccatgccaaatttgtacctaatctcattcatttgtggaaac---ctctttgcagAACTTTGACACCTGGCCATGATCCTGTCCAAAAGGTTACCTTAATCCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA----------------------------------

upper sequence: LOC_Os06g45820.3 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S156_30V6.1 (Physcomitrella patens), 3'ss of exon 4
gtcttgttgcttaccatgaagttgggcatgcaatttgtgggtaagagataatctgcatatttgctaactgtgcttttgtttattacttgcatatcaaaattccgtgcaact-attcatatctggaaatgtattctttgtagaactttgacgcctggccacgaccctgtccaaaagGTTACTTTGATCCCGAGGGGTCAAGCTCGTGGTCTCACATGGTTCATTCCAATGGACGACCCAACGCTCATCTCCAGGCAACAACTGTTCGCCAGAATTG
                 | | ||   | | ||   |     |   |    | |||||  ||   |  || ||      ||      || |    ||     |  |    || ||| |||  |  || ||| |    || || || ||||| || ||||| ||  | || |||||||||||  |||| || ||||||||||||||||||||||| ||||||||||||   || ||||| ||                                   
-----------------gtactttttctttcaccatccaattgcaattgtacctgcagtttcattgtctctggaaaatttctaaggttacggtgcattgacctctaaggcttattaataaatt-aattgtgtgaggtgcagGACCTTGACACCAGGCCATGATGCAGTGCAAAAGGTTACCCTGATTCCTAGGGGTCAAGCTCGTGGTCTCACCTGGTTCATTCCAGGCGAGGACCCCACC----------------------------------

upper sequence: LOC_Os06g45820.3 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S178_66V6.1 (Physcomitrella patens), 3'ss of exon 5
gtcttgttgcttaccatgaagttgggcatgcaatttgtgggtaagagataatctgcatatttgctaactgtgcttttgtttattacttgcatatcaaaattccgtgcaactattcatatctggaaatgtattctttgtagaactttgacgcctggccacgaccctgtccaaaagGTTACTTTGATCCCGAGGGGTCAAGCTCGTGGTCTCACATGGTTCATTCCAATGGACGACCCAACGCTCATCTCCAGGCAACAACTGTTCGCCAGAATTG
                                        ||||    |   |   | ||      | ||| |   |   |||  || |     ||   || |    ||||| |||  |      || | | |   | |||||||| || || ||||||||  | || |||||||| ||| | |||||||||||||||||||| |||||||| |||||||| ||   ||| || || ||                                   
----------------------------------------gtaatttcttcacaatacatgcatctattgtccaaattgatatccctggttcggcagggttgca---aactaatcagtt------atatttgcgacgcagAACTTTAACCCCAGGCCACGATGCAGTGCAAAAGGTGACTCTCATCCCGAGGGGTCAAGCTCGCGGTCTCACCTGGTTCATCCCTGGGGAAGATCCTACT----------------------------------

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 75 (downstream exon)
Score: 165

CGTGGTCGGACAGCAATTTCCTCAAAGGAGATTGATGATTCAATTGACAGAATAGTGGCTGGTATGGAAGGAACTGTGATGACAGATGGGAAGAGCAAAAgtcttgttgc ... tgtccaaaagGTTACTTTGATCCCGAGGGGTCAAGCTCGTGGTCTCACATGGTTCATTCCAATGGACGACCCAACGCTCATCTCCAGGCAACAACTGTTCGCCAGAATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggaaatgtattctttgtagaactttgacgcctggccacgaccctgtccaaaagGTTACTTTGATCCCGAGGGGTCAAGCTCGTGGTCTCACATGGTTCATTCCAATGGACGACCCAACGCTCATCTCCAGGCAACAACTGTTCGCCAGAATTG
                       ctttgac  putative branch site (score: 165)
                                          ccctgtcc  putative PPT
     aatgtatt  TA-rich tract