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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctctgtagctctaagctgttcagtgttaaatatacatgttaatgtatacaaaattaaggatgcaggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA

Basic information

species Oryza sativa
transcript LOC_Os02g39570.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G407044_T02 (Zea mays), 3'ss of exon 8
gtctctgtagctctaagctgtt----cagtgttaaatatacatgttaatgtatacaaaattaaggatgcaggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA
     | | ||| ||||   |      | || |  |  | |||||| ||| ||||     | |   ||||| | |||| | |    ||||||| | | || ||| | | ||||||||| || |||||||| ||||||||||| ||||| || |||||||| ||||||||||| ||||| |||||||||||||| ||||||||||
----atatggctttaagaaatggtaataatgcttgacctgcatgtttatgcatactgttgttatcttgcagctgctaatccagtattgattttgtgttgtacagGCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCTGGTGTCCTCAACATTGTAACAGGAGTCTTTGCTCGCAGGGGCTACAATA

upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 7
gtctctgtagctctaagctgtt--cagtgttaaatatacatgttaatgtatacaaaattaaggatgcaggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA
     |  |  |  ||  || |   | || | ||  | |||||| ||| ||||     | |   ||||| | |||| | |    ||||||| | |||| ||| ||| ||||||| | || ||||| || ||||||||||| |||||||| |||||||||||||||||||| ||||| |||||||||||||| ||||||||||
--acatagatttaaaaaatggtaataatgcttaacctgcatgtttatgaatactgttgttatcttgcagctgctaatccagtattgattttgtgtggtacagGCAACTGGACTTTGCTCGCATACCCTCTCCATCCTTGTGAATGATTGTCCTGGTGTTCTCAACATTGTAACAGGAGTCTTTGCTCGCAGGGGCTACAATA

upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G13290.1 (Glycine max), 3'ss of exon 7
gtctctgtagct---ctaagctgttcagtgttaaatatacatgttaatgtata-caaaattaaggatg-caggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA
    ||||  ||   |||   |||| | ||| | ||   ||||| ||| |  | |||  ||  | ||| || ||| ||   |   |  |||  |   |    ||| | |||||| |||||||||| ||| ||||||| ||||| || |||   ||||| ||||| |||||||||||||| || |||||| | |||||||| || |
tctcctgtgccttcactactatgtttattgt-acattagcatgt-aatattcatcaattttctgaatgacatgtcttactgttggtgggataatgcct---tcagACTAGTGGAATTCGATCACACACTTTATCCATGCTTGTGAACGATGCTCCTGGAGTTCTAAACATTGTTACAGGAGTTTTTGCTAGAAGAGGCTATAACA

upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA05G30130.1 (Glycine max), 3'ss of exon 7
----gtctctgtagctctaagctgttcagtgttaaatatacatgttaatgtatacaaaattaaggatgcaggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA
        || |   | |     ||| ||  |  ||||| ||  | ||| |    ||    | |  ||    |      ||     ||   | |||   | ||| | |||||| |||||||||| ||  ||||||| ||||| || |||   ||||| ||||| |||||||||||||| || |||||| | |||||||| || |
cttcactactatgtttattgtacgtt-agcatgtaatattca--tcaattttatgaatgacatgcttgtgactgtcttactgttggtggaataattcctt-cagACCAGTGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCTGGAGTTCTAAACATTGTTACAGGAGTTTTTGCTAGAAGAGGCTATAACA

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|32948291|gb|BP184863.1|BP184863
EST:     GCTCACTGGGGCGTCCTTGATGATGAAGAT                         TCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCT
genomic: GCTCACTGGGGCGTCCTTGATGATGAAGATgtaagtttca ... tttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCT
EST: gi|32948361|gb|BP184933.1|BP184933
EST:     CCATGAACCAAGTACTTGATGCTCACTGGGGCGTCCTTGATGATGAAGAT                         TCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCT
genomic: CCATGAACCAAGTACTTGATGCTCACTGGGGCGTCCTTGATGATGAAGATgtaagtttca ... tttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCT
EST: gi|33682200|gb|CF310439.1|CF310439
EST:     CCATGAACCAAGTACTTGATGCTCACTGGGGCGTCCTTGATGATGAAGAT                         TCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCT
genomic: CCATGAACCAAGTACTTGATGCTCACTGGGGCGTCCTTGATGATGAAGATgtaagtttca ... tttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCT

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: 72 (upstream exon), 70 (downstream exon)
Score: 96

GGCGATGTCTATCCTGTGGAACCTTATGAGGGTTCATCCATGAACCAAGTACTTGATGCTCACTGGGGCGTCCTTGATGATGAAGATgtaagtttca ... tttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatacaaaattaaggatgcaggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA
                            agctaaa  putative branch site (score: 96)
                                        ttttattt  putative PPT
                          taagctaaatatgatt  TA-rich tract