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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttaaaaacatgaatttgtttcatctctttctggcctatgctaacaagatattattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAATGGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATA

Basic information

species Oryza sativa
transcript LOC_Os02g58020.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 6
gtaagtttaaaaacatgaatt-tgtttcatctctttctggcctatgctaacaagatattattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAATGGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATA
|||||||  |||    |  || | |||| || ||| || ||  |||||||     ||| | ||| ||||| ||||||||||| ||||||||||||||| ||||||| ||||||||||| ||||||||||||||||||||||||||||| || ||||||||| | ||||
gtaagttggaaatgtggggttatttttcttcacttgcttgcacatgctaaagctgtatcactttccagAACCATCTTGATCTTCATGCTGTGTTATGGCTAGAAACTTATCTCCTGAAGTGGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATA

upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G10530.1 (Glycine max), 3'ss of exon 5
gtaagtttaaaaacatgaatttgtttcatctctttctg--gcctatgctaacaagat-----------attattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAATGGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATA
|| |  | |  |     | | | |||| |   |    |  ||||  | | | |  ||           ||| | |||||||||||||||||||| |||||||| |||||| | ||| | ||  |  | ||||||||||| ||||| || ||||| || |||||||| || ||| | || |
gtta-ctcatcattcccagtctctttcgtgattcatggatgccttggtttatagaatttatgaattttattttattgcagAATCATCTTGATCTTCATGCTGTCTTATGGCTTGAATCGTACTTGGTTAAATGGCCAAAAACATTTATCGTTGTTTCTCATGCTAGAGAATTTTTAAACA

upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 5
gtaagtttaaaaacatgaatttgtttcatctctttctg--gcctatgctaacaagat-----------attattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAATGGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATA
|| |  | |  |     | ||| ||||||   |    |  ||||  | | | |  ||            || | |||||||||||||||||||| |||||||| |||||| | ||| | ||  |  | ||||||||||| ||||| |||||||| || |||||||| || ||| | || |
gtta-ctcatcattccaagtttctttcatgattcatggatgccttggtttatagaatttatgaattttgttttattgcagAATCATCTTGATCTTCATGCTGTCTTATGGCTTGAATCTTACTTGGTTAAATGGCCAAAAACATTTATTGTTGTTTCTCATGCTAGAGAATTTTTAAACA

upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------gtaagtttaaaaacatgaatttgtttcatctctttctggcctatgctaacaagatattattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAATGGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATA
             ||||| ||      || |  |   |  || |     |  |  |   |       | |  ||| | |||| |||||||||||||||||||| ||||||||||||||||||||   ||| |||||||| ||||| || || || || ||||||||||| ||  | || |
gtgtgttttctttgtaaggtttcccttattagatcaatatattttcaggtttctgacattcttttcctctcttttggtagAACCATCTTGATCTCCATGCTGTCTTATGGTTAGAAACATATCTAACGAAGTGGCCAAAAACATTTATAGTCGTTTCCCATGCTAGGGAATTCTTGAACA

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|218482666|gb|FG970229.1|FG970229
EST:     CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACA                         AATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
genomic: CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACAgtaagtttaa ... tattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
EST: gi|29662747|gb|CB659022.1|CB659022
EST:     CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACA                         AATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
genomic: CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACAgtaagtttaa ... tattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
EST: gi|29644366|gb|CB649373.1|CB649373
EST:     CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACA                         AATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
genomic: CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACAgtaagtttaa ... tattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
EST: gi|24468674|gb|CA305623.1|CA305623
EST:     CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACA                         AATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
genomic: CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACAgtaagtttaa ... tattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
EST: gi|88311922|gb|CI577528.1|CI577528
EST:     CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACA                         AATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
genomic: CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACAgtaagtttaa ... tattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
EST: gi|58602069|gb|CK012597.1|CK012597
EST:     CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACA                         AATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
genomic: CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACAgtaagtttaa ... tattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA

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), 60 (downstream exon)
Score: 57

TAAACGCACAAAACAGTTTTCTGGTGGATGGCGCATGAGAATTGCTCTAGCACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACAgtaagtttaa ... tattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAATGGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgaatttgtttcatctctttctggcctatgctaacaagatattattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAATGGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATA
                               tgctaac  putative branch site (score: 57)
                                            ttatttt  putative PPT
                                  taacaagatattattt  TA-rich tract