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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTGAATATGCGATTAATGTGGTTAAGCACATATACAGTAGCCATGTTGTGTTGCAGTACAACTGTACAAACACTATACCCGAACAACTGCTAGAAAATgtaagcagcaaacaattaagtacaattaaatatgttcttggaggcacagctgtcaactcacactgaagattttttttcatatatgtatgttgattcttgtag

Basic information

species Oryza sativa
transcript LOC_Os03g12590.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g12590.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G012501_T01 (Zea mays), 5'ss of exon 15
GACTGAATATGCGATTAATGTGGTTAAGCACATATACAGTAGCCATGTTGTGTTGCAGTACAACTGTACAAACACTATACCCGAACAACTGCTAGAAAATgtaagcagcaaacaattaagtacaattaaatatgttcttggaggcacagctgtcaactcacactgaagattttttttcatatatgtatgttgattcttgtag
 |||||||||||  ||| ||||||||| ||||| ||     || |  |||| ||||||||||| ||| |||||||||||   ||||||||||||||| ||||||||| | |   |||        | || ||| |||||  |||   |  |||  ||||||||||||| ||     |  || |||||| ||| |||||  ||
AACTGAATATGCTGTTAGTGTGGTTAAACACATTTATGACGGCTACATTGTATTGCAGTACAATTGTGCAAACACTATAGAAGAACAACTGCTAGAAGATgtaagcatcta--catt--------tcaagtattttcttcaaggactaaatgtttactcacactgaaggtt-----tggtaaatgtat-ttgcttctttcag

upper sequence: LOC_Os03g12590.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA06G01520.1 (Glycine max), 5'ss of exon 15
GACTGAATATGCGATTAATGTGGTTAAGCACATATACAGTAGCCATGTTGTGTTGCAGTACAACTGTACAAACACTATACCCGAACAACTGCTAGAAAATgtaagcagcaaacaattaagtacaattaaatatgttcttggaggcacagctgtcaactcacactgaagattttttttcatatatgtatgttgattcttgtag
||| ||||||||  |||||||  |||| ||||| |    ||| ||||||||||| ||||||||||| |||||||| ||||| || ||| || | ||| ||||||      || | |  ||     | |||| |  |          || ||   |  ||    | |  ||||||    || ||                   
GACAGAATATGCTGTTAATGTCATTAAACACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCACAAACACGATACCAGAGCAATTGTTGGAACATgtaa----tgaatattatagatgcttcaaattttcttaaaataatccaactccaaggtctttgtaattatttttccctat-tacag----------------

upper sequence: LOC_Os03g12590.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA04G01470.1 (Glycine max), 5'ss of exon 15
GACTGAATATGCGATTAATGTGGTTAAGCACATATACAGTAGCCATGTTGTGTTGCAGTACAACTGTACAAACACTATACCCGAACAACTGCTAGAAAATgtaagcagcaaacaattaagtacaattaaatatgttcttggaggca--cagctgtcaactcacactgaagattttttttcatatatgtatgttgattcttgtag
||| ||||||||  |||||||  |||| ||||| |    ||| ||||||||||| ||||||||||| |||||||| ||||| || ||| || | ||| ||||||  |  |     |||   |   || ||  | ||| |  |   |  || ||   |  ||    | |  |||||| |  || ||                   
GACAGAATATGCAGTTAATGTCATTAAACACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCACAAACACGATACCAGAGCAATTGTTGGAAGATgtaatgaata-----ttatagatgcttcaaatttttcataaaataatccaactccaaggtctttgtaattatttttctctat-tacag----------------

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|14191672|gb|AU183883.1|AU183883
EST:     TGTTGCAGTACAACTGTACAAACACTATACCCGAACAACTGCTAGAAAAT                         GTGACTGTTTATGTTGATGCCACTGATGCTGAGGAATTTTCAGAAGTTTGT
genomic: TGTTGCAGTACAACTGTACAAACACTATACCCGAACAACTGCTAGAAAATgtaagcagca ... attcttgtagGTGACTGTTTATGTTGATGCCACTGATGCTGAGGAATTTTCAGAAGTTTGT
EST: gi|58663414|gb|CK052100.1|CK052100
EST:     TGTTGCAGTACAACTGTACAAACACTATACCCGAACAACTGCTAGAAAAT                         GTGACTGTTTAGTGTTGATGCCACTGATGCTGAGGAATTTTCAGAAGTTTG
genomic: TGTTGCAGTACAACTGTACAAACACTATACCCGAACAACTGCTAGAAAATgtaagcagca ... attcttgtagGTGACTGTTTA-TGTTGATGCCACTGATGCTGAGGAATTTTCAGAAGTTTG
EST: gi|14571493|gb|BI118861.1|BI118861
EST:     ACAAACACTATACCCGAACAACTGCTAGAAAAT                         GTGACTGTTTATGTTGATGCCACTGATGCTGAGGAATTTTCAGAAGTTTGT
genomic: ACAAACACTATACCCGAACAACTGCTAGAAAATgtaagcagca ... attcttgtagGTGACTGTTTATGTTGATGCCACTGATGCTGAGGAATTTTCAGAAGTTTGT
EST: gi|58654518|gb|CK043198.1|CK043198
EST:     TGTTGCAGTACAACTGTACAAACACTATACCCGAACAACTGCTAGAAAAT                         GTGACTGTTTATGTTGATGCCACTGATGCTGAGGAATTTTCAGAAGTTTGT
genomic: TGTTGCAGTACAACTGTACAAACACTATACCCGAACAACTGCTAGAAAATgtaagcagca ... attcttgtagGTGACTGTTTATGTTGATGCCACTGATGCTGAGGAATTTTCAGAAGTTTGT
EST: gi|58667540|gb|CK056226.1|CK056226
EST:     TGTTGCAGTACAACTGTACAAACACTATACCCGAACAACTGCTAGAAAAT                         GTGACTGTTTATGTTGATGCCACTGATGCTGAGGAATTTTCAGAAGTTTGT
genomic: TGTTGCAGTACAACTGTACAAACACTATACCCGAACAACTGCTAGAAAATgtaagcagca ... attcttgtagGTGACTGTTTATGTTGATGCCACTGATGCTGAGGAATTTTCAGAAGTTTGT

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: 74 (upstream exon), 75 (downstream exon)
Score: 36

GACTGAATATGCGATTAATGTGGTTAAGCACATATACAGTAGCCATGTTGTGTTGCAGTACAACTGTACAAACACTATACCCGAACAACTGCTAGAAAATgtaagcagca ... attcttgtagGTGACTGTTTATGTTGATGCCACTGATGCTGAGGAATTTTCAGAAGTTTGTTCAAAGCCACTTAGAAGTTTGCCTTATGATTCACCTGGGCAAATTTTTG




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