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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcataggactttttaaaaatatctaaagttattaacatttacaaatggttagccttaactccgttaaattttcctgtgtagTTGAGCTAGATAAGCCATGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTTAAG

Basic information

species Oryza sativa
transcript LOC_Os10g40140.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g40140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G171406_T02 (Zea mays), 3'ss of exon 2
gtaagttcataggactttttaaaaatatctaaagttattaacatttacaaatggttagccttaactcc---gttaaattttcctgtgtagTTGAGCTAGATAAGCCATGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTTAAG-----------------------------
||||| |    ||| || || |       || | |  ||  ||||  | | ||||||   ||  |  |   ||| |||| |   | ||||||||||| || ||||| |||||||||||||||||||||||||||||||||||||||||||| ||||| |||                             
gtaagctgtgtggatttattga-------tatattcgttcgcatt-gcgattggttaaatttctcctccgcgttgaattcttgcgcgtagTTGAGCTGGAGAAGCCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAGGTCCATGTCTTCCCTGTCCCGTGAAGTTC

upper sequence: LOC_Os10g40140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G171406_T06 (Zea mays), 3'ss of exon 1
gtaagttcataggactttttaaaaatatctaaagttattaacatttacaaatggttagccttaactcc---gttaaattttcctgtgtagTTGAGCTAGATAAGCCATGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTTAAG
||||| |    ||| || || |       || | |  ||  ||||  | | ||||||   ||  |  |   ||| |||| |   | ||||||||||| || ||||| |||||||||||||||||||||||||||||||||||||||||||| ||||| |||
gtaagctgtgtggatttattga-------tatattcgttcgcatt-gcgattggttaaatttctcctccgcgttgaattcttgcgcgtagTTGAGCTGGAGAAGCCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAG

upper sequence: LOC_Os10g40140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G074173_T01 (Zea mays), 3'ss of exon 2
gtaagttcataggactttttaaaaatatc----taaagttattaacatttacaaa---------tggttagccttaactc-cgttaaattttcctgtgtagTTGAGCTAGATAAGCCATGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTTAAG
||||||||   ||| || || | | | ||     ||   | ||   |||    ||           ||| || |   | | |||  |||  |   | | ||||||||| || ||||| |||||||||||||||||||||||||||||||||||||| || || ||||| |||
gtaagttctgcggatttcttgatattttcgttccaattgtgttgtgattggtcaaacctcacttccgttggcatctccccgcgtctaatccttgcgcgcagTTGAGCTGGAGAAGCCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCACCACGTCGCATTCAAG

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|88400668|gb|CI596089.1|CI596089
EST:     TGCCAGCGGAAGGCTGATCTCCATTTACCCAGAGGATCTCACTTTCCTAT                         TTGAGCTAGATAAGCCATGCTATTGCAATCTCAAGGTGGTGAACAACAGCG
genomic: TGCCAGCGGAAGGCTGATCTCCATTTACCCAGAGGATCTCACTTTCCTATgtaagttcat ... tcctgtgtagTTGAGCTAGATAAGCCATGCTATTGCAATCTCAAGGTGGTGAACAACAGCG




















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: 57 (upstream exon), 27 (downstream exon)
Score: 7

GTGTGGCAATGGGTGCCAGCGGAAGGCTGATCTCCATTTACCCAGAGGATCTCACTTTCCTATgtaagttcat ... tcctgtgtagTTGAGCTAGATAAGCCATGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttattaacatttacaaatggttagccttaactccgttaaattttcctgtgtagTTGAGCTAGATAAGCCATGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTTAAG
                                          ttttcctgt  CT-rich tract
     ttaacatttacaaat  TA-rich tract