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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttgtgtcattttgcacattcgaaagggttatcttgtcaaatgctgaccaatgtcctattaatttttgcagTGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAAT

Basic information

species Oryza sativa
transcript LOC_Os12g13590.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g13590.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM5G823484_T01 (Zea mays), 3'ss of exon 7
----------------------------gtatccttgtgtcattttgcacattcgaaagggttatcttgtcaaatgctgaccaatgtcctattaatttttgcagTGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAAT
                               ||| ||   |||| |  |  || | |  |  |  |||   | ||  || |  |  |  |||||    ||| ||||||||  ||||| |||||||||| || ||||| || ||||| ||||||||||||||||||||||| || |||||||| ||||| |||||| | |||||
aatcgaaatatttgccaatgttttgatccactccatgaaccattatttatcttggcagagccttgcttcatacatagtgccttactttttatta----ttgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT
















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|33689209|gb|CF317448.1|CF317448
EST:     TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTAGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
genomic: TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgt ... atttttgcagTGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
EST: gi|87029720|gb|CI274401.1|CI274401
EST:     TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
genomic: TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgt ... atttttgcagTGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
EST: gi|66920327|gb|CX107175.1|CX107175
EST:     TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
genomic: TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgt ... atttttgcagTGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
EST: gi|88974506|gb|CI022047.1|CI022047
EST:     TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
genomic: TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgt ... atttttgcagTGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
EST: gi|58666677|gb|CK055363.1|CK055363
EST:     GGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
genomic: GGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgt ... atttttgcagTGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
EST: gi|33689213|gb|CF317452.1|CF317452
EST:     TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTAGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
genomic: TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgt ... atttttgcagTGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
EST: gi|87029773|gb|CI274454.1|CI274454
EST:     TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
genomic: TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgt ... atttttgcagTGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG

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), 28 (downstream exon)
Score: 7

GGAAATCGCTTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgt ... atttttgcagTGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattcgaaagggttatcttgtcaaatgctgaccaatgtcctattaatttttgcagTGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAAT
                                        tattaat  putative branch site (score: 7)
                                              tttttgc  CT-rich tract
                                     tcctattaattttt  TA-rich tract