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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttcactactaccatatatagaactcgatgccctttataggtcatcaatattggtttcaagtcttgtggagcaaattatgtttgattgtggttaatatactccatttctgcagTCCTTTTATCTACCATGGGCAATGCTTGGGTTGGATGTGATATTTGGCTCAGAGATACTCCCTGGCCTTCTGGGAATTCTCGTTGGACACACGTACTACT

Basic information

species Oryza sativa
transcript LOC_Os05g09550.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g09550.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G117388_T01 (Zea mays), 3'ss of exon 5
gtaagcttcactactaccatatatagaactcgatgccctttataggtcatcaatattggtttca--agtcttgtggagcaaattatgtttgattgtggttaatatactccatttctgcagTCCTTTTATCTACCATGGGCAATGCTTGGGTTGGATGTGATATTTGGCTCAGAGATACTCCCTGGCCTTCTGGGAATTCTCGTTGGACACACGTACTACT
              |    || |    |  |   |  || |  |   || | ||  | | |  |  || | |||| |     ||||| ||  |||| | |  ||  |||   || |||||||||||||||| |||||||| |||||    ||||||||||||||||| |||    || | ||||| |||||||| ||  | ||||||||    |||||||
-------------ttgaagtaaaggagatccatggatctctcca---cacccatcctaggtgaagcagacctgtgaact---ttatgattagttgttgatg-tactctcttcttttgcagTCCTTTTATCTTCCATGGGCTATGCTCTTATTGGATGTGATATTTGGGTCATCATTAATGCCTGGACTTCTGGGTATCATGGTTGGACATCTCTACTACT
















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|29671730|gb|CB668005.1|CB668005
EST:     GAGAATATCCGAATTCTCAGATCAGCATGTATGGCCTTGTCCAACTGAGG                         TCCTTTTATCTACCATGGGCAATGCTTGGGTTGGATGTGATATTTGGCTCA
genomic: GAGAATATCCGAATTCTCAGATCAGCATGTATGGCCTTGTCCAACTGAGGgtaagcttca ... atttctgcagTCCTTTTATCTACCATGGGCAATGCTTGGGTTGGATGTGATATTTGGCTCA
EST: gi|27578253|gb|CB000948.1|CB000948
EST:     GAGAATATCCGAATTCTCAGATCAGCATGTATGGCCTTGTCCAACTGAGG                         TCCTTTTATCTACCATGGGCAATGCTTGGGTTGGATGTGATATTTGGCTCA
genomic: GAGAATATCCGAATTCTCAGATCAGCATGTATGGCCTTGTCCAACTGAGGgtaagcttca ... atttctgcagTCCTTTTATCTACCATGGGCAATGCTTGGGTTGGATGTGATATTTGGCTCA
EST: gi|218492921|gb|FG948483.1|FG948483
EST:     GAGAATATCCGAATTCTCAGATCAGCATGTATGGCCTTGTCCAACTGAGG                         TCCTTTTATCTACCATGGGCAATGCTTGGGTTGGATGTGATATTTGGCTCA
genomic: GAGAATATCCGAATTCTCAGATCAGCATGTATGGCCTTGTCCAACTGAGGgtaagcttca ... atttctgcagTCCTTTTATCTACCATGGGCAATGCTTGGGTTGGATGTGATATTTGGCTCA
EST: gi|44669030|gb|CR282464.1|CR282464
EST:     GAGAATATCCGAATTCTCAGATCAGCATGTATGGCCCTGTCCAACTGAGG                         TCCTTTTATCTACCATGGGCAATGCTTGGGTTGGATGTGATATTTGGCTCA
genomic: GAGAATATCCGAATTCTCAGATCAGCATGTATGGCCTTGTCCAACTGAGGgtaagcttca ... atttctgcagTCCTTTTATCTACCATGGGCAATGCTTGGGTTGGATGTGATATTTGGCTCA
EST: gi|86501898|gb|CI144531.1|CI144531
EST:     GAGAATATCCGAATTCTCAGATCAGCATGTATGGCCTTGTCCAACTGAGG                         TCCTTTTATCTACCATGGGCAATGCTTGGGTTGGATGTGATATTTGGCTCA
genomic: GAGAATATCCGAATTCTCAGATCAGCATGTATGGCCTTGTCCAACTGAGGgtaagcttca ... atttctgcagTCCTTTTATCTACCATGGGCAATGCTTGGGTTGGATGTGATATTTGGCTCA
EST: gi|38476086|gb|CF960219.1|CF960219
EST:     GAGAATATCCGAATTCTCAGATCAGCATGTATGGGCGGGTCCAACTGAGG                         TCCTTTTATCTACCATGGGCAATGCTTGGGTTGGATGTGATATTTGGCTCA
genomic: GAGAATATCCGAATTCTCAGATCAGCATGTATGGCCTTGTCCAACTGAGGgtaagcttca ... atttctgcagTCCTTTTATCTACCATGGGCAATGCTTGGGTTGGATGTGATATTTGGCTCA

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), 69 (downstream exon)
Score: 48

TTATTTCTTGGGAGTACCCATGGTCAGCATGCTTCTTTATGTCTGGAGCAGAGAATATCCGAATTCTCAGATCAGCATGTATGGCCTTGTCCAACTGAGGgtaagcttca ... atttctgcagTCCTTTTATCTACCATGGGCAATGCTTGGGTTGGATGTGATATTTGGCTCAGAGATACTCCCTGGCCTTCTGGGAATTCTCGTTGGACACACGTACTACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtcttgtggagcaaattatgtttgattgtggttaatatactccatttctgcagTCCTTTTATCTACCATGGGCAATGCTTGGGTTGGATGTGATATTTGGCTCAGAGATACTCCCTGGCCTTCTGGGAATTCTCGTTGGACACACGTACTACT
                               ggttaat  putative branch site (score: 48)
                                         ctccatttct  putative PPT
              aaattatgtttgatt  TA-rich tract