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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgatatgtttgatatgcttgcatttttctatcagtttatttcatacaaggtatttcttgtcaaaagtctgtttcctccgttctaattcctctttagaatccagTGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCCAGGGATAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGAC

Basic information

species Oryza sativa
transcript LOC_Os10g35960.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G085747_T05 (Zea mays), 3'ss of exon 8
gtatatgatatgtttgatatgcttgcatttttctatcagtttatttcatacaaggtatttcttgtcaaaagtctgtttcctccgttctaattcctctttagaatccagTGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCCAGGGATAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGAC
|||| |||||||||||| ||  ||| |   ||   | ||  || || |||     | ||  ||||||||| | || ||| | | ||||||||||||||||||||||||||||||||||||||||||||  |||||||||                                                                     
gtatctgatatgtttgacatttttgtaaaatttccttagCCTACTTTATATGGAATGTTCATTGTCAAAAATGTGGTTCGTACATTCTAATTCCTCTTTAGAATCCAGTGCTGGGATAGGTGTGCTTAGCATGGCTAAA---------------------------------------------------------------------

upper sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G085747_T04 (Zea mays), 3'ss of exon 8
gtatatgatatgtttgatatgcttgcatttttctatcagtttatttcatacaaggtatttcttgtcaaaagtctgtttcctccgttctaattcctctttagaatccagTGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCCAGGGATAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGAC
|||| |||||||||||| ||  ||| |   ||   | ||  || || |||     | ||  ||||||||| | || ||| | | ||||||||||||||||||||||||||||||||||||||||||||  |||||||||||||| ||| |||||||||| |||||  |||| | ||||||||||||||||||||||||||||||||||
gtatctgatatgtttgacatttttgtaaaatttccttagcctactttatatggaatgttcattgtcaaaaatgtggttcgtacattctaattcctctttagaatccagTGCTGGGATAGGTGTGCTTAGCATGGCTAAACAGGCAATGTTAAGGATGCCTGGGATCCACAGAACCGGGGAAGGGCATAATCAATTCTGGGTTCTGGAC

upper sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G085747_T02 (Zea mays), 3'ss of exon 9
gtatatgatatgtttgatatgcttgcatttttctatcagtttatttcatacaaggtatttcttgtcaaaagtctgtttcctccgttctaattcctctttagaatccagTGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCCAGGGATAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGAC
|||| |||||||||||| ||  ||| |   ||   | ||  || || |||     | ||  ||||||||| | || ||| | | ||||||||||||||||||||||||||||||||||||||||||||  |||||||||||||| ||| |||||||||| |||||  |||| | |||||||||||||||||||||||||||       
gtatctgatatgtttgacatttttgtaaaatttccttagcctactttatatggaatgttcattgtcaaaaatgtggttcgtacattctaattcctctttagAATCCAGTGCTGGGATAGGTGTGCTTAGCATGGCTAAACAGGCAATGTTAAGGATGCCTGGGATCCACAGAACCGGGGAAGGGCATAATCAATTCTGGGT-------

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|58596497|gb|CK007025.1|CK007025
EST:     GGGAGCTGGAAG                         TGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCC
genomic: GGGAGCTGGAAGgtatatgata ... tagaatccagTGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCC
EST: gi|58673493|gb|CK062179.1|CK062179
EST:     CCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAGCTGGAAG                         TGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCC
genomic: CCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAGCTGGAAGgtatatgata ... tagaatccagTGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCC
EST: gi|58665242|gb|CK053928.1|CK053928
EST:     CCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAGCTGGAAG                         TGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCC
genomic: CCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAGCTGGAAGgtatatgata ... tagaatccagTGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCC
EST: gi|58601869|gb|CK012397.1|CK012397
EST:     GCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAGCTGGAAG                         TGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCC
genomic: CCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAGCTGGAAGgtatatgata ... tagaatccagTGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCC
EST: gi|58659006|gb|CK047686.1|CK047686
EST:     CCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAGCTGGAAG                         TGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCC
genomic: CCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAGCTGGAAGgtatatgata ... tagaatccagTGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCC
EST: gi|29624067|gb|CB629078.1|CB629078
EST:     CCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAGCTGGAAG                         TGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGC
genomic: CCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAGCTGGAAGgtatatgata ... tagaatccagTGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGC
EST: gi|29687359|gb|CB683634.1|CB683634
EST:     CCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAGCTGGAAG                         TGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCT
genomic: CCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAGCTGGAAGgtatatgata ... tagaatccagTGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCT
EST: gi|29624065|gb|CB629076.1|CB629076
EST:     CCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAGCTGGAAG                         TGCTGGGATAGGTGTGCTTAATATGGCTAAA
genomic: CCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAGCTGGAAGgtatatgata ... tagaatccagTGCTGGGATAGGTGTGCTTAATATGGCTAAA
EST: gi|29678813|gb|CB675088.1|CB675088
EST:     CCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAGCTGGAAG                         TGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCC
genomic: CCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAGCTGGAAGgtatatgata ... tagaatccagTGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCC

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: 70 (upstream exon), 74 (downstream exon)
Score: 52

CAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAAGGTCGACCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAGCTGGAAGgtatatgata ... tagaatccagTGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCCAGGGATAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtatttcttgtcaaaagtctgtttcctccgttctaattcctctttagaatccagTGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCCAGGGATAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGAC
                               ttctaat  putative branch site (score: 52)
                  tctgtttcctccgttc  CT-rich tract
                               ttctaatt  TA-rich tract