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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaataaaatcttgccgcccactttctttgctctctctccatgaagtaccttagcttagtcaacctgttatcttgcactgacacatatatatttctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG

Basic information

species Oryza sativa
transcript LOC_Os02g58730.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G375002_T03 (Zea mays), 3'ss of exon 3
gcaataaaatcttgccgcccactttctttgctctctctccatgaagtac-------cttagcttag----tcaacctgt-tatcttgcac-tgacacatatatatttctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG
|||||||  | |  | ||||||||||||  | |   | |  |  | | |        |||  ||||    |  || ||  | |||||||  | ||   |  || |   | ||  |||||| | |||||||||||||| ||||||||||| ||||| ||||| || ||||| ||||| ||||
gcaataatctttccctgcccactttcttgccccggccccggtttaatgcattcttatttattttagcttcttgacttgcatttcttgcatattacctgtgcatgtcgttttttccagTGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTG

upper sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G35020.3 (Arabidopsis thaliana), 3'ss of exon 5
----gcaataaaatcttgccgcccactttctttgctctctctccatgaagtaccttagcttagtcaacctgttatcttgcactgacacatatatatttctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG
    |   |    ||||  |    |  |||||| || | |    ||  |||   |    | ||| |  ||| ||   | || |     || |   |||   || | ||||| | |||||| | || ||||||||||||||||| || || || |||||||||||||||||||
gtttgatctgtggtcttctcctgaaacttctttcctgttt---tattcagt--ttacattcagtgattctgatagaatacatttg-gtatcttgcttttgattcttagTGGGTTCCTGAACTGAGACATTATGCTCCTGGTGTTCCCATCATCCTCGTTGGAACAAAGCTTG
















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|86900291|gb|CI296334.1|CI296334
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGC
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGC
EST: gi|3763167|gb|AU029919.1|AU029919
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|33802327|gb|CF327037.1|CF327037
EST:     TGGCCTTTTCTCTGATCAGCGAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|88832933|gb|CI369823.1|CI369823
EST:     CAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: CAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|163919913|gb|EG714915.1|EG714915
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTC
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTC
EST: gi|11233552|gb|AU164964.1|AU164964
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|58593555|gb|CF991863.1|CF991863
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|58594206|gb|CF992514.1|CF992514
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|25807453|gb|CA763414.1|CA763414
EST:     TGGCCTNTTCTCTGATCAGCAAAGCAAGCTACGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|88410858|gb|CI578664.1|CI578664
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATAC-TGAATTA-GGCAT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCAT
EST: gi|218494722|gb|FG969779.1|FG969779
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|163920990|gb|EG710403.1|EG710403
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|14980894|gb|BI305572.1|BI305572
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|117226289|gb|CT846197.1|CT846197
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|86415824|gb|CI029835.1|CI029835
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCCATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|7134822|gb|AU082691.1|AU082691
EST:     CAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: CAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|88362335|gb|CI608726.1|CI608726
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAAT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAAT
EST: gi|218499440|gb|FG950955.1|FG950955
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|218483315|gb|FG958115.1|FG958115
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|218501655|gb|FG956603.1|FG956603
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAA
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAA
EST: gi|30228239|gb|CB966130.1|CB966130
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT

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: 71 (upstream exon), 64 (downstream exon)
Score: 42

CTACAATAGGCTACGCCCGTTGAGCTATCGTGGCGCTGATGTTTTCCTGCTGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttagcttagtcaacctgttatcttgcactgacacatatatatttctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG
                          cactgac  putative branch site (score: 42)
                                          tttctgtt  putative PPT
                                   atatatatttctgtt  TA-rich tract