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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactacactaatgttcaatatttgtttttagaatgatatgcaaaagttgaatgatttctgatcatattttttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG

Basic information

species Oryza sativa
transcript LOC_Os03g21950.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 7
gtactacactaatgttcaatatttgtttttagaatgatatgcaaaagttgaatgatttctgatcatattttttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG
|||||| |||       ||| ||||||||          |  | || || |   | | ||||| || | |||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||
gtactatactg----ctaatgtttgttttc---------tttacaaattaac--actactgataat-tattttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACTGGCTTGAACACCAAGAAAGG

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 8
----gtactacactaatgttcaatatttgtttttagaatgatatgcaaaagttgaatgatttctgatca--tattttttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG
    |    |   ||   ||      |    |||    |  |   | |   |  | |||  ||| |     |     |   ||  |||||||| |||||||||||||| ||||| || || || ||||||||||||||
gtttgggaaatgatatcttttggggatctgatttcctgtacttctccagtttatactgaggtctaacttgctggaaatgtttggccagCTTGCACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGG

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT5G50950.3 (Arabidopsis thaliana), 3'ss of exon 6
gtactacactaatgttc----aatatttgtttttagaatgatatgcaaaagttgaatgatttctgatca--tattttttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG
||     | | || |      |  || || ||| | | | ||   ||||  || | |||  |||||     ||    |   ||   ||||||| |||||||||||||| ||||| || || || ||||||||||||||
gtttggaaatgatatctcttgaggatctgatttcatatt-attctcaaagtttcattgagctctgacttgttagaaatgtttgtctagCTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 8
--gtactacactaa-tgttcaatatttgtttttagaatgatatgcaaaagttgaatgatttctgatcatattttttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG
   | | ||   || | || | | |||   | |    |      | |  ||  |||||   | |   || || ||||   |||||||||| |||||||| ||||| || || || || |||||||| ||||||||
gtctgcaacttgaagtattaagtttttaactgttctttcccccactag-gtctaatga--acagggaatgttgtttg---agcagCTTGCACAAGGTGGCACTGCTGTAGGGACTGGATTGAACACAAAGAAAGG

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ18116 (Selaginella moellendorffii), 3'ss of exon 6
gtactacactaatgttcaatatttgtttttagaatgatatgcaaaagttgaatgatttctgatcatattttttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG
                            |  ||  |   |   |    ||| || | |||      | || |||    ||||||||| |||||||||||||| || ||||| ||| | ||||||||||||||
---------------------------gtaggagcgcgctcttacttctgattgctctcta-----aattcttgt--ggcagCTTGCACAAGGTGGAACTGCCGTGGGAACTGGCCTCAACACTAAGAAAGG

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ09601 (Selaginella moellendorffii), 3'ss of exon 6
gtactacactaatgttcaatatttgtttttagaatgatatgcaaaagttgaatgatttctgatcatattttttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG
                             ||| |       |  |  |    ||||| ||    | ||| ||      ||||||||| |||||||||||||| || ||||| ||| | ||||||||||||||
----------------------------gtaggagcgcgctcgtacttc---tgattgctctctaaattcttgt---ggcagCTTGCCCAAGGTGGAACTGCCGTGGGAACTGGCCTCAACACTAAGAAAGG

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|58692734|gb|CK081421.1|CK081421
EST:     TGAAATATGGAATTGATAGAATNGTTTGTACCTTACCACGGATGTATCAG                         CTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG
genomic: TGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAGgtactacact ... tgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG
EST: gi|33795747|gb|CF323743.1|CF323743
EST:     TGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAG                         CTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTG
genomic: TGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAGgtactacact ... tgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTG
EST: gi|58662738|gb|CK051424.1|CK051424
EST:     TGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAG                         CTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG
genomic: TGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAGgtactacact ... tgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG
EST: gi|33676561|gb|CF304800.1|CF304800
EST:     TGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAG                         CTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGGA
genomic: TGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAGgtactacact ... tgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGGA
EST: gi|33674910|gb|CF303149.1|CF303149
EST:     TGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAG                         CTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG
genomic: TGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAGgtactacact ... tgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG

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: 67 (upstream exon), 66 (downstream exon)
Score: 29

GTGAAATATGGAATTGATAGAATTGTTTGTACCTTACCACGGATGTATCAGgtactacact ... tgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagaatgatatgcaaaagttgaatgatttctgatcatattttttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG
                             ttctgat  putative branch site (score: 29)
                                        ttttttgct  putative PPT
                                tgatcatatttttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactacactaatgttcaatatttgtttttagaatgatatgcaaaagttgaatgatttctgatcatattttttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA