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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaactatcttctaagttttagggggcaaaaccaaaatcatttagatatgcttaatttttactatagttatgttgccaatgatatgtgttcttatttacagGCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTCACTACTGCTTCAGCTATTGTAATTGGTCTGTCACAGATCAAGTATTTCTTG

Basic information

species Oryza sativa
transcript LOC_Os09g06499.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g06499.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G068212_T01 (Zea mays), 3'ss of exon 3
aaactatcttctaagttttagggggcaaaaccaaaatcatttagatatgcttaatttttactatagttatgttgccaatg-atatgtgtt--cttatttacagGCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTCACTACTGCTTCAGCTATTGTAATTGGTCTGTCACAGATCAAGTATTTCTTG
  | ||| |||| | ||| |  |   || |   | |  || | | |||||||  | | |   | | |  |||  ||| |  |||||| ||   || | |||||||| |||||||| ||||| || |||||||||||||| |||||||| |||||||| |||||||| ||||| |||||| | || ||||| ||||||||||| 
--aatattttcttaatttgatagtagaacaaatacacaatcttggtatgcttgttctctgtgagaat-gtgtaaccatttcatatgttttattttgtatacagGCTTGGTTGGCTCATTCGTTTCATTAGCCATTCTGTAATATCTGGGTTCACTACAGCTTCAGCCATTGTTATTGGTTTATCCCAGATAAAGTATTTCTTA

upper sequence: LOC_Os09g06499.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G10590.1 (Glycine max), 3'ss of exon 3
------aaactatcttctaagttttagggggcaaaaccaaaatcatttagatatgcttaatttttactatagttatgttgccaatgatatgtgttcttatttacagGCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTCACTACTGCTTCAGCTATTGTAATTGGTCTGTCACAGATCAAGTATTTCTTG
      |  ||     || ||   |  |   |||| |  || |  ||  || | |    ||||| |  |||       |     || | | || ||  |||| |||||| || ||||||||||| || ||||||||||| || ||||||||||| || || |||||||||||||| |||||| | || ||    || || ||||||
tatatgattctgctggctcagcactcagcatcaaacctgaattttttatgaaagg---gattttaaggataacctacatatacttgttttttggtc--attt-cagGCTTGGATGGCTTATTCGTTTCATTAGCCATTCAGTGATATCTGGCTTTACAACCGCTTCAGCTATTGTCATTGGTTTATCTCAAGCAAAATACTTCTTG

upper sequence: LOC_Os09g06499.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G52270.1 (Glycine max), 3'ss of exon 3
------aaactatcttctaagttttagggggcaaaaccaaaatcatttagatatgcttaatttttactatagttatgttgccaatgatatgtgttcttatttacagGCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTCACTACTGCTTCAGCTATTGTAATTGGTCTGTCACAGATCAAGTATTTCTTG
      |  ||     || ||   |  |   |||  |  || |  ||  || | |    ||||| || |||    | |   || |  | | | ||  |  || |||||| || ||||| ||||| || ||||||||||| || || |||||||| || ||||||||||||||||| |||||| | || ||    || || ||||||
tatatgattctgcaggctcagcactcagtttcaagcctgaattttttatgaaagg---gattttaacgataacc-tatgtacact--tgtcttttggttctttcagGCTTGGATGGCTGATTCGTTTCATTAGCCATTCAGTGATTTCTGGCTTTACAACTGCTTCAGCTATTGTCATTGGTTTATCTCAAGCGAAATACTTCTTG

upper sequence: LOC_Os09g06499.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G12520.1 (Arabidopsis thaliana), 3'ss of exon 3
aaactatcttctaagttttagggggcaaaaccaaaatcatttagatatgcttaatttttactatagttatgttgccaatgatatgtgttcttattta---cagGCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTCACTACTGCTTCAGCTATTGTAATTGGTCTGTCACAGATCAAGTATTTCTTG
              || ||    | |    |     |  |  |   |  | |  | |||  | ||||  |    | | |  |  || |  || || |   |||||| || ||||||||||| || || || || || ||||| ||||| || || |||||||||||| ||||||||||  | || ||  | || || ||| | 
--------------gtatttatagtcttctctttgtttgtgcaaggaatcctg-tattttttgtagtgttagaacaagttgttcgtttgttttttcaacccagGCTTGGATGGCTTATTCGTTTCATAAGTCACTCAGTCATTTCTGGATTTACAACTGCTTCAGCTGTTGTAATTGGGTTATCCCAACTGAAATACTTCCTA

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|29643060|gb|CB648067.1|CB648067
EST:     TTATTGGCATTCATGGTTGGTGTATTAGAATGCTTGATGGGATTGCTAAG                         GCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTCAC
genomic: TTATTGGCATTCATGGTTGGTGTATTAGAATGCTTGATGGGATTGCTAAGgtaattctat ... ttatttacagGCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTCAC
EST: gi|29678820|gb|CB675095.1|CB675095
EST:     TTATTGGCATTCATGGTTGGTGTATTAGAATGCTTGATGGGATTGCTAAA                         GCTCGGTTGGCTTATTCGATT-ATTAGCCATTCTGTCATATCTGGCTTCAC
genomic: TTATTGGCATTCATGGTTGGTGTATTAGAATGCTTGATGGGATTGCTAAGgtaattctat ... ttatttacagGCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTCAC
EST: gi|29613614|gb|CB618627.1|CB618627
EST:     ATGGGATTGCTAAG                         GCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTTAC
genomic: ATGGGATTGCTAAGgtaattctat ... ttatttacagGCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTCAC
EST: gi|29614648|gb|CB619661.1|CB619661
EST:     TTATTGGCATTCATGGTTGGTGTATTAGAATGCTTGATGGGATTGCTAAG                         GCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTTAC
genomic: TTATTGGCATTCATGGTTGGTGTATTAGAATGCTTGATGGGATTGCTAAGgtaattctat ... ttatttacagGCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTCAC
EST: gi|29674506|gb|CB670781.1|CB670781
EST:     TTATTGGCATTCATGGTTGGTGTATTAGAATGCTTGATGGGATTGCTAAC                         GCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTCAC
genomic: TTATTGGCATTCATGGTTGGTGTATTAGAATGCTTGATGGGATTGCTAAGgtaattctat ... ttatttacagGCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTCAC

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), 71 (downstream exon)
Score: 10

TCGGTGGTATTGTTGATTCATCTAGTGAGCTGTACACAGAATTAGCCATATTATTGGCATTCATGGTTGGTGTATTAGAATGCTTGATGGGATTGCTAAGgtaattctat ... ttatttacagGCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTCACTACTGCTTCAGCTATTGTAATTGGTCTGTCACAGATCAAGTATTTCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgcttaatttttactatagttatgttgccaatgatatgtgttcttatttacagGCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTCACTACTGCTTCAGCTATTGTAATTGGTCTGTCACAGATCAAGTATTTCTTG
   gcttaat  putative branch site (score: 10)
                                          ttcttattt  putative PPT
     ttaatttttactatag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaactatcttctaagttttagggggcaaaaccaaaatcatttagatatgcttaatttttactatagttatgttgccaatgatatgtgttcttatttacagGCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTCACTACTGCTTCAGCTATTGTAATTGGTCTGTCACAGATCAAGTATTTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - -aaaccaa
- - - - - - - - - - - - - - - - - - - - - - - -tgcttaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgcc