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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgcggtcatgcacttgtaccgtctgaagattctgtgatgtgcctgtatgtaacattgtgaatcttttatcagatttactcataagctgtgtgtttcagGGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGATGTGGTTTCCAATGACTTCGTTGGTGATGCAAG

Basic information

species Oryza sativa
transcript LOC_Os02g07490.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 11
-actgcggtcatgcacttgtaccgtctgaagattctgtgatgtgcctgtatgtaacattgtgaatcttttatcagatttactcataagctgtgtgttt-cagGGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGATGTGGTTTCCAATGACTTCGTTGGTGATGCAAG
   ||   | |||||||  | ||        || | | ||    | |||   ||  || |   | | |  |   ||| |   || || || | | ||| |||| | ||||||||||||||||| ||||||||||| || |||||||| |||||||| ||||||||||| || ||||||||| ||||
gtgtgttctgatgcact-attcctaagatttatgcagagagaaccatgtgcatattatcgaccaacctacagtggatct-tacacaatcttttttttttcagGACGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGATGTTGTTTCCAATGATTTTGTTGGTGATTCAAG

upper sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 11
actgcggtcatgcacttgtaccgtctgaagattctgtgatgtgcctgtatgta-acattgtga---atcttttatcagat-ttactcataagctgtgtgtttcagGGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGATGTGGTTTCCAATGACTTCGTTGGTGATGCAAG
   | | || |||  | |||    || |   || ||    | ||    |||   | |||   |   ||| |      ||| |||  ||  |  | | | || |||||| ||||||||||||||||| ||||||||||| || |||||||| ||||| || ||||||||||| || ||||||||| | ||
---gtgctc-tgctgtggtatt-cctaagatttgtgcagagagcaaccatgcgcatattaccagccatcctacggtggatcttatgcagcatatcttttttccagGGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG

upper sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 11
-----actgcggtcatgcacttgtaccgtctgaagatt-ctgtgatgtgcctgtatgtaacattgtgaatcttttatcaga-tttactcataagctgtgtgtttcagGGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGATGTGGTTTCCAATGACTTCGTTGGTGATGCAAG
      ||   |   |    || |   ||||  |   | |||||||    |||||  |||| || ||  |  ||| |  || ||| ||  | |    | ||    |||   || ||||||||  ||||||||||||| || || |||||||| |||||||| || || |||||||| ||||||||| ||||
gtatgtctattgcgttttttttttttggtctccactctgctgtgattgttctgtac-taaccttttgcttgatttctatgactttgctactgaaaaatatg---aagGTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG

upper sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G79530.1 (Arabidopsis thaliana), 3'ss of exon 11
-actgcggtcatgcacttgtaccgtctga--agattctgtgat-gtgcctgtatgtaacattgtgaatcttttatcagatttac-tcataagctgtgtgtttc----agGGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGATGTGGTTTCCAATGACTTCGTTGGTGATGCAAG
   |||  || |  | || ||  | | ||  ||||   || || |   |  |||     | |||  | || |||  |   |  | |  |    |||     ||    |||   || ||||| ||  | || ||||| ||||| || ||||||||||| ||||| || |||||||| ||||| |||||| ||||
gtatgct-tcctaaaattttattgcccgaccagatatcgtcatcgaaacattatcgtttaatgtagaactcttaataacctctcatggtttaatgtaaacctctaacagGCATGCCTCAGAAGGACCTCTTAAAGGCATTCTCGGGTACACAGATGAAGATGTCGTCTCCAATGATTTCGTCGGTGATTCAAG

upper sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv19s0085g00600.t01 (Vitis vinifera), 3'ss of exon 11
---------actgcggtcatgcacttgtaccgtctgaagat---tctgtgatgtgcctgtatgtaacattgtgaatctttta--tcagatttactcataagctgtgtgtttcagGGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGATGTGGTTTCCAATGACTTCGTTGGTGATGCAAG
             |  ||   | ||    |  |||    ||   ||| | |||  |  |||||    ||    ||   || |  | |  |||     | |  |      |  |||   || ||||||||  || |||| |||||||| || ||||| ||||||||||| || |||||||| || ||||||||  ||||
gtatactctctctctctctctctctctctctatctatctatctatctatcatgcccaagtatgatttatcccaaaatattaaaattatctttctctttgaatttccaactaaagGTATGCCTCAGAGGGGCCATTGAAGGGTATTCTTGGATACACGGATGAGGATGTTGTCTCCAATGATTTTGTTGGTGACTCAAG

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|86413519|gb|CI019104.1|CI019104
EST:     TGCCGGATTGAAAAAAGTGCATCCTATGACGATGTGAAAGCAGCCATCAA                         GGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGA
genomic: TGCCGGATTGAAAAAAGTGCATCCTATGACGATGTGAAAGCAGCCATCAAgtatgtagga ... tgtgtttcagGGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGA
EST: gi|58675895|gb|CK064582.1|CK064582
EST:     TGCCGGATTGAAAAAAGTGCATCCTATGACGATGTGAAAGCAGCCATCAA                         GGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGA
genomic: TGCCGGATTGAAAAAAGTGCATCCTATGACGATGTGAAAGCAGCCATCAAgtatgtagga ... tgtgtttcagGGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGA
EST: gi|29677604|gb|CB673879.1|CB673879
EST:     TGCCGGATTGAAAAAAGTGCATCCTATGACGATGTGAAAGCAGCCATCAA                         GGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGA
genomic: TGCCGGATTGAAAAAAGTGCATCCTATGACGATGTGAAAGCAGCCATCAAgtatgtagga ... tgtgtttcagGGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGA
EST: gi|58680325|gb|CK069012.1|CK069012
EST:     TGCCGGATTGAAAAAAGTGCATCCTATGACGATGTGAAAGCAGCCATCAA                         GGGCAGCATCAGAGGGTG
genomic: TGCCGGATTGAAAAAAGTGCATCCTATGACGATGTGAAAGCAGCCATCAAgtatgtagga ... tgtgtttcagGG-CAGCATCAGAGGGTG
EST: gi|89164374|gb|CI101462.1|CI101462
EST:     TGCCGGATTGAAAAAAGTGCATCCTATGACGATGTGAAAGCAGCCATCAA                         GGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGA
genomic: TGCCGGATTGAAAAAAGTGCATCCTATGACGATGTGAAAGCAGCCATCAAgtatgtagga ... tgtgtttcagGGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGA
EST: gi|88903442|gb|CI088980.1|CI088980
EST:     TATGACGATGTGAAAGCAGCCATCAA                         GGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGA
genomic: TATGACGATGTGAAAGCAGCCATCAAgtatgtagga ... tgtgtttcagGGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGA
EST: gi|66925358|gb|CX112206.1|CX112206
EST:     GCCGGGATTGAAAAAAGTGCATCCTATGACGATGTGAAAGCAGCCATCAA                         GGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGA
genomic: GCC-GGATTGAAAAAAGTGCATCCTATGACGATGTGAAAGCAGCCATCAAgtatgtagga ... tgtgtttcagGGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGA
EST: gi|218505391|gb|FG946304.1|FG946304
EST:     TGCCGGATTGAAAAAAGTGCATCCTATGACGATGTGAAAGCAGCCATCAA                         GGCAGCATCAGAGGGTGCACTGAAAGGTATTCT
genomic: TGCCGGATTGAAAAAAGTGCATCCTATGACGATGTGAAAGCAGCCATCAAgtatgtagga ... tgtgtttcagGGCAGCATCAGAGGGTGCACTGAAAGGTATTCT
EST: gi|86599430|gb|CI251388.1|CI251388
EST:     TGCCGGATTGAAAAAAGTGCATCCTATGACGATGTGAAAGCAGCCATCAA                         GGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGA
genomic: TGCCGGATTGAAAAAAGTGCATCCTATGACGATGTGAAAGCAGCCATCAAgtatgtagga ... tgtgtttcagGGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGA

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), 74 (downstream exon)
Score: 36

GTATGGCCTTCCGAGTTCCAACACCAAATGTGTCTGTTGTCGACTTGACCTGCCGGATTGAAAAAAGTGCATCCTATGACGATGTGAAAGCAGCCATCAAgtatgtagga ... tgtgtttcagGGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGATGTGGTTTCCAATGACTTCGTTGGTGATGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatgtaacattgtgaatcttttatcagatttactcataagctgtgtgtttcagGGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGATGTGGTTTCCAATGACTTCGTTGGTGATGCAAG
   atgtaac  putative branch site (score: 36)
                    ttttatcagattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgcggtcatgcacttgtaccgtctgaagattctgtgatgtgcctgtatgtaacattgtgaatcttttatcagatttactcataagctgtgtgtttcagGGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGATGTGGTTTCCAATGACTTCGTTGGTGATGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
actgcgg
- - - -tcatgca
- - - - - - - - tgtaccg
- - - - - - - - - - - - - - -gattctg
- - - - - - - - - - - - - - - - - - - - gtgcctg