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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatgttacccttatgcattttattatgttagcagacttcctaatgctttagtagtccatagacttcacacggctgaattttactctgacatgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGGAGGACATTGCAATTGTACTCATCAGTCAATAT

Basic information

species Oryza sativa
transcript LOC_Os04g05080.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g05080.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G26580.1 (Glycine max), 3'ss of exon 3
--tttatgttacccttat-gcattttattatgttagcagacttcctaatgctttagtagtccatagacttcacacggctgaattttactctgacatgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGGAGGACATTGCAATTGTACTCATCAGTCAATAT
  ||| ||| |    | | |  || |    | ||    | |    | |        |  | |    |||  |      || || | |          || |||||||||| |||||||||||||| ||||| || || || || || |||||||||||  |||||||||| || || || ||||||
tgtttgtgtcaatagtgtcgtgttctgaagtatttttggtcagtttgaaatcaagttgattc---tactctaggtttttgtatatcatgactttgattttcagAAACAACCGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGGAGGATGTTGCAATTGTGCTGATTAGCCAATAT

upper sequence: LOC_Os04g05080.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G09570.1 (Glycine max), 3'ss of exon 3
tttatgttacccttatgcattttattatgtta-gcagacttcctaatgctttagtagtccatagacttcacac--ggctgaattttactctgacatg---ttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGGAGGACATTGCAATTGTACTCATCAGTCAATAT
      ||     | |  ||  ||| |||||  | ||  ||  |  |   || | | || |     || || |  || |    ||||   |||| |    || |||||||||| |||||||||||||| ||||| || || || || || |||||||||||  |||||||||| || || || ||||||
------ttgtgtgtgtcaatagtatcatgttctgaagtatttttggtcagtttgaaatcaagttgatttactctaggtttttgtttatcatgactttgattttcagAAACAACTGTCAAACAAATTGAGGATGCATTCAAAGAATTTACAACAAGGGAGGATGTTGCAATTGTGCTGATTAGCCAATAT

upper sequence: LOC_Os04g05080.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv05s0062g00210.t01 (Vitis vinifera), 3'ss of exon 3
----tttatgttacccttatgcattttattatgttagcagacttcctaatgctttagtagtccatagacttcacacggctga--attttactctgacatgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGGAGGACATTGCAATTGTACTCATCAGTCAATAT
     ||  |  ||   | | |  ||  |||| | || |        | |   | | | |||     | ||||   |||| |  |  | | | ||   | |   ||||||||| || ||||||||||||||||| || ||||| ||||| |||| ||| |||||||| ||  |  | || || ||||||
gtgaattgggcaacttgtgtacccttatttatttcagtatctaatgaagtttatcaatggtc-----atttcat-tggctaatgaggtcattttgttctttcttagAAACAACTGTAAAACAAATTGAAGATGCATTCAAGGAATTCACCACAAAGGAAGACATTGCTATCATTTTAATAAGCCAATAT

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|88530107|gb|CI457444.1|CI457444
EST:     GATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
genomic: GATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACAgtaataactt ... catgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
EST: gi|33659255|gb|CF281868.1|CF281868
EST:     TGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACAgtaataactt ... catgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
EST: gi|313079217|gb|HO663798.1|HO663798
EST:     TGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATTGAAGATGCATTTAAGGAGTTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACAgtaataactt ... catgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
EST: gi|88973977|gb|CI002639.1|CI002639
EST:     TGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACAgtaataactt ... catgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
EST: gi|88533493|gb|CI461060.1|CI461060
EST:     TGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACAgtaataactt ... catgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
EST: gi|88536484|gb|CI466240.1|CI466240
EST:     TGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACAgtaataactt ... catgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
EST: gi|112786061|gb|EE591978.1|EE591978
EST:     TGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACAgtaataactt ... catgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
EST: gi|33659484|gb|CF282097.1|CF282097
EST:     CGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACAgtaataactt ... catgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
EST: gi|33659483|gb|CF282096.1|CF282096
EST:     CGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACAgtaataactt ... catgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
EST: gi|33809423|gb|CF330591.1|CF330591
EST:     TGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACAgtaataactt ... catgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
EST: gi|88522596|gb|CI449496.1|CI449496
EST:     CAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
genomic: CAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACAgtaataactt ... catgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
EST: gi|88275457|gb|CI395308.1|CI395308
EST:     GATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
genomic: GATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACAgtaataactt ... catgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
EST: gi|55437989|gb|CV732288.1|CV732288
EST:     TGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACAgtaataactt ... catgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGG

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: 68 (upstream exon), 60 (downstream exon)
Score: 46

GACACGGTGACTGGGTTTTAGTTGGCTGGAGTTGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACAgtaataactt ... catgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGGAGGACATTGCAATTGTACTCATCAGTCAATAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctttagtagtccatagacttcacacggctgaattttactctgacatgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGGAGGACATTGCAATTGTACTCATCAGTCAATAT
                                       ctctgac  putative branch site (score: 46)
                              tgaatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttatgttacccttatgcattttattatgttagcagacttcctaatgctttagtagtccatagacttcacacggctgaattttactctgacatgttacagAAACAACAGTCAAACAAATTGAAGATGCGTTTAAGGAGTTCACTACAAGGGAGGACATTGCAATTGTACTCATCAGTCAATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
-ttatgtt
- - - - - - ttatgca
- - - - - - - - - - - - - - - - - - - - -ctaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cggctga