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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattatataaatggttatgtcgtctttcaaatatttactgatttgtgcaaacaaacagcttctcactcatatatcaaaaacaaccttttttgctcctcagATGAAGATTCCAATGGCGAAATAGATAAACAAGAATTGAAGCATTGTTTCCAAAAGTTGGAAATTTCATTCACAGAGGAGGAGATAAATGACCTCTTTGA

Basic information

species Oryza sativa
transcript LOC_Os06g40720.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g40720.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G006790_T01 (Zea mays), 3'ss of exon 2
---tattatataaatggttatgtcgtctttcaaatatttactgat--ttgtgcaaacaaacagcttctcactcatatatcaaaaacaaccttttttgctcctcagATGAAGATTCCAATGGCGAAATAGATAAACAAGAATTGAAGCATTGTTTCCAAAAGTTGGAAATTTCATTCACAGAGGAGGAGATAAATGACCTCTTTGA
   |   ||||   | |   ||   |  |  | | | ||| |  |     ||  |     ||  |||||  | || | |||| ||       ||||||     |||||||||||| |||||||||||||||||| | ||| |||| |||||||| |||||| ||||||| |||||||||||||||||||||  ||| ||||||||
ttgtggaatattcgttgacttgcgctaatggagacaattatttttgacactgtcagttttcatgttctcgttgatgtgtcaagaagtggtgcttttgc-----agATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTCAAAAGCTGGAAATCTCATTCACAGAGGAGGAGATATGTGATCTCTTTGA

upper sequence: LOC_Os06g40720.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G006790_T03 (Zea mays), 3'ss of exon 2
tattatataaatggttatgtcgtctttcaaatatttactgat--ttgtgcaaacaaacagcttctcactcatatatcaaaaacaaccttttttgctcctcagATGAAGATTCCAATGGCGAAATAGATAAACAAGAATTGAAGCATTGTTTCCAAAAGTTGGAAATTTCATTCACAGAGGAGGAGATAAATGACCTCTTTGA------
    ||||   | |   ||   |  |  | | | ||| |  |     ||  |     ||  |||||  | || | |||| ||       ||||||     |||||||||||| |||||||||||||||||| | ||| |||| |||||||| |||||| ||||||| |||||||||||||||||||||  ||| ||||||||      
---aatattcgttgacttgcgctaatggagacaattatttttgacactgtcagttttcatgttctcgttgatgtgtcaagaagtggtgcttttgc-----agatgaagATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTCAAAAGCTGGAAATCTCATTCACAGAGGAGGAGATATGTGATCTCTTTGAAGCTTG
















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|88415313|gb|CI586519.1|CI586519
EST:     GAAAATCGATGAGAGCTTGAGGAAATGCAAGATCATCTTCGAGCAATTCG                         ATGAAGATTCCAATGGCGACATAGATAAACAAGAATTGAACCATTGTTTCC
genomic: GAAAATCGATGAGAGCTTGAGGAAATGCAAGATCATCTTCGAGCAATTCGgtgagattcg ... tgctcctcagATGAAGATTCCAATGGCGAAATAGATAAACAAGAATTGAAGCATTGTTTCC
EST: gi|88373009|gb|CI640460.1|CI640460
EST:     GAAAATCGATGAGAGCTTGAGGAAATGCAAGATCATCTTCGAGCAATTCG                         ATGAAGATTCCAATGGCGAAATA
genomic: GAAAATCGATGAGAGCTTGAGGAAATGCAAGATCATCTTCGAGCAATTCGgtgagattcg ... tgctcctcagATGAAGATTCCAATGGCGAAATA
EST: gi|88302426|gb|CI668272.1|CI668272
EST:     GAAAATCGATGAGAGCTTGAGGAAATGCAAGATCATCTTCGAGCAATTCG                         ATGAAGATTCCAATGGCGAAATAGATAAACAAGAAT
genomic: GAAAATCGATGAGAGCTTGAGGAAATGCAAGATCATCTTCGAGCAATTCGgtgagattcg ... tgctcctcagATGAAGATTCCAATGGCGAAATAGATAAACAAGAAT
EST: gi|88368777|gb|CI649985.1|CI649985
EST:     GAAAATCGATGAGAGCTTGAGGAAATGCAAGATCATCTTCGAGCAATTCG                         ATGAAGATTCCAATGGCGAAATAGA
genomic: GAAAATCGATGAGAGCTTGAGGAAATGCAAGATCATCTTCGAGCAATTCGgtgagattcg ... tgctcctcagATGAAGATTCCAATGGCGAAATAGA
EST: gi|88973647|gb|CI718075.1|CI718075
EST:     GAAAATCGATGAGAGCTTGAGGAAATGCAAGATCATCTTCGAGCAATTCG                         ATGAAGATTCCAATGGCGA
genomic: GAAAATCGATGAGAGCTTGAGGAAATGCAAGATCATCTTCGAGCAATTCGgtgagattcg ... tgctcctcagATGAAGATTCCAATGGCGA
EST: gi|88441153|gb|CI602175.1|CI602175
EST:     GAAAATCGATGAGAGCTTGAGGAAATGCCAGATCATCTTCGAGCAATTCG                         ATGAAGATTGCAATGGCGAAATAGATAAACAAGAATT
genomic: GAAAATCGATGAGAGCTTGAGGAAATGCAAGATCATCTTCGAGCAATTCGgtgagattcg ... tgctcctcagATGAAGATTCCAATGGCGAAATAGATAAACAAGAATT
EST: gi|88973656|gb|CI718084.1|CI718084
EST:     GAAAATCGATGAGAGCTTGAGGAAATGCAAGATCATCTTCGAGCAATTCG                         ATGAAGATTCCAATGGNGAAAT
genomic: GAAAATCGATGAGAGCTTGAGGAAATGCAAGATCATCTTCGAGCAATTCGgtgagattcg ... tgctcctcagATGAAGATTCCAATGGCGAAAT
EST: gi|88580296|gb|CI697213.1|CI697213
EST:     GAAAATCGATGAGAGCTTGAGGAAATGCAAGATCATCTTCGAGCAATTCG                         ATGAAGATTCCAATGGCGAAATAGAT
genomic: GAAAATCGATGAGAGCTTGAGGAAATGCAAGATCATCTTCGAGCAATTCGgtgagattcg ... tgctcctcagATGAAGATTCCAATGGCGAAATAGAT
EST: gi|58671024|gb|CK059710.1|CK059710
EST:     GAAAATCGATGAGAGCTTGAGGAAATGCAAGATCATCTTCGAGCAATTCG                         ATGAAGATTCCAATGGCGAAATAGATAAACAAGAATTGAAGCATTGTTTCC
genomic: GAAAATCGATGAGAGCTTGAGGAAATGCAAGATCATCTTCGAGCAATTCGgtgagattcg ... tgctcctcagATGAAGATTCCAATGGCGAAATAGATAAACAAGAATTGAAGCATTGTTTCC

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: 74 (upstream exon), 71 (downstream exon)
Score: 40

TCGCACGGGACTTCACTCAAGTCGTTCGATAGCATCATCATGAAGTTTCCGAAAATCGATGAGAGCTTGAGGAAATGCAAGATCATCTTCGAGCAATTCGgtgagattcg ... tgctcctcagATGAAGATTCCAATGGCGAAATAGATAAACAAGAATTGAAGCATTGTTTCCAAAAGTTGGAAATTTCATTCACAGAGGAGGAGATAAATGACCTCTTTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaaacaaacagcttctcactcatatatcaaaaacaaccttttttgctcctcagATGAAGATTCCAATGGCGAAATAGATAAACAAGAATTGAAGCATTGTTTCCAAAAGTTGGAAATTTCATTCACAGAGGAGGAGATAAATGACCTCTTTGA
              ttctcac  putative branch site (score: 40)
                                      ccttttttgctcctc  putative PPT
                       atatatcaaaaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattatataaatggttatgtcgtctttcaaatatttactgatttgtgcaaacaaacagcttctcactcatatatcaaaaacaaccttttttgctcctcagATGAAGATTCCAATGGCGAAATAGATAAACAAGAATTGAAGCATTGTTTCCAAAAGTTGGAAATTTCATTCACAGAGGAGGAGATAAATGACCTCTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - ttactga
- - - - - - - - - - - - - - - - - - - - -tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaacaa