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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgacgttgttgtttcttgattcttgatgatgacgatagatgctttatgccctattttggatgatgatgatgttcgtttgtctgaattttggtttgtgcagGTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG

Basic information

species Oryza sativa
transcript LOC_Os02g15550.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g15550.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G120578_T02 (Zea mays), 3'ss of exon 1
gtatgtgacgttgttgtttcttgattcttgatgatgacgatagatgctttatgccctattttggatgatgatgatgttcgtttgtctgaattttggtttgtgcagGTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG
   |  | |  || | |  |||| ||| |||     || ||   |  ||    |  |  | |      ||   || ||  |    |   |||   |  |||||||||||| | ||||| || ||||||||||||||||| ||||||||||
--gtacgcccctggt-tcccttgcttcatgacatgtactattttttattaccactgtcatctcttaactggctattttattccaccctgattgctgcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG

upper sequence: LOC_Os02g15550.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G060896_T04 (Zea mays), 3'ss of exon 2
gtatgtgacgttgttgtttcttgattcttgatgatgacgatagatgctttatgccctattttggatgatgatgatgttcgtttgtctgaattttggtttgtgcagGTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG
   |  | |    |||  ||||| ||  | | |  || ||| ||| |   | || | ||||          |  |||| |     |   ||| | |  | |||||| ||| | |||||||| ||||||||||||||||||||||||||||
--gtaggcctcgattg--tcttgcttggtaacgtagatgat-gatacagca-gcacaattt--------attactgtttgac--ccctgattgttgcctctgcagGCAAAGCCAGCAAAGTTCAGTATTACAATAACCCGATGTGGCCAG
















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|218497061|gb|FG955846.1|FG955846
EST:     CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCG                         GTAAAACGAGCAAAGTGCAGTATTACAATAACACGATGTGGCCAG
genomic: CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCGgtatgtgacg ... gtttgtgcagGTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG
EST: gi|13165585|gb|AU174382.1|AU174382
EST:     CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCG                         GTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG
genomic: CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCGgtatgtgacg ... gtttgtgcagGTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG
EST: gi|58602035|gb|CK012563.1|CK012563
EST:     CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCG                         GTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG
genomic: CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCGgtatgtgacg ... gtttgtgcagGTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG
EST: gi|29642051|gb|CB647058.1|CB647058
EST:     CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCG                         GTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG
genomic: CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCGgtatgtgacg ... gtttgtgcagGTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG
EST: gi|29672898|gb|CB669173.1|CB669173
EST:     CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCG                         GTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG
genomic: CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCGgtatgtgacg ... gtttgtgcagGTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG
EST: gi|11025755|gb|AU162356.1|AU162356
EST:     CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCG                         GTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG
genomic: CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCGgtatgtgacg ... gtttgtgcagGTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG
EST: gi|88306532|gb|CI671284.1|CI671284
EST:     CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCG                         GTAAAACGAGCAAAGTGCAGTATTA
genomic: CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCGgtatgtgacg ... gtttgtgcagGTAAAACGAGCAAAGTGCAGTATTA
EST: gi|29664250|gb|CB660525.1|CB660525
EST:     CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCG                         GTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG
genomic: CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCGgtatgtgacg ... gtttgtgcagGTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG
EST: gi|88442871|gb|CI694277.1|CI694277
EST:     CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCG                         GTAAAACGAGCAAAGTGCAGTATTACAAT
genomic: CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCGgtatgtgacg ... gtttgtgcagGTAAAACGAGCAAAGTGCAGTATTACAAT
EST: gi|88352695|gb|CI678715.1|CI678715
EST:     CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCG                         GTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGGCAGGAG
genomic: CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCGgtatgtgacg ... gtttgtgcagGTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAGGAG
EST: gi|88371982|gb|CI681499.1|CI681499
EST:     CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCG                         GTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG
genomic: CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCGgtatgtgacg ... gtttgtgcagGTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG
EST: gi|29667240|gb|CB663515.1|CB663515
EST:     CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCG                         GTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG
genomic: CCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCGgtatgtgacg ... gtttgtgcagGTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG

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: 73 (upstream exon), 71 (downstream exon)
Score: 38

CCTTGCTGCGTCAAGGCCAGGGCGGCGGCGCCTGAATCCGAGGCCAAGTGCCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCGgtatgtgacg ... gtttgtgcagGTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgccctattttggatgatgatgatgttcgtttgtctgaattttggtttgtgcagGTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG
                                    tgaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgacgttgttgtttcttgattcttgatgatgacgatagatgctttatgccctattttggatgatgatgatgttcgtttgtctgaattttggtttgtgcagGTAAAACGAGCAAAGTGCAGTATTACAATAACCCGATGTGGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG