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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtgcaattcctgtctgataggtgtccaatccccctttgttaatgttttattttgtcccctagaagacattgttagatggtttcccctccaccgcggtgttacacaataaatgtcgtgtcttaccattgcatttacgttttcttttacagAAATATATGCCTGGGAAGAAGGTGGAAGATATCAACCATAATTATGTTGAGTGCCTGATGTACATTTTTCACCATTTAGCCCATAAG

Basic information

species Oryza sativa
transcript LOC_Os02g20930.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g20930.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G059039_T01 (Zea mays), 3'ss of exon 10
gtctgtgcaattcctg--tctgataggt------gtccaatccccctttgttaatgttttattttgtcccctagaagacattgttagatggtttcccctc-caccgcggtgttacacaataa-atgtcgtgt-cttaccattg--catt----tacgttttcttttacagAAATATATGCCTGGGAAGAAGGTGGAAGATATCAACCATAATTATGTTGAGTGCCTGATGTACATTTTTCACCATTTAGCCCATAAG
   |   || ||| |   ||||||| ||      | |  | | |  ||| |  | |||||  ||| | |     ||||    |||  |||  ||| | |   | |    ||||   || | | || |  | | | |||  |||  ||||    |||  |||   || ||||| ||||||||||||||||||||||||||||||||||||||||||||||||||| || | |||| |||||| ||||| || || |||
-gttagacacttcttaattctgatatgttttaaggcctgagcacaatttttctaggttttcattt-ttcatcgaaagatgaggtttaatgacttctcttgataacagattgtttagcattgatattttttatacatacttttgagcattctgttactgtttgagttgcagAAGTATATGCCTGGGAAGAAGGTGGAAGATATCAACCATAATTATGTTGAGTGCTTGCTATACACTTTTCATCATTTGGCTCACAAG

upper sequence: LOC_Os02g20930.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G014577_T01 (Zea mays), 3'ss of exon 10
gtctgtgcaattcctgtct--gataggtgtccaatccccctttgttaatgttttattttgtcccctag-----aagacattgttagatggtttcccctccaccgcggtgttacacaataaatgtcgtgtcttaccattgcatttacgttttcttttacagAAATATATGCCTGGGAAGAAGGTGGAAGATATCAACCATAATTATGTTGAGTGCCTGATGTACATTTTTCACCATTTAGCCCATAAG
||  || || ||| |   |   ||| || ||  |  ||        | |  |  |  ||    |  |      | ||| |  || | |      |  |  | |    |||||     |       || | | | ||||   || ||  |||   || ||||||||||||||||||||||||||||| ||||||||||||||||||||||| ||| || |||||| || ||| ||||| || ||||||
gttagtacacttcttaatttaaatatgtatctgaggcctgagcacaattactcaacgttagtactcaactgtaatgacttcttttggtaacagactatttagcatt-tgttattttttctgcacagt-tttgagcattctgtt-actgtttgagttgcagAAATATATGCCTGGGAAGAAGGTGGACGATATCAACCATAATTATGTTGAATGCTTGCTGTACACTTATCATCATTTGGCTCATAAG
















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|88364130|gb|CI610474.1|CI610474
EST:     CAGCACAAGATGCACGGCAGCTGCTTCCCCCTGTTGTTCAATTGCTCAAG                         AAATATATGCCTGGGAAGAAGGTGGAAGATATCAACCATAATTATGTTGAG
genomic: CAGCACAAGATGCACGGCAGCTGCTTCCCCCTGTTGTTCAATTGCTCAAGgtctgtgcaa ... tcttttacagAAATATATGCCTGGGAAGAAGGTGGAAGATATCAACCATAATTATGTTGAG




















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), 75 (downstream exon)
Score: 43

GAAGAAACTGGATTTGCTCAAAACAGTTGCTGCAAGCTCACCATATGCTACAGCACAAGATGCACGGCAGCTGCTTCCCCCTGTTGTTCAATTGCTCAAGgtctgtgcaa ... tcttttacagAAATATATGCCTGGGAAGAAGGTGGAAGATATCAACCATAATTATGTTGAGTGCCTGATGTACATTTTTCACCATTTAGCCCATAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgttacacaataaatgtcgtgtcttaccattgcatttacgttttcttttacagAAATATATGCCTGGGAAGAAGGTGGAAGATATCAACCATAATTATGTTGAGTGCCTGATGTACATTTTTCACCATTTAGCCCATAAG
                      gtcttac  putative branch site (score: 43)
                                    tttacgttttctttt  putative PPT
                                          ttttctttta  TA-rich tract