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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatagtaatgtcttttaaccacaattttactctcttttttaatttcgtttcacatctttaccctgaaatttgaaataacttgcagGTCCAAATAACACCGTACCTATTCATTGGTATATAATGACCAGCCCCTTCACCGATGACATCACTCGCAAATTCTTCGAAAGCCGTAAATACTTTGGCTT

Basic information

species Oryza sativa
transcript LOC_Os04g52370.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G019986_T04 (Zea mays), 3'ss of exon 5
gtgatagta--atgtcttttaaccacaattttactctcttttttaatttcgtttcacatctttaccct--gaaatttgaaataacttgcagGTCCAAATAACACCGTACCTATTCATTGGTATATAATGACCAGCCCCTTCACCGATGACATCACTCGCAAATTCTTCGAAAGCCGTAAATACTTTGGCTT
|| |||||   |   || | | |  | | || | |   |   |    |||  |||| ||  | || ||   ||| |   ||||||||||||| || | |||||| || |  || || |||||||||||||| ||||||||||| ||||    |||||||||||||||||||| ||||| |||||||||| |
gtaatagtttcaaacctgtcatcttctagtt-atttattacctcttcttctcttcagattatcacactcaaaaaatgttaataacttgcagGCCCGAGTAACACTGTGCTGATCCACTGGTATATAATGACAAGCCCCTTCACAGATGCTTCCACTCGCAAATTCTTCGAAACCCGTAGATACTTTGGCCT

upper sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv01s0011g01420.t01 (Vitis vinifera), 3'ss of exon 5
gtgatagtaatgtcttttaaccacaattttactctcttttttaatttcgtttcacatctttaccctgaaatttgaaataacttgcagGTCCAAATAACACCGTACCTATTCATTGGTATATAATGACCAGCCCCTTCACCGATGACATCACTCGCAAATTCTTCGAAAGCCGTAAATACTTTGGCTT
      |||| ||  ||   |  || |    || | | |||  ||||| ||| ||||  |  || |   |||| |  | |||||||||  ||  |      || || ||||||||||| || ||||| || || || || |||||  |||| |||||||| || ||||||| ||||||||||||| |
------gtaaggttatt---ctgcatt----ctgtttgtttgtatttcatttgacatgctgcccttattatttta--ttacttgcagGCTCAGGTGGTTTTGTGCCAATTCATTGGTACATTATGACGAGTCCATTTACTGATGATGTCACCCGCAAATTTTTTGAAAGCCATAAATACTTTGGCCT
















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|396941374|gb|HO188583.1|HO188583
EST:     ACTCCAAGCTGAACGGATTTTGTGTGTTCAAAAGCTTGCTGCTCAATCAAGTGATA                    
genomic: ACTCCAAGCTGAACGGATTTTGTGTGTTCAAAAGCTTGCTGCTCAATC-----A-Agtgatagtaa ... taact




















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: 29

GTATCGGACTTCCGTCTGGAAAGTCGCTTTTCCAACTCCAAGCTGAACGGATTTTGTGTGTTCAAAAGCTTGCTGCTCAATCAAgtgatagtaa ... taacttgcagGTCCAAATAACACCGTACCTATTCATTGGTATATAATGACCAGCCCCTTCACCGATGACATCACTCGCAAATTCTTCGAAAGCCGTAAATACTTTGGCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcttttttaatttcgtttcacatctttaccctgaaatttgaaataacttgcagGTCCAAATAACACCGTACCTATTCATTGGTATATAATGACCAGCCCCTTCACCGATGACATCACTCGCAAATTCTTCGAAAGCCGTAAATACTTTGGCTT
                                          aaataac  putative branch site (score: 29)
                                   aaatttgaaataactt  TA-rich tract