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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcgggttcccctctcccactcgctagctaggaggaggaggcgagcggctgattcctgattggttggttcccgtgggttttttggttgcagGTGGAGGGGCGGGTGGTGTCGGCGATTGGCCCCGGCCTCCTCGTCCTTGTCGGCGTCCACGAGGCCGACACCGACGCCGACGCTGACTACAT

Basic information

species Oryza sativa
transcript LOC_Os01g14040.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14040.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G100260_T03 (Zea mays), 3'ss of exon 1
gtgagcgggttcccctctcccactcgctagctaggaggaggaggcgagcggctgattcctgattggttggttcccgtgggttttttggttgcagGTGGAGGGGCGGGTGGTGTCGGCGATTGGCCCCGGCCTCCTCGTCCTTGTCGGCGTCCACGAGGCCGACACCGACGCCGACGCTGACTACAT
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gtgagcgcgctctccagtgc-act-gcaattcgctcggaa------------tcttccctgaatgct---tctctgtggg-------gtcgcagGTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACAT
















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|88395326|gb|CI611243.1|CI611243
EST:     AGAGGGAGATGAGGGCCGTGGTGCAGCGTGTCCTCTCGGCAAGCGTCGAG                         GTGGAGGGGCGGGTGGTGTCGGCGATTGGCCCCGGCCTCCTCGTCCTTGTC
genomic: AGAGGGAGATGAGGGCCGTGGTGCAGCGTGTCCTCTCGGCAAGCGTCGAGgtgagcgggt ... ttggttgcagGTGGAGGGGCGGGTGGTGTCGGCGATTGGCCCCGGCCTCCTCGTCCTTGTC
EST: gi|88692898|gb|CI736473.1|CI736473
EST:     AGAGGGAGATGAGGGCCGTGGTGCAGCGTGTCCTCTCGGCAAGCGTCGAG                         GTGGAGGGGCGGGTGGTGTCGGCGATTGGCCCCGGCCTCCTCGTCCTTGTC
genomic: AGAGGGAGATGAGGGCCGTGGTGCAGCGTGTCCTCTCGGCAAGCGTCGAGgtgagcgggt ... ttggttgcagGTGGAGGGGCGGGTGGTGTCGGCGATTGGCCCCGGCCTCCTCGTCCTTGTC
EST: gi|58690528|gb|CK079215.1|CK079215
EST:     AGAGGGAGATGAGGGCCGTGGTGCAGCGTGTCCTCTCGGCAAGCGTCGAG                         GTGGAGGGGCGGGTGGTGTCGGCGATTGGCCCCGGCCTCCTCGTCCTTGTC
genomic: AGAGGGAGATGAGGGCCGTGGTGCAGCGTGTCCTCTCGGCAAGCGTCGAGgtgagcgggt ... ttggttgcagGTGGAGGGGCGGGTGGTGTCGGCGATTGGCCCCGGCCTCCTCGTCCTTGTC
EST: gi|88422041|gb|CI611661.1|CI611661
EST:     AGAGGGAGATGAGGGCCGTGGTGCAGCGTGTCCTCTCGGCAAGCGTCGAG                         GTGGAGGGGCGGGTGGTGTCGGCGATTGGCCCCGGCCTCCTCGTCCTTGTC
genomic: AGAGGGAGATGAGGGCCGTGGTGCAGCGTGTCCTCTCGGCAAGCGTCGAGgtgagcgggt ... ttggttgcagGTGGAGGGGCGGGTGGTGTCGGCGATTGGCCCCGGCCTCCTCGTCCTTGTC

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: 35 (upstream exon), 61 (downstream exon)
Score: 11

GGCGCCGCACGCGAAGCCCGGAGATCCGGCTGCGGCGGAGGCGAGAAGGAAGAGGGAGATGAGGGCCGTGGTGCAGCGTGTCCTCTCGGCAAGCGTCGAGgtgagcgggt ... ttggttgcagGTGGAGGGGCGGGTGGTGTCGGCGATTGGCCCCGGCCTCCTCGTCCTTGTCGGCGTCCACGAGGCCGACACCGACGCCGACGCTGACTACAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaggcgagcggctgattcctgattggttggttcccgtgggttttttggttgcagGTGGAGGGGCGGGTGGTGTCGGCGATTGGCCCCGGCCTCCTCGTCCTTGTCGGCGTCCACGAGGCCGACACCGACGCCGACGCTGACTACAT
                 tcctgat  putative branch site (score: 11)
                                         tttttt  putative PPT
                                         tttttt  TA-rich tract