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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtataaccagtttttgcggtggtcctgttctgcttatactattgtggggttaattcattgattgttttcagGAACTTAATTTTCAAAGTGAGGGATCTGTGCTTCATTATGGCCAGTTGCTTCAAAATTGTACAATACATTCAGTATGGGATGAACTAAAGGTTTCTTGTA

Basic information

species Oryza sativa
transcript LOC_Os03g31550.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g31550.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G050984_T01 (Zea mays), 3'ss of exon 4
gtaagtataaccagtttttgcgg-tggtcctgttctgcttatactattgtggggttaattcatt-gattgttttcagGAACTTAATTTTCAAAGTGAGGGATCTGTGCTTCATTATGGCCAGTTGCTTCAAAATTGTACAATACATTCAGTATGGGATGAACTAAAGGTTTCTTGTA
||||| |||| |      || |  |||  |||  ||  | | ||||||||| | ||||   ||| || | ||  ||||||||||||||||| | ||| |||  |||||| ||||||||||||||||| || ||||||||||||  |||||| |||||||||||||| |  |||||||
gtaagcataaacttgcgctgtgaatggcactggccttgtcaaactattgtgagattaacctatttgagtcttgacagGAACTTAATTTTCACAATGATGGAGTTGTGCTACATTATGGCCAGTTGCTCCAGAATTGTACAATAAGTTCAGTTTGGGATGAACTAAAAGCATCTTGTA
















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|58695695|gb|CK084382.1|CK084382
EST:     AGCACATGGCTACAGAACTCAAGCGAAGTCCTGAGGAGATAAAA                         GAACTTAATTTTCAAAGTGAGGGATCTGTGCTTCATTATGGCCAGTTGCTT
genomic: AGCACATGGCTACAGAACTCAAGCGAAGTCCTGAGGAGATAAAAgtaagtataa ... ttgttttcagGAACTTAATTTTCAAAGTGAGGGATCTGTGCTTCATTATGGCCAGTTGCTT
EST: gi|86903777|gb|CI302423.1|CI302423
EST:     GGATTCAGCACATGGCTACAGAACTCAAGCGAAGTCCTGAGGAGATNAAA                         GAACTTAATTTTCAAAGTGAGGGATCTGTGCTTCATTATGGCCAGTTGCTT
genomic: GGATTCAGCACATGGCTACAGAACTCAAGCGAAGTCCTGAGGAGATAAAAgtaagtataa ... ttgttttcagGAACTTAATTTTCAAAGTGAGGGATCTGTGCTTCATTATGGCCAGTTGCTT
EST: gi|88411025|gb|CI606244.1|CI606244
EST:     GGATTCAGCACATGGCTACAGAACTCAAGCGAAGTCCTGAGGAGATAAAA                         GAACTTAATTTTCAAAGTGAGGGATCTGTGCTTCATTATGGCCAGTTGCTT
genomic: GGATTCAGCACATGGCTACAGAACTCAAGCGAAGTCCTGAGGAGATAAAAgtaagtataa ... ttgttttcagGAACTTAATTTTCAAAGTGAGGGATCTGTGCTTCATTATGGCCAGTTGCTT
EST: gi|58683895|gb|CK072582.1|CK072582
EST:     GGATTCAGCACATGGCTACAGAACTCAAGCGAAGTCCTGAGGAGATAAAA                         GAACTTAATTTTCAAAGTGAGGGATCTGTGCTTCATTATGGCCAGTTGCTT
genomic: GGATTCAGCACATGGCTACAGAACTCAAGCGAAGTCCTGAGGAGATAAAAgtaagtataa ... ttgttttcagGAACTTAATTTTCAAAGTGAGGGATCTGTGCTTCATTATGGCCAGTTGCTT

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: 75 (upstream exon), 74 (downstream exon)
Score: 56

TGCTTTCAGAGGTTTTGGTGGTCCACAAGCTATGCTGATTGCAGAGAATTGGATTCAGCACATGGCTACAGAACTCAAGCGAAGTCCTGAGGAGATAAAAgtaagtataa ... ttgttttcagGAACTTAATTTTCAAAGTGAGGGATCTGTGCTTCATTATGGCCAGTTGCTTCAAAATTGTACAATACATTCAGTATGGGATGAACTAAAGGTTTCTTGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggtggtcctgttctgcttatactattgtggggttaattcattgattgttttcagGAACTTAATTTTCAAAGTGAGGGATCTGTGCTTCATTATGGCCAGTTGCTTCAAAATTGTACAATACATTCAGTATGGGATGAACTAAAGGTTTCTTGTA
                                       cattgat  putative branch site (score: 56)
                                             ttgttttc  CT-rich tract
                                 ttaattcattgatt  TA-rich tract