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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagccagcagaactaagttgtttcctttttacaagcaaaaatatatttgtattctagaaaacaatggcttgaatactctaaataatgttatgtcttgataaatatgattgtcatgaaacttccagATAAATTGAAGGAGCATTTCTCTTCATATGGGAAGGTAGTTGAGCATCAGATAATGCTTGACCATGGCACTGGGCGGTCACGAGGCTTTGGCTTTGTCAC

Basic information

species Oryza sativa
transcript LOC_Os06g37000.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g37000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G104481_T01 (Zea mays), 3'ss of exon 4
gtagccagcagaactaagttgtttcctttttacaagcaaaaatatatttgtatt----ctagaaaacaatggcttgaatactctaa-----ataat-gttatgtcttgataa----------atatg--------attgtcatgaaacttccagATAAATTGAAGGAGCATTTCTCTTCATATGGGAAGGTAGTTGAGCATCAGATAATGCTTGACCATGGCACTGGGCGGTCACGAGGCTTTGGCTTTGTCAC
||| | |||    || |    | |  | ||| ||||||||||    | || |||     |  |||  |    ||| |||   | |      ||||| |||  | ||||  ||          | |||        |||   ||||| |||||||||||||| |||||||| ||||| || || |||||||| |||||||||||||| |||||||| ||| ||||||| || ||||| |||||||| ||||||||
gta-caagcgttgctgaaacctcttttgttt-caagcaaaaaatattctgcattgaaattgcaaattataaacttcaatgagccaccagctataattgttgggccttgcaaacattcatttcaaatgctagcaatattaatatgaaccttccagATAAATTAAAGGAGCACTTCTCATCGTACGGGAAGGTGGTTGAGCATCAGATTATGCTTGATCATAGCACTGGACGTTCACGGGGCTTTGGATTTGTCAC

upper sequence: LOC_Os06g37000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G064518_T01 (Zea mays), 3'ss of exon 4
gtagccagcagaactaagttgtttcctttttacaagcaaaa-atatat-----ttgtatt---ctagaaa-acaatggcttgaat------------actctaaataatgttatgtcttg-ataaatatgattgtcatgaaacttccagATAAATTGAAGGAGCATTTCTCTTCATATGGGAAGGTAGTTGAGCATCAGATAATGCTTGACCATGGCACTGGGCGGTCACGAGGCTTTGGCTTTGTCAC
||| | |||   ||| |    |||  | |||  |||||||| ||||       |||||||   || | || | |||  |||  ||            ||  | || |   || | ||      ||| ||||||   ||||| ||| |||||||||| |||||||| ||||| || ||||||||||| |||||||||||||| |||||||||||| ||||||| || ||||| |||||||| ||||||||
gta-caagcgacactgaaacattttttgtttgtaagcaaaagatatggcaacattgtattgaactggcaatataataactttgatcagccaccagctaccttgaaaacatttgtttcaaatgcaaacatgattaatatgaaccttgcagATAAATTAAAGGAGCACTTCTCATCGTATGGGAAGGTGGTTGAGCATCAGATTATGCTTGACCATAGCACTGGACGCTCACGTGGCTTTGGATTTGTCAC
















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|163928021|gb|EG709469.1|EG709469
EST:     TAAAACGAGAAAAATCTTTGTTGGTGGTATTCCACCATCTCTTACTGAAG                         ATAAATTGAAGGAGCATTTCTCTTCATATGGGAAGGTAGTTGAGCATCAGA
genomic: TAAAACGAGAAAAATCTTTGTTGGTGGTATTCCACCATCTCTTACTGAAGgtagccagca ... aaacttccagATAAATTGAAGGAGCATTTCTCTTCATATGGGAAGGTAGTTGAGCATCAGA




















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: 45

GAAGTTAAAAGGACTGTCCCGAGGGAGGAAATGTCGTCGAAAGATGGTCCTAAAACGAGAAAAATCTTTGTTGGTGGTATTCCACCATCTCTTACTGAAGgtagccagca ... aaacttccagATAAATTGAAGGAGCATTTCTCTTCATATGGGAAGGTAGTTGAGCATCAGATAATGCTTGACCATGGCACTGGGCGGTCACGAGGCTTTGGCTTTGTCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatactctaaataatgttatgtcttgataaatatgattgtcatgaaacttccagATAAATTGAAGGAGCATTTCTCTTCATATGGGAAGGTAGTTGAGCATCAGATAATGCTTGACCATGGCACTGGGCGGTCACGAGGCTTTGGCTTTGTCAC
                                                cttcc  CT-rich tract
        taaataatgttatgtc  TA-rich tract