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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATAGACCTTCTTGGGCCAGTGGATGAACTATTTATTGATACATACGACAGATTTGAACCTACTAATGACCCATCTTCAGACAATTGTTTCATCTCAACAgtaagtcatcgcagaaatatcaagtgtatgtaggttagacatatgaccaaaaaactgcatttgaaataaacatttaattcgatttgcttttcag

Basic information

species Oryza sativa
transcript LOC_Os07g16970.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g16970.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G047431_T01 (Zea mays), 5'ss of exon 10
GATAGACCTTCTTGGGCCAGTGGATGAACTATTTATTGATACATACGACAGATTTGAACCTACTAATGACCCATCTTCAGACAATTGTTTCATCTCAACAgtaagtcatcgcagaaatatcaagtgtatgtaggttagacatatgaccaaaaaactgcatttgaaataaacatttaattcgatttgcttttcag
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GATCGATCTTCTTGGGAAGGTGGACGAGTTATTTATCGACATATATGACAGATATGAACCTACCAATGACTCATCAGCAGACAATTGTTTCATCTCAACAgtaag-catt------atctgacacgcacctttgataga---attttcaaatatccttattt-------ccatttcaattaactaccttttcag
















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|88218519|gb|CI218368.1|CI218368
EST:     GATTTGAACCTACTAATGACCCATCTTCAGACAATTGTTTCATCTCAACA                         AGTTATGATGCCACAACACACTTTGAGTCTACTGTGATGGATGTTCTTTCC
genomic: GATTTGAACCTACTAATGACCCATCTTCAGACAATTGTTTCATCTCAACAgtaagtcatc ... tgcttttcagAGTTATGATGCCACAACACACTTTGAGTCTACTGTGATGGATGTTCTTTCC
EST: gi|44676146|gb|CR289580.1|CR289580
EST:     GATTTGAACCTACTAATGACCCATCTTCAGACAATTGTTTCATCTCAACA                         AGTTATGATGCCACAACACACTTTGAGTCTACTGTGATGGATGTTCTTTCC
genomic: GATTTGAACCTACTAATGACCCATCTTCAGACAATTGTTTCATCTCAACAgtaagtcatc ... tgcttttcagAGTTATGATGCCACAACACACTTTGAGTCTACTGTGATGGATGTTCTTTCC
EST: gi|88257202|gb|CI359590.1|CI359590
EST:     CTTCAGACAATTGTTTCATCTCAACA                         AGTTATGATGCCACAACACACTTTGAGTCTACTGTGATGGATGTTCTTTCC
genomic: CTTCAGACAATTGTTTCATCTCAACAgtaagtcatc ... tgcttttcagAGTTATGATGCCACAACACACTTTGAGTCTACTGTGATGGATGTTCTTTCC
EST: gi|86838203|gb|CI343373.1|CI343373
EST:     CCATCTTCAGACAATTGTTTCATCTCAACA                         AGTTATGATGCCACAACACACTTTGAGTCTACTGTGATGGATGTTCTTTCC
genomic: CCATCTTCAGACAATTGTTTCATCTCAACAgtaagtcatc ... tgcttttcagAGTTATGATGCCACAACACACTTTGAGTCTACTGTGATGGATGTTCTTTCC
EST: gi|86838076|gb|CI343326.1|CI343326
EST:     TCAGACAATTGTTTCATCTCAACA                         AGTTATGATGCCACAACACACTTTGAGTCTACTGTGATGGATGTTCTTTCC
genomic: TCAGACAATTGTTTCATCTCAACAgtaagtcatc ... tgcttttcagAGTTATGATGCCACAACACACTTTGAGTCTACTGTGATGGATGTTCTTTCC
EST: gi|29624787|gb|CB629798.1|CB629798
EST:     GATTTGAACCTACTAATGACCCATCTTCAGACAATTGTTTCATCTCAACA                         AGTTATGATGCCACAACACACTTTGAGTCTACTGTGATGGATGTTCTTTCC
genomic: GATTTGAACCTACTAATGACCCATCTTCAGACAATTGTTTCATCTCAACAgtaagtcatc ... tgcttttcagAGTTATGATGCCACAACACACTTTGAGTCTACTGTGATGGATGTTCTTTCC
EST: gi|88840159|gb|CI079613.1|CI079613
EST:     TAATGACCCATCTTCAGACAATTGTTTCATCTCAACA                         AGTTATGATGCCACAACACACTTTGAGTCTACTGTGATGGATGTTCTTTCC
genomic: TAATGACCCATCTTCAGACAATTGTTTCATCTCAACAgtaagtcatc ... tgcttttcagAGTTATGATGCCACAACACACTTTGAGTCTACTGTGATGGATGTTCTTTCC

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: 66 (upstream exon), 63 (downstream exon)
Score: 15

GATAGACCTTCTTGGGCCAGTGGATGAACTATTTATTGATACATACGACAGATTTGAACCTACTAATGACCCATCTTCAGACAATTGTTTCATCTCAACAgtaagtcatc ... tgcttttcagAGTTATGATGCCACAACACACTTTGAGTCTACTGTGATGGATGTTCTTTCCATCTATACAAAGATCACCGGAAAG




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