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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttggaacataaaactcgaaaaaagaatttctccaattcctttcctgaactaattagataaacacaatttccatccagATATTGTAACGGTCATGTTTGTTGGAAATTTCATTGGCATCGTGTGCGCACGATCATTACACTACCAATTTTATTCCTG

Basic information

species Oryza sativa
transcript LOC_Os01g07720.4
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07720.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G066362_T01 (Zea mays), 3'ss of exon 10
gtatgttggaacataaaactcgaaaaaagaatttc--tccaat------tcctttcctgaactaattagataaacacaatttccatccagATATTGTAACGGTCATGTTTGTTGGAAATTTCATTGGCATCGTGTGCGCACGATCATTACACTACCAATTTTATTCCTG
||  |||  | |  ||  ||| ||  ||  ||  |  ||| ||      |    | ||||||||| |||| |   |||| ||  |||||||||||||||| || ||||||||||| || ||||||||| | ||||| || |||||||| ||||||||||| ||||||||
gtgcgttaaaccgcaattctcaaactaatcataccattccgatctatgctttccttctgaactaactagacatgtacaacttgaatccagATATTGTAACTGTTATGTTTGTTGGCAACTTCATTGGCGTTGTGTGTGCCCGATCATTGCACTACCAATTCTATTCCTG
















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|88247507|gb|CI247356.1|CI247356
EST:     TGGACAGTTAATTTTTGCCAAGCCCAAACTGTCAACTCTTAACAAAGAAC                         ATATTGTAACGGTCATGTTTGTTGGAAATTTCATTGGCATCGTGTGCGCAC
genomic: TGGACAGTTAATTTTTGCCAAGCCCAAACTGTCAACTCTTAACAAAGAACgtatgttgga ... ttccatccagATATTGTAACGGTCATGTTTGTTGGAAATTTCATTGGCATCGTGTGCGCAC
EST: gi|33800779|gb|CF326261.1|CF326261
EST:     TGGACAGTTAATTTTTGCCAAGCCCAAACTGTCAACTCTTAACAAAGAAC                         ATATTGTAACGGTCATGTTTGTTGGAAATTTCATTGGCATCGTGTGCGCAC
genomic: TGGACAGTTAATTTTTGCCAAGCCCAAACTGTCAACTCTTAACAAAGAACgtatgttgga ... ttccatccagATATTGTAACGGTCATGTTTGTTGGAAATTTCATTGGCATCGTGTGCGCAC
EST: gi|163925452|gb|EG711565.1|EG711565
EST:     TGGACAGTTAATTTTTGCCAAGCCCAAACTGTCAACTCTTAACAAAGAAC                         ATATTGTAACGGTCATGTTTGTTGGAAATTTCATTGGCATCGTGTGCGCAC
genomic: TGGACAGTTAATTTTTGCCAAGCCCAAACTGTCAACTCTTAACAAAGAACgtatgttgga ... ttccatccagATATTGTAACGGTCATGTTTGTTGGAAATTTCATTGGCATCGTGTGCGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaatttctccaattcctttcctgaactaattagataaacacaatttccatccagATATTGTAACGGTCATGTTTGTTGGAAATTTCATTGGCATCGTGTGCGCACGATCATTACACTACCAATTTTATTCCTG
                        aactaat  putative branch site (score: 2)
                                            tttccatcc  putative PPT
                        aactaattagataaa  TA-rich tract