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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataagtagcagttacagactggtgatatcgaacaaattggactattatgtttgcaattacatatctaagaaataaattaaatctcattttgtttctgtagTCAGGTTTGTGATTCACCACAGCCTTAGTAAATCTATGGAAACATACTACCAG

Basic information

species Oryza sativa
transcript LOC_Os11g48090.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g48090.4 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA09G34860.1 (Glycine max), 3'ss of exon 10
ataagtagcagttacagactggtgatatcgaacaaattggactattatgtttgcaattacatatctaaga--aataa-attaaatctcattttgtttc-tgtagTCAGGTTTGTGATTCACCACAGCCTTAGTAAATCTATGGAAACATACTACCAG
 | | | |   || || ||||   ||  | |    |   |  |||| | |||||  |  | |   | |     |||| ||| |||   |  |  |||| ||||||||||||||| || || |||||  | |||||||| ||||||||||||||||||
-tgaat-gtttttgca-actgac-atccccagtggacgtgcatattgtatttgctttaccttcattgaagctgataacatttaatgctagatattttcatgtagTCAGGTTTGTCATCCATCACAGTTTGAGTAAATCAATGGAAACATACTACCAG

upper sequence: LOC_Os11g48090.4 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv02s0087g00070.t01 (Vitis vinifera), 3'ss of exon 10
ataagtagcagttacagactggtgatatcgaacaaattggactatt-----atgtttgca-attacatatctaagaaataaattaaatctcattttgtttctgtagTCAGGTTTGTGATTCACCACAGCCTTAGTAAATCTATGGAAACATACTACCAG
 |  || | | || || | || |  ||    |     ||   ||||     ||| ||||   | |  ||| ||  | |   | |||||   | |   |   ||||||||||||||| || || |||||||| |||||||| ||||| ||||||||||||
-tgtgt-gaacttgcata-tgttattactctatgtggtgtgatattcagtcatgcttgcctgtcatgtatttattataattaataaat---agtggttgcttgtagTCAGGTTTGTCATCCATCACAGCCTAAGTAAATCAATGGAGACATACTACCAG
















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|29682976|gb|CB679251.1|CB679251
EST:     GTGGCGTTTGGAATGGGAATCAACAAGCCAGATG                         TCAGGTTTGTGATTCACCACAGCCTTAGTAAATCTATGGAAACATACTACC
genomic: GTGGCGTTTGGAATGGGAATCAACAAGCCAGATGgtgcgttaag ... gtttctgtagTCAGGTTTGTGATTCACCACAGCCTTAGTAAATCTATGGAAACATACTACC
EST: gi|58596568|gb|CK007096.1|CK007096
EST:     GTGGCGTTTGGAATGGGAATCAACAAGCCAGATG                         TCAGGTTTGTGATTCACCACAGCCTTAGTAAATCTATGGAAACATACTACC
genomic: GTGGCGTTTGGAATGGGAATCAACAAGCCAGATGgtgcgttaag ... gtttctgtagTCAGGTTTGTGATTCACCACAGCCTTAGTAAATCTATGGAAACATACTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtttgcaattacatatctaagaaataaattaaatctcattttgtttctgtagTCAGGTTTGTGATTCACCACAGCCTTAGTAAATCTATGGAAACATACTACCAG
                                    tctcattttgtttct  CT-rich tract
         aattacatatctaaga  TA-rich tract