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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtacagttgaccatctagctagctagtttgaccgcaaccatactaaatctaatttacatgctattctcgttcagGATTGTGAGAGGCGGTCAATAGCAAAGTTATTCCATCATCGATCAGAAGAGAGACGCAGCAGTCCACAACTAACAAGATGACAGAGATTCTTTCGGAATG

Basic information

species Oryza sativa
transcript LOC_Os11g09170.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g09170.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G011404_T01 (Zea mays), 3'ss of exon 6
gtgggtacagttgaccatctagctagctagtttga---ccgcaaccat-actaaatctaatttacatg---------------------------ctattct-----cgttcagGATTGTGAGAGGCGGTCAATAGCAAAGTTATTCCATCATCGATCAGAAGAGAGACGCAGCAGTCCACAACTAACAAGATGACAGAGATTCTTTCGGAATG
||||| || |||||||  | |  |||||| || ||     |||| | | | | | |   | ||  |||                            | ||||       |||||||||||||||| || |||||||| ||| |||||||||| ||  |||||||||||| || |||| ||||| ||||||||||||| |   |   | |  |||
gtgggcacggttgaccgccgaagtagctacttcgaaaattgcaagcgttagtcatttcgacttcaatggatgattttgtttgagaatttatttaattgttctacaaattttcagGATTGTGAGAGACGATCAATAGCGAAGCTATTCCATCACCGGACAGAAGAGAGACACAACAGTGCACAATTAACAAGATGACACATCCTTCCTAGTGATG
















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|88196984|gb|CI196834.1|CI196834
EST:     CCGGAGAAGCCATTTCGCCTTAATATGTTTAAG                         GATTGTGAGAGGCGGTCGATAGCAAAGTTATTCCATCATCGATCAGAAGAG
genomic: CCGGAGAAGCCATTTCGCCTTAATATGTTTAAGgtgggtacag ... tctcgttcagGATTGTGAGAGGCGGTCAATAGCAAAGTTATTCCATCATCGATCAGAAGAG
EST: gi|87024607|gb|CI259322.1|CI259322
EST:     AGCTTAGAAGAATGAACCCGGAGAAGCCATTTCGCCTTAATATGTTTAAG                         GATTGTGAGAGGCGGTCAATAGCAAAGTTATTCCATCATCGATCAGAAGAG
genomic: AGCTTAGAAGAATGAACCCGGAGAAGCCATTTCGCCTTAATATGTTTAAGgtgggtacag ... tctcgttcagGATTGTGAGAGGCGGTCAATAGCAAAGTTATTCCATCATCGATCAGAAGAG
EST: gi|88197548|gb|CI197398.1|CI197398
EST:     AGCTTAGAAGAATGAACCCGGAGAAGCCATTTCGCCTTAATATGTTTAAG                         GATTGTGAGAGGCGGTCAATAGCAAAGTTATTCCATCATCGATCAGAAGAG
genomic: AGCTTAGAAGAATGAACCCGGAGAAGCCATTTCGCCTTAATATGTTTAAGgtgggtacag ... tctcgttcagGATTGTGAGAGGCGGTCAATAGCAAAGTTATTCCATCATCGATCAGAAGAG
EST: gi|86859373|gb|CI278805.1|CI278805
EST:     GAAGAATGAACCCGGAGAAGCCATTTCGCCTTAATATGTTTAAG                         GATTGTGAGAGGCGGTCAATAGCAAAGTTATTCCATCATCGATCAGAAGAG
genomic: GAAGAATGAACCCGGAGAAGCCATTTCGCCTTAATATGTTTAAGgtgggtacag ... tctcgttcagGATTGTGAGAGGCGGTCAATAGCAAAGTTATTCCATCATCGATCAGAAGAG
EST: gi|87018951|gb|CI256836.1|CI256836
EST:     AGCTTAGAAGAATGAACCCGGAGAAGCCATTTCGCCTTAATATGTTTAAG                         GATTGTGAGAGGCGGTCAATAGCAAAGTTATTCCATCATCGATCAGAAGAG
genomic: AGCTTAGAAGAATGAACCCGGAGAAGCCATTTCGCCTTAATATGTTTAAGgtgggtacag ... tctcgttcagGATTGTGAGAGGCGGTCAATAGCAAAGTTATTCCATCATCGATCAGAAGAG
EST: gi|86479541|gb|CI122174.1|CI122174
EST:     GAATGAACCCGGAGAAGCCATTTCGCCTTAATATGTTTAAG                         GATTGTGAGAGGCGGTCAATAGCAAAGTTATTCCATCATCGATCAGAAGAG
genomic: GAATGAACCCGGAGAAGCCATTTCGCCTTAATATGTTTAAGgtgggtacag ... tctcgttcagGATTGTGAGAGGCGGTCAATAGCAAAGTTATTCCATCATCGATCAGAAGAG
EST: gi|88236846|gb|CI234697.1|CI234697
EST:     GAATGAGCCCGGAGAAGCCATTTCGCCTTAATATGTTTAAG                         GATTGTGAGAGGCGGTCAATAGCAAAGTTATTCCATCATCGATCAGAAGAG
genomic: GAATGAACCCGGAGAAGCCATTTCGCCTTAATATGTTTAAGgtgggtacag ... tctcgttcagGATTGTGAGAGGCGGTCAATAGCAAAGTTATTCCATCATCGATCAGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagctagtttgaccgcaaccatactaaatctaatttacatgctattctcgttcagGATTGTGAGAGGCGGTCAATAGCAAAGTTATTCCATCATCGATCAGAAGAGAGACGCAGCAGTCCACAACTAACAAGATGACAGAGATTCTTTCGGAATG
                                            ttctcgttc  CT-rich tract
                    atactaaatctaattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtacagttgaccatctagctagctagtttgaccgcaaccatactaaatctaatttacatgctattctcgttcagGATTGTGAGAGGCGGTCAATAGCAAAGTTATTCCATCATCGATCAGAAGAGAGACGCAGCAGTCCACAACTAACAAGATGACAGAGATTCTTTCGGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG