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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctagtccatgaatgctcaaatgtatttaaggtctttatgttgcttgaaatcatctaatcatgtcagatggtttatcatgttgttgatgatccttttcagGATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAAAAACCAGGGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAG

Basic information

species Oryza sativa
transcript LOC_Os08g42740.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42740.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G100913_T02 (Zea mays), 3'ss of exon 7
-gctagtccatgaatgctcaaatgtatttaa---ggtctttatgttgcttgaaatcatctaatcatgtcagatggtttatcatgttgttgatgatccttttcagGATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAAAAACCAGGGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAG
   ||    || | ||    ||||| ||||      || || ||   ||| ||||    | |  | ||    |   |  | ||| ||| | | ||| |||||||||||||||||||||||||||| || ||||| |||||||| ||||||||||||||||||||||||||||||||||| ||||| || ||||| ||||| || 
atttaactgataattgt--gaatgtttttattttattccttgtggcacttcaaattgcatgaaaaggtttattatgtatttatgctgt-gttcatc-ttttcagGATACTGGCTAATTCTAAGCCCTGTCCAAAGTGCAAACGGCCAATAGAGAAAAACCAGGGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAA

upper sequence: LOC_Os08g42740.3 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 7
gctagtccatgaatgctcaaatgtatttaaggtctttatgttgcttgaaatcat-ctaatcatgtcagatggtttatcatgttgttgatgatccttttcagGATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAAAAACCAGGGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAG
   |  ||||    | |    | | ||  |  || |    ||       ||||| ||   ||| |    | |||  |  |    |  ||  |   |||||||||  |||| ||||| ||||| || |||||||||||||| |||||||||||||||||||| || |||||||| || ||||| ||||| || |||||||||
-gaaaaccattttcggtttcttctcttccatctcctagcattagggtgcatcatgcttcacattttgttttgttgctgctaagttccatattgaatttcagGATTTTGGCAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAAAAACCAGGGTTGTATGCATATTACGTGCACCCCACCATGTAAATTTGAG

upper sequence: LOC_Os08g42740.3 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S178_72V6.3 (Physcomitrella patens), 3'ss of exon 7
gctagtccatgaatgctcaaatgtatttaaggtctttatgttgcttgaaatcatctaatcatgtcagatggtttatcatgttgttgatgatcctttt-cagGATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAAAAACCAGGGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAG
   |     | | |  |  | |               |||  | |   | |     | |  | ||| ||  | |    |  | || ||  || || | |||||| ||||| ||    || || ||||| ||||| ||  |||| || || |||||||| || ||||||||||| |||||||| ||||||||||||||||||
aacaacttttcagtagttgactaaggaaggcagtccgatgaagttctcattttatcatttgtttca-atcatctgaagtcattttcattttcattgtgcagGATTCTGGCAAACAGCAAACCCTGCCCTAAATGTAAGAGACCGATTGAAAAAAACCAAGGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAG

upper sequence: LOC_Os08g42740.3 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S156_28V6.1 (Physcomitrella patens), 3'ss of exon 7
gctagtccatgaatgctcaaatgtatttaaggtctttatgttgcttgaaatcatctaatcatgtcagatggtttat-catgttgttgatgatcctttt----cagGATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAAAAACCAGGGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAG
|||| || |   |  ||| ||| | | || |       ||   ||||||   || |  || |     |||   ||| | | ||  | ||     ||||    |||||| || || ||    || || ||||| ||||| ||| | ||||| ||||||||||| || || ||||| || |||||||| || |||||||||||||||
gctattcta---accctctaatctctatatgtaagaagtga-acttgaagatatttg-tcttagagaatgacctattcttattcattatcgctgttttaaaacagGATTCTTGCAAACAGCAAACCCTGCCCCAAATGTAAAAGGCCAATTGAGAAAAACCAAGGGTGTATGCACATTACTTGCACACCTCCTTGCAAATTTGAG

upper sequence: LOC_Os08g42740.3 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S9_199V6.1 (Physcomitrella patens), 3'ss of exon 8
gctagtccatgaatgctcaaatgtatttaaggtctttatgttgcttgaaatcatctaatcatgtcagatggtttatcatgttgttgatgatcctttt---cagGATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAAAAACCAGGGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAG
   | |    |   |  |  || |  |   |   ||| | ||     | | |   |  |    ||| || || | ||   || ||    ||  ||||   |||||| || || ||    || || || || ||||| ||| | ||||| || || || || || |||||||| || |||||||| ||||||||||||||||||
--aaatatgcgttcgagctgatattctgtcgacttttttcttagagaataactcatcctttattcatattgtgt-tcccttttttatcaatttttttgaacagGATTCTTGCGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAAGAATCAAGGCTGCATGCACATTACTTGCACACCACCTTGCAAATTTGAG

upper sequence: LOC_Os08g42740.3 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 3'ss of exon 7
--gctagtccatgaatgctcaaatgtat-ttaaggtctttatgttgcttgaaatcatctaatcatgtcagatggtttatcatgttgttgatgatcctttt-cagGATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAAAAACCAGGGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAG
   | |  |||  | |  | |    ||  || ||| |  | || ||       |   ||  | || |   | |  |||   |  | |   |  || ||   |||||| || || ||    || || ||||| || || ||  | ||||| ||||||||||| || ||||||||||| |||||||||||||||||||||  ||||
ggaccaaacca--actcttaagtcatagatttaggacaatgtgatgaagttccttgcct--ttatatttaacgcattagtgttatctcctttttctttgagcagGATTCTTGCAAACAGCAAACCTTGCCCCAAGTGTAAGAGGCCAATTGAGAAAAACCAAGGCTGCATGCATATCACTTGCACTCCACCTTGCAAACATGAG

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|86885710|gb|CI309837.1|CI309837
EST:     GTTTCTAGGTGGATATTAAAGAATAGCGCAGAATCTGAAAATATGAACTG                         GATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAA
genomic: GTTTCTAGGTGGATATTAAAGAATAGCGCAGAATCTGAAAATATGAACTGgtatggttca ... tccttttcagGATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAA
EST: gi|29635023|gb|CB640032.1|CB640032
EST:     GTTTCTAGGTGGATATTAAAGAATAGCGCAGAATCTGAAAATATGAACTG                         GATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAA
genomic: GTTTCTAGGTGGATATTAAAGAATAGCGCAGAATCTGAAAATATGAACTGgtatggttca ... tccttttcagGATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAA
EST: gi|29643283|gb|CB648290.1|CB648290
EST:     GTTTCTAGGTGGATATTAAAGAATAGCGCAGAATCTGAAAATATGAACTG                         GATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAA
genomic: GTTTCTAGGTGGATATTAAAGAATAGCGCAGAATCTGAAAATATGAACTGgtatggttca ... tccttttcagGATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAA
EST: gi|29622679|gb|CB627690.1|CB627690
EST:     GTTTCTAGGTGGATATTAAAGAATAGCGCAGAATCTGAAAATATGAACTG                         GATACTGGCTAATTCTAAGCCGTGCCCGANATGCAAACGACCAATAGAGAA
genomic: GTTTCTAGGTGGATATTAAAGAATAGCGCAGAATCTGAAAATATGAACTGgtatggttca ... tccttttcagGATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAA
EST: gi|29671896|gb|CB668171.1|CB668171
EST:     GTTTCTAGGTGGATATTAAAGAATAGCGCAGAATCTGAAAATATGAACTG                         GATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAA
genomic: GTTTCTAGGTGGATATTAAAGAATAGCGCAGAATCTGAAAATATGAACTGgtatggttca ... tccttttcagGATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAA
EST: gi|29669832|gb|CB666107.1|CB666107
EST:     GTTTCTAGGTGGATATTAAAGAATAGCGCAGAATCTGAAAATATGAACTG                         GATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAA
genomic: GTTTCTAGGTGGATATTAAAGAATAGCGCAGAATCTGAAAATATGAACTGgtatggttca ... tccttttcagGATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAA
EST: gi|29643281|gb|CB648288.1|CB648288
EST:     GTTTCTAGGCCGATATTAAAGAATAGCGCAGAATCTGAAAATATGAACTG                         GATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAA
genomic: GTTTCTAGGTGGATATTAAAGAATAGCGCAGAATCTGAAAATATGAACTGgtatggttca ... tccttttcagGATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAA
EST: gi|29677672|gb|CB673947.1|CB673947
EST:     GTTTCTAGGTGGATATTAAAGAATAGCGCAGAATCTGAAAATATGAACTG                         GATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAA
genomic: GTTTCTAGGTGGATATTAAAGAATAGCGCAGAATCTGAAAATATGAACTGgtatggttca ... tccttttcagGATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaatcatctaatcatgtcagatggtttatcatgttgttgatgatccttttcagGATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAAAAACCAGGGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAG
                                             tccttttc  CT-rich tract
                          tttatcat  TA-rich tract