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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttgatcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttatcatgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG

Basic information

species Oryza sativa
transcript LOC_Os06g36770.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 6
----gttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttgatcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttatcat--gcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG
    | | ||||  ||  || ||||| ||| | |||          ||    | |  |   |  || | |    || ||   |  ||| |   ||||   |  |     ||  ||||||  | | | | |  ||   | |||  ||||||| | |||| ||| |  |||| ||||||||||||||||||||||| ||| |||||||| ||||||||||| || ||||| ||||  |||||
gtaagctatactcgacaact-tatatatta-ttaac---------tttagcatttgaaattgtacttgta----taacttttaagtgaaattatgcaaaactgca-gctatttagtcca--actcatttctctttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G20830.1 (Glycine max), 3'ss of exon 5
gttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttgatcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttat----catgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG
                                        | || | || |  |   |  ||||    || |||      |  || |||||   |  |   | |  |  ||  | |  |  |   | ||  || |     ||| ||||  | || || ||    |   |  | ||| |||| ||  | |||||||| |||||||||||||| |||||||| ||||| ||||  || ||
----------------------------------------atttta-gtatgtagtggagctagt-tttcaagcc--ttgacaattacttgtttgaaactttgtagtttag--cgagttctaacacgttgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGATGGCTCGATGCCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
gttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttgatcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttat----catgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG
                                          ||  ||| |  |   |  ||||    || |||      |  || |||||   |  |   | |  |  |||  |    | ||  ||||  || |     ||| ||||  | || || ||    |   | || ||| |||||||  | |||||||| |||||||||||||| |||||||| ||||| ||||  || ||
-----------------------------------------atttttgtatgtagtggagctagt-tttcaagcc--ttgacaattacttgtttgaaactttgtagtttagtg-agtgctaac-acattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 7
gttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttgatcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttatcatgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG
                                     ||| | |    |     | |     |    ||      | |||   |||      |      |  ||    |     | | ||     |||||   || || |||||  | || || ||   || || ||| |||||||||||| | |||||||| |||||||||||||| |||||||| || || ||||  || ||
------------------------------------catggccttcactaccactgattaggaattgattcttaagtcatgcaatattacttaatattgctcatttgtagactaatagtt-----catttgacat-atacagGTAACTAGCCATGAGTCGAGCCCTGTGGCTAGATGTCGAAGAGTATATGCTCATGCTCATGATTATCATATTAATTCAATCTCAAATAACAG

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 5
gttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttg-atcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttatcatgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG
                                          ||| |  |||   ||    |||   |      |     ||   |||    |  | |||  | || || | |   || ||    |  |||||    ||  ||||| | || || ||    |||||||| |||||||| ||| | || ||||| ||||||||||||||||||||||| || || || |  |  ||
------------------------------------------ttgtttccttttgtcgtaactaaagctcagtaccaaattagtctaatgcactagtcaatttgtgttctactt-gaacttatgggtgtttctgcatatatagGTTACCAGCCAGGAGACTAACCTTGTGGCTAGATGCCGAAGAGTGTATGCCCATGCTCATGATTACCATATTAATTCAATCTCCAATAGCAG

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|2310581|gb|C26736.1|C26736
EST:     ACATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGTGGTA                         GTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCA
genomic: ACATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGTGGTAgttgtactta ... tatcatgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCA
EST: gi|58660482|gb|CK049162.1|CK049162
EST:     ATATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGT-G--                         GTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCA
genomic: ACATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGTGGTAgttgtactta ... tatcatgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCA
EST: gi|66912957|gb|CX099805.1|CX099805
EST:     ATATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGTGGTA                         GTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCA
genomic: ACATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGTGGTAgttgtactta ... tatcatgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCA
EST: gi|33796287|gb|CF324010.1|CF324010
EST:     ACATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGTGGTA                         GTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCA
genomic: ACATTTTGTTTCCACCTGGAGGCTACCCGTCATTACGTTTGCCTGTGGTAgttgtactta ... tatcatgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgcacggcaacctatgatcaagtccaaaattgactgcatttcttatcatgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG
                             aattgac  putative branch site (score: 3)
                                        tttcttatc  putative PPT
                                       atttcttat  TA-rich tract