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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttgtagtcctgcatgaggcattaaattttatgtttgaagatgctgctatttcttttttacccagcatctaattttcttttggtgttggcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCACTTCGCCCCATTGTTCAGTGCCAAACACTTAAGTACAACATGAAGTCTAG

Basic information

species Oryza sativa
transcript LOC_Os06g02510.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g02510.3 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G49010.5 (Arabidopsis thaliana), 3'ss of exon 2
tatttgtagtcctgcatgaggcattaaattttatgtttgaagatgctgctatttcttttttacccagcatctaattttcttttggtgttggcttttgca--gCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCACTTCGCCCCATTGTTCAGTGCCAAACACTTAAGTACAACATGAAGTCTAG
  || |||||  |      | ||  |  | | || ||   |  |   | | |   |||      ||   |||     |||| |  ||||   || | ||  || ||||||||||| ||||||||||||||||| || || ||||||||||| || |||||  |||| ||  | || || ||||||||||||||||||   ||
-gttagtagtagta---atgtcaacacttctgatattgtcatgtttcgttttaagtttacactacaatctctttgggtcttattatgttatgttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTCTCCGCCCTGTTGTGCATGGTCAGACTCTTAAGTACAACATGAAGGTCAG

upper sequence: LOC_Os06g02510.3 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 2
tatttgtagtcctgcatgaggcattaaattttatgtttgaagatgctgctatttcttttttacccagcatctaattttcttttggtgttggcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCACTTCGCCCCATTGTTCAGTGCCAAACACTTAAGTACAACATGAAGTCTAG
            |     || |  || ||||| |  || || ||| |  |  |  |  |||    ||  | |  || | || ||   |  | |||  ||||||| || ||||| ||||||||||||||||| || || || ||||| || || || ||  |||||||  | || ||||||||||||||||||||   |||
----------gttagtaaagtctctacattttctactttaa-atgattttgctcttaattttaatagtgtatgtttcttttgtgtgatgtgttttctcagCTAGACAGAAGAAGGCTGTGAAGATCTTCCCTCGTCCCACCTCTGGTCCTCTCCGACCTGTTGTTCATGGTCAGACACTTAAGTACAACATGAAAGTTAG

upper sequence: LOC_Os06g02510.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv13s0047g01160.t01 (Vitis vinifera), 3'ss of exon 1
-tatttgtagtcctgcatgaggcattaaattttatgtttgaagatgctgctatttcttttttacccagcatctaattttcttttggtgttggcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCACTTCGCCCCATTGTTCAGTGCCAAACACTTAAGTACAACATGAAGTCTAG
  || | |  |  ||         ||| |||||   | |    |   ||  ||    |||| ||  ||| |  ||||   ||||  ||    | | | ||||||| || ||||||||||||||||| ||||| ||||| |||  |||||||||||||||  |||||||  | |||||  | ||||||||||||||    ||
tcatgtttgattttgtccagtcttttatattttgaatatttgtaccatgtgatgctattttaactgagc-ttaaattggtttttcatgaaaccatctccagCTAGACAGAAGAAAGCTGTGAAGATTTTCCCTCGCCCCACTGTTGGACCACTTCGCCCACTTGTTCATGGACAAACTTTGAAGTACAACATGAAAGTCAG

upper sequence: LOC_Os06g02510.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv14s0006g00820.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------tatttgtagtcctgc--atgag---gcattaaattttatgtttgaagatgctgctatttcttttttacccagcatctaattttctt-ttggtgttggcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCACTTCGCCCCATTGTTCAGTGCCAAACACTTAAGTACAACATGAAGTCTAG
                                  | |||   ||| |||  || ||   |   |||   || ||||| |  ||   |||   |  || |   |  |||| |  ||  | | |  ||  |  | | | |||||||||||||||| ||||||||||||||||| || || || |||||||||||||| || ||||| ||  | ||||| || |||||||| |||||   |||
gtagctacttaaccattttaaaatggaaatggtgtttttcctgtcttgctaattagttggtcataatgattctgtttcattatcaagcttgcttattctgtgctcgcattttcttgacatgtctgttataccatctccagCTAGGCAAAAGAAGGCTGTGAAGATCTTCCCACGGCCCACGTCTGGACCACTTCGACCTATTGTCCATGGGCAAACTCTGAAGTACAATATGAAAGTTAG

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|58595081|gb|CF993389.1|CF993389
EST:     TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
EST: gi|218504798|gb|FG948126.1|FG948126
EST:     TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
EST: gi|163920526|gb|EG709582.1|EG709582
EST:     TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
EST: gi|86498221|gb|CI140854.1|CI140854
EST:     CCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: CCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
EST: gi|7212765|gb|D40121.2|D40121
EST:     TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
EST: gi|5667631|gb|AU077891.1|AU077891
EST:     TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
EST: gi|117233207|gb|CT848039.1|CT848039
EST:     TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
EST: gi|25801409|gb|CA757370.1|CA757370
EST:     TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
EST: gi|29686266|gb|CB682541.1|CB682541
EST:     TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
EST: gi|58682724|gb|CK071411.1|CK071411
EST:     TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctatttcttttttacccagcatctaattttcttttggtgttggcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCACTTCGCCCCATTGTTCAGTGCCAAACACTTAAGTACAACATGAAGTCTAG
                       atctaat  putative branch site (score: 3)
                                              cttttgc  putative PPT
                       atctaattttctttt  TA-rich tract