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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_Os06g02510.3
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|218504798|gb|FG948126.1|FG948126
EST:     TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
EST: gi|33811788|gb|CF331781.1|CF331781
EST:     TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
EST: gi|163920526|gb|EG709582.1|EG709582
EST:     TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
EST: gi|58682724|gb|CK071411.1|CK071411
EST:     TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
EST: gi|86498221|gb|CI140854.1|CI140854
EST:     CCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: CCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
EST: gi|117233207|gb|CT848039.1|CT848039
EST:     TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
EST: gi|58665756|gb|CK054442.1|CK054442
EST:     TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
EST: gi|58677962|gb|CK066649.1|CK066649
EST:     TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGGGCTACTTCTGGACCAC
genomic: TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
EST: gi|29686266|gb|CB682541.1|CB682541
EST:     TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
EST: gi|58595081|gb|CF993389.1|CF993389
EST:     TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
EST: gi|25801409|gb|CA757370.1|CA757370
EST:     TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCG                         CTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCAC
genomic: TGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... 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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 72 (upstream exon), 75 (downstream exon)
Score: 88

CACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgat ... gcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCACTTCGCCCCATTGTTCAGTGCCAAACACTTAAGTACAACATGAAGTCTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctatttcttttttacccagcatctaattttcttttggtgttggcttttgcagCTAGGCAAAAGAAAGCTGTGAAGATCTTCCCCCGCCCTACTTCTGGACCACTTCGCCCCATTGTTCAGTGCCAAACACTTAAGTACAACATGAAGTCTAG
                       atctaat  putative branch site (score: 88)
                                              cttttgc  putative PPT
                       atctaattttctttt  TA-rich tract