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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAATGGCGTGCTCTGCTTGATGAGATGGCTGTGGTGGCTACAAAGGAATACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttttgtttcttcataatcatcagacttggaacatttcatataatgcatttaaggcacttagctaaacattgttcatttcaggcaaaacctttgtaaattaattttctttacatttttcatgaaatcag

Basic information

species Oryza sativa
transcript LOC_Os08g27840.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g27840.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA13G34560.1 (Glycine max), 5'ss of exon 9
AGAATGGCGTGCTCTGCTTGATGAGATGGCTGTGGTGGCTACAAAGGAATACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttttgtttcttcataatcatcagacttggaacatttcatataatgcatttaaggcacttagctaaacattgttcatttcaggcaaaacctttgtaaattaattttctttacatttttcatgaaatcag
||||||||||||| || | ||| ||||||||||  | |||||  |||||||||| ||||| || ||| |||||||||||||||| |||||||||||||| || ||       ||   |  ||| || |  | ||  |  | ||      || ||||  | |  |||| |  |  |      |  | |  ||||| |||  |     || ||                        
AGAATGGCGTGCTTTGATGGATCAGATGGCTGTCATTGCTACTGAGGAATACCGTTCCATTGTATTCAAGGAACCACGCTTTGTTGAGTATTTCCGCCTGgtaaggaccacatt---tagtaaacaacttaatta-agtactt------attcatt--aagttcttatcagatgacatgagaccttattcaaaaacttgattgtgaaacttg-----------------------

upper sequence: LOC_Os08g27840.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA12G35840.1 (Glycine max), 5'ss of exon 8
AGAATGGCGTGCTCTGCTTGATGAGATGGCTGTGGTGGCTACAAAGGAATACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttttgtttcttcataatcatcagacttggaacatttcatataatgcatttaaggcacttagctaaacattgttcatttcaggcaaaacctttgtaaattaattttctttacatttttcatgaaatcag
||||||||||||| || | ||| ||||||||||  | |||||  |||||||||| ||||| || ||| |||||||||||||||| |||||||||||||| || ||       |||  | |  | | | |  |  | |    |||||  | | | | | ||      |  | | | ||||| ||   |  |   |   |   | ||                              
AGAATGGCGTGCTTTGATGGATCAGATGGCTGTCATTGCTACTGAGGAATACCGTTCCATTGTATTCAAGGAACCACGCTTTGTTGAGTATTTCCGCCTGgtaaggaccacatttagtaaacaac-ttaatcaagtacttattcattgagttcttatcagatgac-atatgagc-ttgttaat---aaacttgattgtgaaacatg-----------------------------

upper sequence: LOC_Os08g27840.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA06G33380.1 (Glycine max), 5'ss of exon 8
AGAATGGCGTGCTCTGCTTGATGAGATGGCTGTGGTGGCTACAAAGGAATACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttttgtttcttcataatcatcagacttggaacatttcatataatgcatttaaggcacttagctaaacattgttcatttcaggcaaaacctttgtaaattaattttctttacatttttcatgaaatcag
||||||||| ||| || | ||||||||||||||  | || ||  |||| ||||||||||| || ||| | |||||||| ||||| |||||||||||||| || ||      ||| || ||         || ||||     || | ||  |   |||||  |   ||  |||| |||||  ||||       |   | |||||| |   ||| || |   ||             
AGAATGGCGGGCTTTGATGGATGAGATGGCTGTCATTGCCACTGAGGAGTACCGGTCCATTGTGTTCAAAGAACCACGATTTGTTGAGTATTTCCGCCTGgtaag------gttactaca--------ggaattgg-----tttaaatt-tatttttaattcctataaataaatattgtgaattttgattttagtttgtgtaaaatg--ttttttgatggtt-------------

upper sequence: LOC_Os08g27840.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA20G09810.1 (Glycine max), 5'ss of exon 9
AGAATGGCGTGCTCTGCTTGATGAGATGGCTGTGGTGGCTACAAAGGAATACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttttgtttcttcataatcatcagacttggaacatttcatataatgcatttaaggcacttagctaaacattg--ttcatttcaggcaaaacctttgtaaattaattttctttacatttttcatgaaatcag
 |||||| | ||| || | ||||||||||||||  | || ||  |||| ||||||||||| || ||| | |||||||| ||||| |||||||||||||| || ||      ||| || || ||  ||  |   |  || || |  |    | | | | |   |  | | | ||  |||  || | ||| || ||||  ||| |   ||  ||||  |                    
GGAATGGAGGGCTTTGATGGATGAGATGGCTGTCATTGCCACTGAGGAGTACCGGTCCATTGTGTTCAAAGAACCACGATTTGTTGAGTATTTCCGCCTGgtaag------gttcctacagaa--attgg---ttaaatatgtttt----tacttcttataaatatgg-tgaattttgattttagttcgggtaaaatgttttttg-ttggttttggt--------------------

upper sequence: LOC_Os08g27840.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT3G14940.1 (Arabidopsis thaliana), 5'ss of exon 9
AGAATGGCGTGCTCTGCTTGATGAGATGGCTGTGGTGGCTACAAAGGAATACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttttgtttcttcataatcatcagacttggaacatttcatataatgcatttaaggcacttagctaaacattg-ttcatttcaggcaaaacctttgtaaattaattttctttacatttttcatgaaatcag
 || ||||||||| |||||||||| ||||| || || || ||  |||||||||| ||  |||| ||||| ||||| || || ||||||||||||||||| || ||| ||       ||||||   |||  | ||  | ||     | |  ||  ||| | | || ||   || | ||| ||   ||   |||                                            
CGAGTGGCGTGCTTTGCTTGATGAAATGGCGGTTGTTGCAACTGAGGAATACCGATCTGTCGTTTTCCAAGAACCTCGATTCGTCGAGTATTTCCGCCTCgtaagtattca-----ttcatatcaatccaaatttcaccaaagtttttg-tgtgttttaagtacctaa--aaccgttggtttggttt--gcag-------------------------------------------

upper sequence: LOC_Os08g27840.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv12s0028g02180.t01 (Vitis vinifera), 5'ss of exon 8
AGAATGGCGTGCTCTGCTTGATGAGATGGCTGTGGTGGCTACAAAGGAATACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagt---gttttgtttcttcataatcatcagacttggaacatttcatataatgcatttaaggcacttagctaaacattgttcatttcaggcaaaacctttgtaaattaattttctttacatttttcatgaaatcag
|||||||||||| ||  | ||||||||||||||  | || || |||||||| || ||||| |||||||||||||| |||||||| || ||||||||||| || |||    || | ||||| |  | |  |  ||  |   | | |     | ||  ||  |    |  |   |  |  || | ||||  ||    |   ||                                     
AGAATGGCGTGCACTCATGGATGAGATGGCTGTCATTGCCACCAAGGAATATCGTTCCATTGTCTTCCAGGAACCCCGCTTTGTTGAATATTTCCGCCTGgtaagtttgattatatttctaccaacttcttggaggtctcagaatgttgttgatcaat--agcatatatgagttgatcttctgcattctagatcgatagttc------------------------------------

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|58695193|gb|CK083880.1|CK083880
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
EST: gi|14571360|gb|BI118728.1|BI118728
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAACATAGGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
EST: gi|25778121|gb|CA752873.1|CA752873
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAACATAGGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
EST: gi|5667216|gb|AU077502.1|AU077502
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAATATANGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
EST: gi|25778152|gb|CA752904.1|CA752904
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAACATAGGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
EST: gi|42591805|gb|CK738291.1|CK738291
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAACATAGGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
EST: gi|33799325|gb|CF325521.1|CF325521
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAATAT
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATAT
EST: gi|29672056|gb|CB668331.1|CB668331
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
EST: gi|27547042|gb|CA765088.2|CA765088
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAACATAGGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
EST: gi|58667732|gb|CK056418.1|CK056418
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
EST: gi|29660927|gb|CB657202.1|CB657202
EST:     ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC
genomic: ACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCC

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: 65

AGAATGGCGTGCTCTGCTTGATGAGATGGCTGTGGTGGCTACAAAGGAATACCGGTCCATCGTCTTCCAGGAACCACGCTTTGTCGAGTATTTCCGCCTTgtgagtgttt ... atgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGTGGTGGCATCGAGTCACTCCGTGCCATCCCATGGA




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