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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCCAACCGACATTACTTTTTCCTCCACTGAGACATGCCGAAGGAGTTGAACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtgtttcctgcacctacttgctacctattctgtatttgatgtattcaatttcctttttatcagttttctcgaaatatatgctaataggcttgt...

Basic information

species Oryza sativa
transcript LOC_Os01g08700.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g08700.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM5G844173_T01 (Zea mays), 5'ss of exon 10
CTCCCAACCGACATTACTTTTTCCTCCACTGAGACATGCCGAAGGAGTTGAACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtgtttcctgc------acctacttgctacctattctgtatttgatgtattcaatt-tcctttttatcagttttctcgaaatatatgctaataggcttgt
 |||||||| ||  | |||||||| |||||| ||||||| |||||||||||  | |||||||| ||||||||||||||||||||||| || || |  |||||||||| | |||  |        |||   ||    | |  |    |    | | || | ||  |  ||   |   ||    |  || || | ||||| |       
TTCCCAACCAACGCTGCTTTTTCCACCACTGCGACATGCTGAAGGAGTTGACGTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAAACAGgtatgcaatattttttctctcaaaaccattttaaagctttctaaagaagctacggatacgatgataattgacacttgtccagtgaaagtaca-gctaaaat------

upper sequence: LOC_Os01g08700.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G107101_T01 (Zea mays), 5'ss of exon 11
CTCCCAACCGACATTACTTTTTCCTCCACTGAGACATGCCGAAGGAGTTGAACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtgtttcctgcacctacttgctacctattctgtatttgatgt--attcaatttcctttttatcagttttctcgaaatatatgctaataggcttgt--
 |||||||| ||  | |||||||| ||||||||||||||||||||||||||| | |||||||| ||||||||||||||||||||||| || || | ||||||||    | ||||    |   | ||   |    ||||  |  || |||  || | ||     | |   || |      |   | || |  ||    | | |  
TTCCCAACCAACGCTGCTTTTTCCACCACTGAGACATGCCGAAGGAGTTGAAGTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAAGCAGgtata---tttttctcaaaaacattttaaaagctttctaaagatgctgtggatacgatgataatgtagacactaaaactgttgtcta-gtgaaagaacatcttc
















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|29659877|gb|CB656152.1|CB656152
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|33675353|gb|CF303592.1|CF303592
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|58688253|gb|CK076940.1|CK076940
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|58688764|gb|CK077451.1|CK077451
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|29631643|gb|CB636652.1|CB636652
EST:     AACTCCATCATGAGCTACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|29678221|gb|CB674496.1|CB674496
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|33676336|gb|CF304575.1|CF304575
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|58687558|gb|CK076245.1|CK076245
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCAC
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCAC
EST: gi|29635195|gb|CB640204.1|CB640204
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|29662456|gb|CB658731.1|CB658731
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|58606034|gb|CK034067.1|CK034067
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|29683422|gb|CB679697.1|CB679697
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|29664618|gb|CB660893.1|CB660893
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|58605455|gb|CK033488.1|CK033488
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|29657250|gb|CB653525.1|CB653525
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|33799165|gb|CF325440.1|CF325440
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|33801382|gb|CF326562.1|CF326562
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|33798134|gb|CF324927.1|CF324927
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|29623544|gb|CB628555.1|CB628555
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|29658233|gb|CB654508.1|CB654508
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|58695779|gb|CK084466.1|CK084466
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT

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: 74 (upstream exon), 55 (downstream exon)
Score: 81

CTCCCAACCGACATTACTTTTTCCTCCACTGAGACATGCCGAAGGAGTTGAACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATTGCTTCCATGCTATGTGCTCATGGTCCCGATGTTGAGTGGAGAATATGTA




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