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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttattgatctcctgatatggctgtgtaatcgcaaaattactactccactactagttagtgtggagtaatgaactgagctgattgttgggacaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATGGGCCTGGAGCCCGGCGAGGCCTTCACCGTCCGCAACATCGCCAACATGG

Basic information

species Oryza sativa
transcript LOC_Os01g45274.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g45274.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G094165_T07 (Zea mays), 3'ss of exon 3
---------cttattgatctcctgatatggctgtgtaatcgcaaaattactactccactactagttagtgtggagtaatgaactgagctgattgttgggacaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATGGGCCTGGAGCCCGGCGAGGCCTTCACCGTCCGCAACATCGCCAACATGG
            | ||  || |   | |   | | | ||      | | |  |||  ||  | |      ||      |||  |   ||   |   ||      ||||||||||||||||| | ||| ||||||| ||||||||||||||||||||| |||||||| |||||||||||||||||||||| ||||||||||||  |||||
ccgcgcgcgggaactggactgc-attttttttctattatttttggactcc--ctcttcttttcgccgacctgagacggtgatttcccctctcttccgg------tgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTGGGCCTGCAGCCCGGCGAGGCCTTCACCGTGCGCAACATCGCCGCCATGG

upper sequence: LOC_Os01g45274.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G348512_T01 (Zea mays), 3'ss of exon 3
-----cttattgatctcctgatatggctgtgtaatcgcaaaattactactccactactagttagtgtggagtaatgaactgagctgattgttgggacaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATGGGCCTGGAGCCCGGCGAGGCCTTCACCGTCCGCAACATCGCCAACATGG
      |        | |  |    || | | |   |     ||  |  | | ||  | |   |  ||  |   |  | |||  ||  || ||  |   |||||||||||||||||| | ||| ||||||| ||||||||||||||||||||| |||||||| | ||||||||||||||  |||||||||||||||||| |||||
tcggaatcggaagagtacatactccgccgggcagctgttg--ttgattgttctctgtt-gccggcttgttgccgtcca-tgaattggctgctgc-atgcatgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTGGGCCTGCACCCCGGCGAGGCCTTTGCCGTCCGCAACATCGCCAGCATGG

upper sequence: LOC_Os01g45274.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G121878_T01 (Zea mays), 3'ss of exon 10
cttattgatctcctgatatggctgtgtaatcgcaaaattactactccactactagttagtgtggagtaatgaactgagctgattgttgggacaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATGGGCCTGGAGCCCGGCGAGGCCTTCACCGTCCGCAACATCGCCAACATGG
 |   ||     || | |     | | |   ||   |||  |  | | |      || |  ||   | |             ||| |  |    |||||||||||||||||| | ||| ||||||| || |||||||| ||||||||| |||||||| |||||||||||||||||||||| |||||||| |||  |||||
gtcgctgcatagctaacaaccgcgggaaccggcctgattttttgtgctccttctttttgcctgacctgacatgacagtgattttgctatgctgcatgcagTACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTGGGCCTGCAGCCCGGCGAGGCCTTCACCGTTCGCAACATAGCCGCCATGG

upper sequence: LOC_Os01g45274.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G121878_T06 (Zea mays), 3'ss of exon 4
cttattgatctcctgatatggctgtgtaatcgcaaaattactactccactactagttagtgtggagtaatgaactgag-ctgattgttgggacaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATGGGCCTGGAGCCCGGCGAGGCCTTCACCGTCCGCAACATCGCCAACATGG
 |   | |   ||        | |    | |      || |       || ||   |  | |     |    || | | |||||| |     |   ||||||||||||||||| | ||| ||||||| ||||||||||||||||||||  |||||||| ||||||||||||| |||||||||||||||||||||  |||||
atcgataagagccatgggaaaccgatcgaacttggttttgcgtacgtgctcctccctcttttcaccgacctgacggtgactgatt-tcccctccgctgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACACTGGGCCTGCAGCCCGGCGAGGCATTCACCGTCCGCAACATCGCCTCCATGG

upper sequence: LOC_Os01g45274.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G348512_T06 (Zea mays), 3'ss of exon 3
cttattgatctcctgatatggctgtgtaatcgcaaaattactactccactactagttagtgtgg-agtaatgaactgagctgattgttgggacaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATGGGCCTGGAGCCCGGCGAGGCCTTCACCGTCCGCAACATCGCCAACATGG
   || |    ||         ||  |   ||             || ||  | |      ||   || |   | |   |     |   | |    |||||||| |||||||| | ||| ||||||| ||||||||||||||||||||| |||||||| |||||||||||||||||||||||||||||||||||  |||||
gccatgggaaaccgatcgaacttggttttgcgtgctccagtcctccctcttttcgccgacctgacggtgactgatttcccct-ccgcctgcattgttgcagTACGTGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTGGGCCTGCAGCCCGGCGAGGCCTTCACCGTCCGCAACATCGCCGCCATGG

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|38471649|gb|CF955780.1|CF955780
EST:     CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|38471231|gb|CF955362.1|CF955362
EST:     CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGG-CGGGCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|38476030|gb|CF960163.1|CF960163
EST:     GAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACGCTCGCGTGTGCCCGTCGGTGACCATG
genomic: GAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|29615754|gb|CB620766.1|CB620766
EST:     CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|38475997|gb|CF960130.1|CF960130
EST:     CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|38477597|gb|CF961730.1|CF961730
EST:     ACAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACAGTGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCAT
genomic: ACAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACA-TGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCAT
EST: gi|38479707|gb|CF963796.1|CF963796
EST:     CAAGAAG-CGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGAGTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|38475423|gb|CF959556.1|CF959556
EST:     GCTCTTCGAGCCG-TCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCGGGCGGTGACCATG
genomic: GCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|38483318|gb|CF967120.1|CF967120
EST:     GCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: GCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|58613056|gb|CK040768.1|CK040768
EST:     GCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: GCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|36355243|gb|CF589207.1|CF589207
EST:     CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|38480149|gb|CF964238.1|CF964238
EST:     ACAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTGTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: ACAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|11442940|gb|BF430837.1|BF430837
EST:     CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|29684733|gb|CB681008.1|CB681008
EST:     CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|11442915|gb|BF430814.1|BF430814
EST:     CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|58594834|gb|CF993142.1|CF993142
EST:     ACAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGGCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: ACAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|29682804|gb|CB679079.1|CB679079
EST:     ACAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: ACAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|11442622|gb|BF430525.1|BF430525
EST:     CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|38475550|gb|CF959683.1|CF959683
EST:     CAAGAAGCCGGAGCTCTTCGAGCCGCTCAGGGGCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|38481454|gb|CF965543.1|CF965543
EST:     CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|4715140|gb|AU056257.1|AU056257
EST:     CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|29684734|gb|CB681009.1|CB681009
EST:     AGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: AGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|29664042|gb|CB660317.1|CB660317
EST:     CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|38473166|gb|CF957298.1|CF957298
EST:     CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|58585665|gb|CF983973.1|CF983973
EST:     GAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
EST: gi|38482639|gb|CF966593.1|CF966593
EST:     CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGGCGGCCAGGCACCCAAG                         TACATGGTGTTCTACGTGCGCCGACTCTCGTCGTGTGCCCAGTCGGTAGAC
genomic: CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCT-CGTGCGCCGACTCTCG-CGTGTGCCC-GTCGGT-GAC
EST: gi|38480358|gb|CF964447.1|CF964447
EST:     CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAG                         TACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG
genomic: CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgct ... acaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccactactagttagtgtggagtaatgaactgagctgattgttgggacaaatgcagTACATGGTGTTCTCGTGCGCCGACTCTCGCGTGTGCCCGTCGGTGACCATGGGCCTGGAGCCCGGCGAGGCCTTCACCGTCCGCAACATCGCCAACATGG
                               agctgat  putative branch site (score: 4)
                     taatgaa  TA-rich tract