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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcacagttatgatgtatctctgctgctaatcaagtggcacgattttctgtgtttatcagcaacttttcatttgatcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCA

Basic information

species Oryza sativa
transcript LOC_Os03g50480.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G109383_T01 (Zea mays), 3'ss of exon 5
gtatcacagttatgat--gtatctctgctgctaatcaagtggca-cgattttctgtgtttatcagcaacttttcatttgatcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCA
||| |    |||      ||||||||| ||| |||||||||      ||  ||| |||| ||     || | ||||  || |||  ||||||||||| |||||||| ||||||| ||||||||| ||||| |||||||| ||||| || ||||| ||||||||||||||||||||  ||||||| ||||
gtacctattttactgctagtatctctgatgcaaatcaagtgctggtcatgctctatgtt-attgaatacatctcatc-gaactttccagGACTTCGGGATCAAATACAACATGGGAAATGGTGGGCCTGCTCCTGAATCTGTTACCGACAAGATTTTCTCTAATACAACGACAATCTCTGAATACCTCA

upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 5
gtatcacagttatgat--gtatctctgctgctaatcaagtggcacg-attttctgtgtttatcagcaacttttcatttgatcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCA
||| ||   |||      || ||| || ||| ||||||||| |||  ||  ||| |||| ||     ||   ||| | || |||  |||||||| || |||||||| || |||| |||||||||||||||||||||||| ||||| || ||||| ||||||||||||||||||||  ||||||| ||||
gtaccaagtttactgctagtgtctttgttgcaaatcaagtgccacacatgctctatgtt-attgaatacgcctcact-gaactttccagGACTTTGGTATCAAATACAATATGGGAAATGGTGGACCTGCCCCTGAATCCGTTACCGACAAGATTTTCTCTAATACAACGACAATCTCTGAATACCTCA

upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------------gtatcacagttatgat-gtatctctgctgctaatcaagtggcacgattttctgtgtttatcagcaacttttcatttgatct--tggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCA
                                                         |||| |     ||  | | |||  |  || ||| | |   |  |   | ||||  |  ||  ||   ||| |   |  |||  |  ||||| |||||||| || || || ||||||||||||||||| || ||||||||  | ||||||||||| | |   || |||| |||||| |  || || |  |
gtcagttctctttttgttctcactcttttgtgcttgttcattcgataccctcacttagtattatttgaatcctagcatcagttttgttaaactatatgttcatctctctgcttccatatgctgatttcctgctattctattcacagGATTTCGGAATTAAGTACAATATGGAAAATGGTGGACCAGCTCCTGAATCAATCACTGATAAGATTTACGAGAACACAAAGACAATCAAGGAGTACCCAA

upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------------------------------------gtatcacagttatgatgtatctctgctgctaatcaagtggcacgattttctgtgtttatcagcaacttttcatttgatcttg-gcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCA
                                                            ||||| |  ||||  |||   | |  |  |||| |  |  |  |||      |     | ||      |||  |    ||||  ||||| || ||||||||||| || ||||||||||| |||||||| ||||||||  | |||||||| || | |   || || | |||||| |  || || |  |
gtccgttctgttcttgttccatctctactgtgctatcctttcatttgaactattcgttttgtatctct-ttatt-tgttctttttttaataataagatatctagatggataataagactaagaggtgattccataccccttgtacagGATTTTGGAATCAAATACAATATGGAAAATGGAGGACCTGCTCCTGAATCAATCACTGATAAAATTTACGAGAACACTAAGACAATCAAGGAGTACCCAA

upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 6
--------------gtatcacagttatgatgtatctctgctgctaatcaagtggcacgattttctgtgtttatcagcaacttttcatttgatcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCA
                || | | ||||  | | |   |     | ||      ||| |||| |   | |||||      |  |   ||    | | |||||| || ||||| || || ||||||||||||||||||||||| |  ||  |  |||||||||||||||     || ||||   | || |  || ||| | |
tgaacgtttgaagcagataaaatttattttatttgattcggatttatggtagtgcatgattcttgttctttatttttttccctgtgttcttcccttgcagGATTTTGGAATTAAGTACAACATGGAAAATGGTGGACCTGCTCAAGAGGCAATTACTGATAAGATCTATGAGAACACAAAATCCATAAAGGAGTATATAA

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|33675938|gb|CF304177.1|CF304177
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58688355|gb|CK077042.1|CK077042
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58675297|gb|CK063984.1|CK063984
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|29612833|gb|CB617846.1|CB617846
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|29689598|gb|CB685873.1|CB685873
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|29671540|gb|CB667815.1|CB667815
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|29664693|gb|CB660968.1|CB660968
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58654844|gb|CK043524.1|CK043524
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCGGAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58682481|gb|CK071168.1|CK071168
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58670502|gb|CK059188.1|CK059188
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58666397|gb|CK055083.1|CK055083
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|29682384|gb|CB678659.1|CB678659
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|33676013|gb|CF304252.1|CF304252
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|87015499|gb|CI303105.1|CI303105
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAAT
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAAT
EST: gi|58667231|gb|CK055917.1|CK055917
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATA
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATA
EST: gi|58667790|gb|CK056476.1|CK056476
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58666319|gb|CK055005.1|CK055005
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|29614791|gb|CB619804.1|CB619804
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|29671584|gb|CB667859.1|CB667859
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58668595|gb|CK057281.1|CK057281
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATA
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATA
EST: gi|33675599|gb|CF303838.1|CF303838
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaagtggcacgattttctgtgtttatcagcaacttttcatttgatcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCA
                                   ttttcattt  TA-rich tract