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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaaattgaacgctttcaatgtcttggcaattagtgtacattttggtgatatttcattacttctcaggtcatgtaagaatgtacctattttccttcccagAACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAGATTTTGGTCTGTCAGACTTCATAAAACCAG

Basic information

species Oryza sativa
transcript LOC_Os02g03410.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03410.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G053868_T02 (Zea mays), 3'ss of exon 4
gtagaaattgaacgctttcaatgtcttggcaattagtgtacattttggtgatatttcattacttc-tcaggtcatgtaagaatgtacctattttccttcccagAACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAGATTTTGGTCTGTCAGACTTCATAAAACCAG
||||||||  ||  ||| |||| |||| |||   |||   ||||| |||||||||||| |||||| ||||||||||||||| |||||||||||||||||||||||||||||||||||||| | ||||||||| |||||  ||||||| |||||||||||| ||||||| ||||| || ||||
gtagaaatcaaatactt-caatctctttgcacacagtaagcattt-ggtgatatttcactacttcctcaggtcatgtaagactgtacctattttccttcccagAACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAG

upper sequence: LOC_Os02g03410.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G08180.1 (Glycine max), 3'ss of exon 5
gtagaaattgaacgctttcaatgtcttggcaattagtgtacattttggtgatatttcattacttctcaggtcatgtaagaatgtacctattttccttcccagAACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAGATTTTGGTCTGTCAGACTTCATAAAACCAG
             |   ||||  |    |  ||   |   || | ||| | | | | |||       |    || | | | | | ||| ||| | | |  |||| || |||||||| |||||||| || || |||||||||||||| || ||||||||| |||| || || |||||||| |
-----------gtgtggtcaagtttgctggcatatctacgcaatatggagttgtgtaattttactcta---tatattaaatttttcctctttgcatgc--agAATTTTCTTTTCAAGTCAACCAAAGAAGATTCACCTTTAAAGGCTACCGATTTTGGTTTGTCTGATTTTATAAAACCTG

upper sequence: LOC_Os02g03410.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 6
gtagaaattgaacgctttca-atgtcttggcaattagtgtacattttggtg-atatttcattacttctcaggtcatgtaagaatgtacctattttccttcccagAACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAGATTTTGGTCTGTCAGACTTCATAAAACCAG
|||  | |  | | | ||   || |||    |||| ||||  | |  | |  ||| | |   |      |  | || ||  ||| |   ||  |    |  ||||| || ||||| ||||||||||| || || |||||||||||||| || ||||||||| ||||||| ||||||||||| |
gtatga-tcaagcacatttgcatatctgccaaatttgtgtgaaatgagatctatactactagatgctatacataatatattaatatttttacctattcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG

upper sequence: LOC_Os02g03410.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G37100.1 (Glycine max), 3'ss of exon 5
gtagaaattgaacgctttcaatgtcttggcaattagtgtacattttggtgatatttcattacttctcaggtcatgtaagaatgtacctattttccttcccagAACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAGATTTTGGTCTGTCAGACTTCATAAAACCAG
                   |  |||  |     |||  ||  | |  |  ||||    ||   | |      ||  |  ||  |     ||   |||  ||||| || |||||||| |||||||| || || |||||||||||||| || ||||||||| |||| || ||||||||||| |
-----------------gtatggtcaagttcgctagcata--tctacgcaatatggatttgtatatgctactatacattaaaatt----ttcctctttgcagAATTTTCTTTTCAAGTCAACCAAAGAAGATTCACCTTTAAAGGCTACCGATTTTGGTTTGTCTGATTTCATAAAACCTG

upper sequence: LOC_Os02g03410.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 4
gtagaaattgaacgctttca-atgtcttggcaattagtgtacattttggtgatatttcattacttctcaggtcatgtaagaatgtacctattttccttcccagAACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAGATTTTGGTCTGTCAGACTTCATAAAACCAG
|||  | |  | | | ||   || |||    |||| ||||  | |  | |  |||   | ||  |   |  | ||  |  |||||   ||  |    |  ||||| || ||||| ||||||| ||| || || |||||||||||||| |||||||||||| ||||||| ||||||||||| |
gtatga-tcaagcacatttgcatatctgccaaatttgtgtgaactgagatc-tatactactagatgctatataatagattaatgtttttacctattcttgcagAATTTTCTTTTTAAATCAATCAAAGAAGATTCACCTTTAAAGGCCACAGATTTTGGTTTGTCAGATTTCATAAAACCTG

upper sequence: LOC_Os02g03410.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 4
----gtagaaattgaacgctttcaatgtcttggcaattagtgtacattttggtgatatttcattacttctcaggtcatgtaagaatgtacctattttccttcccagAACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAGATTTTGGTCTGTCAGACTTCATAAAACCAG
    |||  | |        ||||||| ||||| |||   || | ||     ||  |   |||   |  |||  | | | |    | |      || || || ||||| || || |||||||||||| | || |  ||| || ||||||| ||||||||||||||||| ||||||||||| ||||
gtaggtacgattcagtttgattcaatg-cttggaaat---tgcaaatccatatgtgaaagcatc-ttcatcactttaagaagagttatgatcccttaccctctcagAATTTTCTGTTCAAATCAACCGAAGAAGGTTCATCTCTAAAGGCTACAGATTTTGGTCTGTCGGACTTCATAAAGCCAG

upper sequence: LOC_Os02g03410.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 4
gtagaaattgaacgctttcaatgtcttggcaattagtgtacattttggtgatatttcattacttctcaggtcatgtaagaatgtacctattt-tccttcccagAACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAGATTTTGGTCTGTCAGACTTCATAAAACCAG
||| ||  |||| | || |     |    |||  | | |    |||  |       |||||   || | |     |     |  |  | ||| ||      |||| || |||||||| |||||||| |||||||| ||||| ||||| || ||||||||||| |||||||||||||| || |
gtataa--tgaa-gtttgctggcacacatcaa--aattttggctttaatttgtagccattatgcctaatggtgcttccct-tacatttttttatcgcatgtagAATTTTCTTTTCAAGTCAACCAAAGAGGACTCGCCTTTGAAGGCCACGGATTTTGGTCTATCAGACTTCATAAAGCCTG

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|29644214|gb|CB649221.1|CB649221
EST:     CAGCTGAGTGCCATCTGCATGGGCTAGTTCACCGAGATATGAAGCCCGAG                         AACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAG
genomic: CAGCTGAGTGCCATCTGCATGGGCTAGTTCACCGAGATATGAAGCCCGAGgtagaaattg ... tccttcccagAACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAG
EST: gi|29657420|gb|CB653695.1|CB653695
EST:     CAGCTGAGTGCCATCTGCATGGGCTAGTTCACCGAGATATGAAGCCCGAG                         AACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAGAT
genomic: CAGCTGAGTGCCATCTGCATGGGCTAGTTCACCGAGATATGAAGCCCGAGgtagaaattg ... tccttcccagAACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatatttcattacttctcaggtcatgtaagaatgtacctattttccttcccagAACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAGATTTTGGTCTGTCAGACTTCATAAAACCAG
                                    tacctattttccttcc  CT-rich tract
     atttcatta  TA-rich tract