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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_Os02g03410.2
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

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: 47 (upstream exon), 47 (downstream exon)
Score: 3

TTATAGTGAGAAAGATGCTGCAGTGGTGGTGCGGCAGATGCTCAAAGTGGCAGCTGAGTGCCATCTGCATGGGCTAGTTCACCGAGATATGAAGCCCGAGgtagaaattg ... tccttcccagAACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAGATTTTGGTCTGTCAGACTTCATAAAACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatatttcattacttctcaggtcatgtaagaatgtacctattttccttcccagAACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAGATTTTGGTCTGTCAGACTTCATAAAACCAG
                                    tacctattttccttcc  CT-rich tract
     atttcatta  TA-rich tract