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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGAGCACGCCTTATCTCTCATGCTGGCAGTCTTTCAAACCTTGCTAAGTGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAGgttgttaaaactgactgatttcttggtagctctcaaattccaagtaactgtatggaaagttgtttcaaagtactgatcatagagtatacgtcaacttcttatgcttctttactttctcccag

Basic information

species Oryza sativa
transcript LOC_Os03g22880.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g22880.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G110233_T03 (Zea mays), 5'ss of exon 5
TTGGAGCACGCCTTATCTCTCATGCTGGCAGTCTTTCAAACCTTGCTAAGTGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAGgttgttaaaactgactgatttcttggtagctc------tcaaa---ttccaagtaactgtatggaaagttgtttcaaagtactgatcatagagtatacgtca-------------acttcttatgcttctttactttctcccag
||||||| ||||| |||||||||||||||||||||||||||||||| |||||| | || ||||| || || |||||||||||||| ||||| || ||||||||  ||||        || |  ||||  |||      ||||    ||  |  ||||| | |     || |||  ||| || | ||  | ||||| |  |               || |||||  ||| |    | |   ||||
TTGGAGCTCGCCTAATCTCTCATGCTGGCAGTCTTTCAAACCTTGCCAAGTGTGCAGCTTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgtttataaattcttaacatcttatggtttctcactgcttcaatgccttttagttaactctgtaatttgtggttataaactagtcatattcgagtaaatcttgctagtgggaagacacctcttacacttgtcatttgtacaccag

upper sequence: LOC_Os03g22880.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G144995_T01 (Zea mays), 5'ss of exon 5
TTGGAGCACGCCTTATCTCTCATGCTGGCAGTCTTTCAAACCTTGCTAAGTGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAGgttg--------ttaaaactgact---gatttcttggtagctctcaaattccaagt-aactgtatggaaagttgtttcaaagtactgatcatagagtatacgtcaac------------ttcttatgcttctttactttctcccag
||||||| ||||| ||||||||||||||||||||||||||||||||||||||| | |||||||| || || |||||||||||||| ||||| || |||||||||        |||||||    |   | ||||    |   ||   | |||  ||| |||| | |      | |||  | | |  | ||  | |||||    |                  ||||  ||| |    | ||  ||||
TTGGAGCTCGCCTAATCTCTCATGCTGGCAGTCTTTCAAACCTTGCTAAGTGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaattcttaaaacatcttttgggtttcccactgtttcaatagttctcagttaactctgtaatttatggttatacactggtcatacttgagtaagtcttgctagtaggaagatgcccttacacttgtcctttgtccaccag

upper sequence: LOC_Os03g22880.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT3G12860.1 (Arabidopsis thaliana), 5'ss of exon 5
TTGGAGCACGCCTTATCTCTCATGCTGGCAGTCTTTCAAACCTTGCTAAGTGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAGgttgttaaaactgactgatttcttggtagctctcaaattccaagtaactgtatggaaagttgtttcaaagtactgatcatagagtatacgtcaacttcttatgcttctttactttctcccag
|||| ||  |  | || || ||||| || |||||  |||| ||||| ||||| ||  | || || |||||||| || |||||||| ||||||||||||||||             | |    ||| |||   | | |     | | ||  |   | || |   ||    ||  | ||   ||                                        
TTGGGGCTAGGTTGATTTCACATGCAGGAAGTCTGACAAATCTTGCCAAGTGCCCATCTTCAACCCTCCAGATTCTCGGTGCTGAGAAGGCACTTTTCAGgtg--------catttcaagctttgttagtctttacaagtttaattacactgcagtaactaactttg--gtgttaatttcag----------------------------------------

upper sequence: LOC_Os03g22880.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv17s0000g01720.t01 (Vitis vinifera), 5'ss of exon 5
TTGGAGCACGCCTTATCTCTCATGCTGGCAGTCTTTCAAACCTTGCTAAGTGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAGgttgttaaaactgactgatttcttggtagctctcaaattccaagtaactgtatggaaagttgtttcaaagtactgatcatagagtatacgtcaacttcttatgcttctttactttctcccag
|||| |||||  | || |||||||| || |||||  | || ||||| || || ||| |||||||||| ||||| ||||||||||||||||| || |||||||      |   |  | ||| || |          ||||     |   ||    | |   |  || |     ||  |    |  | |    ||  | | | | | |                
TTGGGGCACGGTTGATTTCTCATGCAGGTAGTCTCACTAATCTTGCAAAATGCCCTTCCTCCACTCTTCAGATCCTTGGTGCTGAAAAGGCTCTATTCAGgt------actaggttaattactcgaggatctcttaatttggtatggttgctgaggagtctcatttagtagtctacttgacggttttgacccatgtgcattttcct----------------

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|27546695|gb|CA767278.2|CA767278
EST:     TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAG                         GGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
genomic: TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAGgttgttaaaa ... tttctcccagGGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
EST: gi|86496816|gb|CI139449.1|CI139449
EST:     GGCACTTTTCAG                         GGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
genomic: GGCACTTTTCAGgttgttaaaa ... tttctcccagGGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
EST: gi|218493558|gb|FG968381.1|FG968381
EST:     TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAA                         GGCATTGAAAACTACGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
genomic: TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAGgttgttaaaa ... tttctcccagGGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
EST: gi|218498396|gb|FG949417.1|FG949417
EST:     TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAG                         GGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
genomic: TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAGgttgttaaaa ... tttctcccagGGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
EST: gi|58659454|gb|CK048134.1|CK048134
EST:     TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAG                         GGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
genomic: TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAGgttgttaaaa ... tttctcccagGGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
EST: gi|27576278|gb|CA998972.1|CA998972
EST:     TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAG                         GGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
genomic: TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAGgttgttaaaa ... tttctcccagGGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
EST: gi|396941561|gb|HO188770.1|HO188770
EST:     TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAG                         GGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
genomic: TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAGgttgttaaaa ... tttctcccagGGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
EST: gi|27554440|gb|CA998340.1|CA998340
EST:     TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAG                         GGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
genomic: TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAGgttgttaaaa ... tttctcccagGGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
EST: gi|58657958|gb|CK046638.1|CK046638
EST:     TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAG                         GGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
genomic: TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAGgttgttaaaa ... tttctcccagGGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
EST: gi|89168282|gb|CI109486.1|CI109486
EST:     TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAG                         GGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
genomic: TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAGgttgttaaaa ... tttctcccagGGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
EST: gi|58676954|gb|CK065641.1|CK065641
EST:     TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAG                         GGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC
genomic: TGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAGgttgttaaaa ... tttctcccagGGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTC

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), 75 (downstream exon)
Score: 55

TTGGAGCACGCCTTATCTCTCATGCTGGCAGTCTTTCAAACCTTGCTAAGTGTCCTGCCTCCACTCTCCAGATACTTGGTGCTGAAAAGGCACTTTTCAGgttgttaaaa ... tttctcccagGGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTCATCCTTCATTGGCCGTGCTTCAACCAAGAACAAAGGCAGAATGGCTAGA




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