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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaatttttttatgttttctaagtgtgtcattattttatactattatcatgtttgaattaagttttttttaaacttttgtagTGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAG

Basic information

species Oryza sativa
transcript LOC_Os08g44810.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44810.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G129513_T01 (Zea mays), 3'ss of exon 6
gtatggaatttttttatgttttctaagtgtgtcattattttatactattatcatgtttgaattaagttttttttaaacttttgtagTGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAG
||| | | ||| | ||||||||   | | | | |    ||||| | ||   | ||| | | ||  |  ||        |   | |||||  ||||||| || || ||||| || |||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||||
gtacgta-tttctatatgttttggcaat-tcttaacgatttattccatcgccttgtcttagttgtgggttgccc---ttgacgcagTGCGCTGATTTGTTTGAAAAATGCCCCAAACATACCGGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCAAAGTGCCAG

upper sequence: LOC_Os08g44810.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G33380.1 (Glycine max), 3'ss of exon 8
gtatggaatttttttatgttttctaagtgtgtcatt--attttatactattatcatgtttgaattaagttttttttaaacttttgtagTGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAG
   |    ||   || |  |   |||   ||  |||  || || | |   | | |||      || |  | | ||||||    || |||||||| || ||||| ||||||||||| ||||| || |||||||| |||||||| || ||  | || ||||| || ||||| || || |||
--gtaagcttggctttttatgagtaaacttgaaattgcatgttgtgcctgt-ttatgcaaacgttcatgtgtatttaaa----tgcagTGCATTAATATGCTTGAAGAATGCTCCTAACATTCCTGCAAAAAATTTTCATGCTTTAACTCGTTTAGATGAGAACAGAGCAAAATGTCAG

upper sequence: LOC_Os08g44810.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G34150.2 (Glycine max), 3'ss of exon 6
gtatggaatttttttatgttttctaagtgtgtcatt--attttatactattatcatgtttgaattaagttttttttaaacttttgtagTGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAG
   |    ||   || |  |   |||   ||  |||  |  || | |   | | ||| |    || |  | | ||||||    || |||||||| |||||||| ||||||||||| ||||| || || ||||| |||||||| || ||  | || ||||| || ||||| || || |||
--gtaagcttggctttttatgggtaaacttgaaattgcacgttgtgcctgt-ttatgctaatgttcatgtgtatttaaa----tgcagTGCATTAATTTGCTTGAAGAATGCTCCTAACATTCCTGCCAAAAATTTTCATGCTTTAACTCGTTTAGATGAGAACAGAGCAAAATGTCAG

upper sequence: LOC_Os08g44810.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G58330.3 (Arabidopsis thaliana), 3'ss of exon 4
gtatggaatttttttatgttt---tctaagtgtgtcattattttatactattatcatgtttgaa-ttaagttttttttaaacttttgtagTGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAG
||| |  |  ||  |   ||     ||     | || | ||     || |  ||      |  | || |  |  ||||    | ||  ||||| ||||||||  | || |||||||||||||| || ||||| ||||| |||||  | |||||||| || |||||| | ||||| ||||||
gtaagctacattccttaattcaaccctcttcatatcgtaatcagtgacaaacattggaagtatactttacctcattttgtgttctttcagTGCCTTGATTTGTCTTAAAAATGCTCCCAACATTCCTGCAAAGAACTTCCATGCCCTCACGAGGTTAGACGAAAATCGTGCCAAATGCCAG

upper sequence: LOC_Os08g44810.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv13s0019g05250.t01 (Vitis vinifera), 3'ss of exon 6
---------------------------------------------------------gtatggaatttttttat--gttttctaagtgtgtcattattttatactattatcatgtttgaattaagttttttttaaacttttgtagTGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAG
                                                         || ||   |||||||||   | ||||  |||||   |  |||        | |||| | ||| ||  ||||  |||   | | || ||||||||||| ||  | || |||||||| |||||||| ||||| ||||||||||| ||||| ||||| ||||| |||||||| || || |||
gtaagaagcattgatttttctttcgttcattcttcttttgtgtgagcatgtgtgtgtgtgtgtgttttttttattgatgttcttggtgtgcagtcctttgtcctccctgtcatttatga-ttgtgtttccttt---cctatgcagTGCATTGATATGTATGAAAAATGCTCCAAACATACCTGCAAAGAACTTTCATGCTTTGACTAGGTTAGATGAGAATAGAGCAAAATGTCAG

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|84117267|gb|CD151034.1|CD151034
EST:     GCATCTCGGAATGTGAAGGTCATAGTTGTCGGGAACCCCTGTAACACTAA                         TGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCA
genomic: GCATCTCGGAATGTGAAGGTCATAGTTGTCGGGAACCCCTGTAACACTAAgtatggaatt ... acttttgtagTGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCA
EST: gi|38468692|gb|CF952823.1|CF952823
EST:     GCATCTCGGAATGTGAAGGTCATAGTTGTCGGGAACCCCTGTAACACTAA                         TGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCA
genomic: GCATCTCGGAATGTGAAGGTCATAGTTGTCGGGAACCCCTGTAACACTAAgtatggaatt ... acttttgtagTGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCA
EST: gi|29686259|gb|CB682534.1|CB682534
EST:     GCATCTCGGAATGTGAAGGTCATAGTTGTCGGGAACCCCTGTAACACTAA                         TGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCA
genomic: GCATCTCGGAATGTGAAGGTCATAGTTGTCGGGAACCCCTGTAACACTAAgtatggaatt ... acttttgtagTGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCA
EST: gi|30227998|gb|CB965890.1|CB965890
EST:     GCATCTCGGAATGTGAAGGTCATAGTTGTCGGGAACCCCTGTAACACTAA                         TGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAA-TTTCA
genomic: GCATCTCGGAATGTGAAGGTCATAGTTGTCGGGAACCCCTGTAACACTAAgtatggaatt ... acttttgtagTGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCA
EST: gi|29686257|gb|CB682532.1|CB682532
EST:     GCATCTCGGAATGTGAAGGTCATAGTTGTCGGGAACCCCTGTAACACTAA                         TGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCA
genomic: GCATCTCGGAATGTGAAGGTCATAGTTGTCGGGAACCCCTGTAACACTAAgtatggaatt ... acttttgtagTGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCA
EST: gi|29677717|gb|CB673992.1|CB673992
EST:     GCATCTCGGAATGTGAAGGTCATAGTTGTCGGGAACCCCTGTAACACTAA                         TGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCA
genomic: GCATCTCGGAATGTGAAGGTCATAGTTGTCGGGAACCCCTGTAACACTAAgtatggaatt ... acttttgtagTGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCA

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: 62 (upstream exon), 75 (downstream exon)
Score: 78

GGGAAAGCACTTAACTCCGTGGCATCTCGGAATGTGAAGGTCATAGTTGTCGGGAACCCCTGTAACACTAAgtatggaatt ... acttttgtagTGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattattttatactattatcatgtttgaattaagttttttttaaacttttgtagTGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAG
                                              cttttgt  CT-rich tract
     attttatactattatc  TA-rich tract