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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagactcacaaattgctgtcagtcacatgtggtgcaatttctcatctctagattgtatctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG

Basic information

species Oryza sativa
transcript LOC_Os01g70960.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g70960.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G06700.1 (Glycine max), 3'ss of exon 5
gtgagactcacaaattgctgtcagtcacatgtggtgcaatttctcatctctagattgtatctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG
|| |  || |  | ||| |   ||| |  | |   | | ||||| || | |    | || || |    |   |  ||     |||||||||| | |||||||| ||||||||||||||||| ||||| |||||||||||||| ||||||||||||||||||
gtaatgctaattatttgat---agtaatgtctttggaattttctaatgtatg---tctacctgaaatatatatccttgtgatttttcagGCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGTTATCGTGACCCACCTGCTGGTGTTTCG

upper sequence: LOC_Os01g70960.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 4
gtgagactcacaaattgctgtcagtcacatgtggtgcaatttctcatctctagattgtatctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG
|| |       |   ||||   |    | |  | |    | | |    | || ||  ||  |||   |||    || |  |   |||||||  | |||||||| ||||||||||| ||||| ||||| |||||||||||||| || |||||||||||||||
gtaatgagtgtagtctgctagtaacgtctttagattt--tcttttgcttttatatcataaataat--tttacccttaatgt---ttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGTGACCCTCCTGCTGGTGTTTCG

upper sequence: LOC_Os01g70960.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G22530.2 (Glycine max), 3'ss of exon 4
gtgagactcacaaattgctgtcagtcacatgtggtgcaatttctcatctctagattgtatctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG
|| |       |   ||||   | |    |  | |    | | |    | || || | |  |||   |||    || | ||   |||||||  | |||||||| ||||||||||| ||| | ||||| || ||||||||||| || |||||||||||||||
gtaatgactgtagtctgctagtaatgtttttagattt--tctattgcttttatatcggaaataat--tttacccttaatat---ttcagGCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGTGACCCTCCTGCTGGTGTTTCG

upper sequence: LOC_Os01g70960.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 4
gtgagactcacaaattgctgtcagtcacatgtggtgcaatttctcatctctagattgtatctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG
|| |  || |  | ||| |   ||| | || |  || |||||   |      |  |   |  || | | | |  |||  || |||||||||| | |||||||| ||||||||||||||||| ||||| |||||||||||||| ||||||||||||||||| 
gtaatgctaattatttgat---agtaatatctt-tgaaattttctaatgtatgtctacctgaaaatatatatccttttgat-ttttcagGCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTAACTGGTTATCGTGACCCACCTGCTGGTGTTTCA

upper sequence: LOC_Os01g70960.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 3
gtgagactcacaaattgctgtcagtcacatgtggtgcaatttctcatctctagattgt-atctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG
||  |   | |   ||     || |   ||    |   |    ||||||    | | | ||||||    ||  |   ||  |  || |||||  | ||||||||||| || ||||| ||||||||  | ||||||||||||||||| ||||||||  |||||
gtttggtgctct--ttctctccatttgtatacaattagaaaattcatct----actatgatctaagcaatt--tggctattttcttccagGCACGTCACAATGGCCAAAATTATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCG

upper sequence: LOC_Os01g70960.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 4
gtgagactcacaaattgctgtcagtcacatgtggtgcaatttctcatctctagattgtatctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG
  |  | |   |  ||   ||   |  | | |  || |  || |  ||| |    |  |  | |    ||| ||||    | |||||||||  | |||||||| || |||||||| ||||| || || |||||||| |||||||||||||||||  |||||
--gtaatttctatgttctggtt--tggcttcttatggagattat-gtctatgttatccaagtgatatcttgcttttgt--tcttttcagGCTCGCCACAATGGTCAAAACTATGTATTTGCACTGCTAACTGGTTACCGTGATCCACCTGCTGGCATTTCG

upper sequence: LOC_Os01g70960.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 3
--gtgagactcacaaattgctgtcagtcacatgtggtgcaatttctcatctctagattgtatctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG
   | |   |    |          |  | | |||       |   || | ||| |   || || |||||||||  | |         |||||| | |||||||| ||||| ||||| ||||||||| | |||||||| |||||||| || ||||||||||| 
gtattaattttgttatagatcccttgatagaagtga-atggctgtccacccctaca--ataactgactctttgtcctct---------cagGCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA

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|218495259|gb|FG944818.1|FG944818
EST:     CTAATCACAAAG                         GCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT
genomic: CTAATCACAAAGgtgagactca ... atattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT
EST: gi|29669775|gb|CB666050.1|CB666050
EST:     GATTTTCAAATGGCGGGGCATACCCCCCGGATCTCAGTCTAATCACAAAG                         GCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT
genomic: GATTTTCAAATGGCGGGGCATACCCCCCGGATCTCAGTCTAATCACAAAGgtgagactca ... atattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT
EST: gi|29669904|gb|CB666179.1|CB666179
EST:     GATTTTCAAATGGCGGGGCATACCCCCCGGATCTCAGTCTAATCACAAAG                         GCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT
genomic: GATTTTCAAATGGCGGGGCATACCCCCCGGATCTCAGTCTAATCACAAAGgtgagactca ... atattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT
EST: gi|87021720|gb|CI276119.1|CI276119
EST:     GGATCTCAGTCTAATCACAAAG                         GCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT
genomic: GGATCTCAGTCTAATCACAAAGgtgagactca ... atattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT
EST: gi|55432382|gb|CV729212.1|CV729212
EST:     GATTTTCAAATGGCGGGGCATACCCCCCGGATCTCAGTCTAATCACAAAG                         GCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT
genomic: GATTTTCAAATGGCGGGGCATACCCCCCGGATCTCAGTCTAATCACAAAGgtgagactca ... atattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT
EST: gi|29669776|gb|CB666051.1|CB666051
EST:     GATTTTCAAATGGCGGGGCATACCCCCCGGATCTCAGTCTAATCACAAAG                         GCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT
genomic: GATTTTCAAATGGCGGGGCATACCCCCCGGATCTCAGTCTAATCACAAAGgtgagactca ... atattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT
EST: gi|38481751|gb|CF965826.1|CF965826
EST:     GATTTTCAAATGGCGGGGCATACCCCCCGGATCTCAGTCTAATCACAAAG                         GCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT
genomic: GATTTTCAAATGGCGGGGCATACCCCCCGGATCTCAGTCTAATCACAAAGgtgagactca ... atattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT
EST: gi|313090494|gb|HO213490.1|HO213490
EST:     GATTTTCAAATGGCGGGGCATACCCCCCGGATCTCAGTCTAATCACAAAG                         GCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCTT
genomic: GATTTTCAAATGGCGGGGCATACCCCCCGGATCTCAGTCTAATCACAAAGgtgagactca ... atattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT
EST: gi|117235872|gb|CT847828.1|CT847828
EST:     GATTTTCAAATGGCGGGGCATACCCCCCGGATCTCAGTCTAATCACAAAG                         GCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT
genomic: GATTTTCAAATGGCGGGGCATACCCCCCGGATCTCAGTCTAATCACAAAGgtgagactca ... atattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT
EST: gi|29669905|gb|CB666180.1|CB666180
EST:     GATTTTCAAATGGCGGGGCATACCCCCCGGATCTCAGTCTAATCACAAAG                         GCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT
genomic: GATTTTCAAATGGCGGGGCATACCCCCCGGATCTCAGTCTAATCACAAAGgtgagactca ... atattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGT

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), 63 (downstream exon)
Score: 10

TAAGCTGAGCGACCGTTTCCCACAACCCTACGCAAATGAGCAAGCAGCTCGATTTTCAAATGGCGGGGCATACCCCCCGGATCTCAGTCTAATCACAAAGgtgagactca ... atattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaatttctcatctctagattgtatctaactctttgttttttacatattttcagGCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG
                        atctaac  putative branch site (score: 10)
                                              tattttc  putative PPT
                               tctttgttttttacat  TA-rich tract