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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCCTGACTGGCATTGTTCTGATTGGTGGGATGATACCTTATATTTCTGAGACATTTGCCAGAATCCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacgagattagtacaagcattatacttggtttttggttttctacaccatcgttaggggtgcaggacaaatcttagggattttctgggctctgaaaatagtcttcttgggtgcatacttagaagttgagttttagtaattcctctcgtatggacctgcag

Basic information

species Oryza sativa
transcript LOC_Os03g63520.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63520.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G082976_T01 (Zea mays), 5'ss of exon 3
TGTCCTGACTGGCATTGTTCTGATTGGTGGGATGATACCTTATATTTCTGAGACATTTGCCAGAATCCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacgagatta---------------gtacaagcattatacttg----gtttttggttttctacaccatcgttaggg---------gtgcaggacaaatcttagggattttctgggctctgaaaatagtcttcttgggtgcatacttagaagttgagttttagtaattcc----tctcgtatggacctgcag
|||||| ||| |||||||||||||||| |||||||||||||| ||||| ||||||||||||||||| |||||| |||||||||||||||| |||||||||||| |  ||||               |||  |  ||| ||||       |||||  |||    |    | |||             | |   ||||||| || | ||      ||  | | ||  || |  |    ||    |      ||||      || |||| ||     |||  |||||      ||
TGTCCTAACTAGCATTGTTCTGATTGGAGGGATGATACCTTACATTTCCGAGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaattaccagcgcttataattgtaataaaattgtactccctccattttttatttgtcgcgttttagtttaaaaatgaactagcgggcgacaaatattcgagaacggaaggagtataaatttaatagta--aggcatgtttgagaaagtcttacattggtaactctgacttctgatatggcatgttag

upper sequence: LOC_Os03g63520.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G112609_T01 (Zea mays), 5'ss of exon 3
TGTCCTGACTGGCATTGTTCTGATTGGTGGGATGATACCTTATATTTCTGAGACATTTGCCAGAATCCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacgagattagtacaagcattatacttggtttttggttttctacacc--atcgttaggggtgca-ggacaaatctt--agggattttctgggctctgaaaatagtcttcttgggtgcatacttagaagttgagttttagtaattcctctcgtatggacctgcag
|||||| ||||||||||||||||| || |||||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||  ||||   |||   ||||| |||    |    | |||  |    || ||  || |||   ||| || ||||  |  | |      | ||    | || |  |    |                                                    
TGTCCTAACTGGCATTGTTCTGATCGGAGGGATGATACCTTACATTTCTGAGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacggaatta--ccaatgcttataattgtaaataaaatgtctgaatttaatagtagggcgtgtttggataagtcttccattggtaactctgacttctgatatggcatggcag----------------------------------------------------

upper sequence: LOC_Os03g63520.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA15G11350.3 (Glycine max), 5'ss of exon 3
TGTCCTGACTGGCATTGTTCTGATTGGTGGGATGATACCTTATATTTCTGAGACATTTGCCAGAATCCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacgagattagtacaagcattatacttggtttttggttttctacaccatcgttaggggtgcaggacaaatcttagggattttctgggctctgaaaatagtcttcttgggtgcatacttagaagttgagttttagtaattcctctcgtatggacctgcag
|||  ||||||| ||||||||  |||| || |||||||||||| | || ||| | ||||| | |||  | ||| | ||||| |||||||||||||||||||||       |||   |   |||||      |||   ||||  || || |||||||  ||  |   |||     |  | |       | | ||| ||| ||||||     |  ||                                             
TGTATTGACTGGAATTGTTCTTCTTGGGGGCATGATACCTTATTTATCAGAGTCGTTTGCAAAAATAATATTCCTTAGCAACTCATTGACATTTATGATGgta-------agtcacatttttatat----atttgtatttttcactcc-tcgttag--gtctaactcaacatcaaaagctagctcatgatgtgagaattgtcttcc-aattatat---------------------------------------------

upper sequence: LOC_Os03g63520.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv10s0116g00010.t01 (Vitis vinifera), 5'ss of exon 1
TGTCCTGACTGGCATTGTTCTGATTGGTGGGATGATACCTTATATTTCTGAGACATTTGCCAGAATCCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacgagattagtacaagcattatacttggtttttggttttctacaccatcgttaggggtgcaggacaaatcttagggattttctgg-gctctgaaaatagtcttcttgggtgcatacttagaagttgagttttagtaattcctctcgtatggacctgcag
|||  | || || |||||||| ||||| ||||||||||| ||| | || ||| ||||||| | |||  | ||| ||||||||||||||||||| ||||||||  |  | |  | |     | | || | |    || |||| |     |  || |    ||    |||| | ||  |||| |  ||   |||||       | ||    | || | |                                            
TGTTTTAACGGGGATTGTTCTCATTGGGGGGATGATACCATATGTATCAGAGTCATTTGCAAAAATTATATTCCTGAGCAATTCATTGACATTCATGATGgttagttaatttttctttgctcacacatagaagatg-ttttattggttacagtca---ttgtgcaacaactgttttggatgtcttgttactctg-------tttttcctgttgtacag-------------------------------------------

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|29685610|gb|CB681885.1|CB681885
EST:     AGACATTTGCCAGAATCCTGTTCTTGAGCAATTCATTGACATTTATGATG                         GTTTATGTATGGAGCAAGCACAATCCCTTCATTCATATGAGCTTCTTGGGT
genomic: AGACATTTGCCAGAATCCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacgagatt ... ggacctgcagGTTTATGTATGGAGCAAGCACAATCCCTTCATTCATATGAGCTTCTTGGGT
EST: gi|117223453|gb|CT848631.1|CT848631
EST:     AGACATTTGCCAGAATCCTGTTCTTGAACAATTCATTGACATTTATGATG                         GTTTATGTATGGAGCAAGCACAATCCCTTCATTCATATGAGCTTCTTGGGT
genomic: AGACATTTGCCAGAATCCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacgagatt ... ggacctgcagGTTTATGTATGGAGCAAGCACAATCCCTTCATTCATATGAGCTTCTTGGGT
EST: gi|33683707|gb|CF311946.1|CF311946
EST:     AGACATTTGCCAGAATCCTGTTCTTGAGCAATTCATTGACATTTATGATG                         GTTTATGTATGGAGCAAGCACAATCCCTTCATTCATATGAGCTTCTTGGGG
genomic: AGACATTTGCCAGAATCCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacgagatt ... ggacctgcagGTTTATGTATGGAGCAAGCACAATCCCTTCATTCATATGAGCTTCTTGGG-
EST: gi|88403631|gb|CI575515.1|CI575515
EST:     AGACATTTGCCAGAATCCTGTTCTTGAGCAATTCATTGACATTTATGATG                         GTTTATGTATGGAGCAAGCACAATCCCTTCATTCATATGAGC
genomic: AGACATTTGCCAGAATCCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacgagatt ... ggacctgcagGTTTATGTATGGAGCAAGCACAATCCCTTCATTCATATGAGC
EST: gi|58695719|gb|CK084406.1|CK084406
EST:     AGACATTTGCCAGAATCCTGTTCTTGAGCAATTCATTGACATTTATGATG                         GTTTATGTATGGAGCAAGCACAATCCCTTCATTCATATGAGCTTCTTGGGT
genomic: AGACATTTGCCAGAATCCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacgagatt ... ggacctgcagGTTTATGTATGGAGCAAGCACAATCCCTTCATTCATATGAGCTTCTTGGGT

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: 67 (upstream exon), 75 (downstream exon)
Score: 33

TGTCCTGACTGGCATTGTTCTGATTGGTGGGATGATACCTTATATTTCTGAGACATTTGCCAGAATCCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacgagatt ... ggacctgcagGTTTATGTATGGAGCAAGCACAATCCCTTCATTCATATGAGCTTCTTGGGTTTGTTCACCTTTACTGCTGCTTATTTACCTTGG




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