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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagatagatttatgtaggctagccagaccttgtaaactcttatgttgactagatggtccttaaaatatctaagtttttattattattctgtatatttgagtatttgacctgtttgtttggtgttccag

Basic information

species Oryza sativa
transcript LOC_Os03g17980.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 5
GGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagatag-atttatgtaggctagccagaccttgtaaactcttatgttgactagatggtccttaaaatatctaagtttttattattattctgtatatttgagtatttgacctgtttgtttggtgttccag
||| ||||||||||| ||||| ||||| ||||||||||| |||||||| |||||||||||||||||||||||||| ||||| || |||||||| || ||||||||| || | |||||| |  ||  || |||||| || |  |||  ||         || ||  |  |||      | |   | |  || |     |||                               
GGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgtgagaaagcacttatgtggaata--caaaccttgcaa-caattagatt-------ctgttctggagttatgaccactctctatctggttttacggttttag-----------------------------

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 6
GGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagatagatttatgtaggctagccagacc--ttgtaaactcttatgttgactagatggtccttaaaatatctaagtttttattattattctgtatatttgagtatttgacctgtttgtttggtgttccag
 || ||||| ||||||||||| || ||  | ||||| || |||||||| || ||||| ||||||||||| ||||| || || || ||||| || ||||||||    |  |||||  |    |      |    |||     ||   ||||||||| ||      | ||| |||  ||               || | || ||  || ||  || | |               
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatttaattttatttatttaattaattgagtgatcggctgttgactacat------tcaaacatcccag-----------gccttggacatgtggataattttccagct---------------

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA13G05700.1 (Glycine max), 5'ss of exon 5
GGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagatagatttatgtaggctagccagaccttgtaaactcttatgttgactagatggtccttaaaatatctaagtttttattattattctgtatatttgagtatttgacctgtttgtttggtgttccag
 || ||||| ||||||||||| || ||  | |||||||| || ||||| |||||||| ||||||||||| || || ||||| || |||||||| ||||||||   ||   |||   ||   ||   |    |  || | |    | ||   |  ||||   | |||  |   |   ||  |||      |  | |  |     |||                        
AGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATGAAAACATTCCCAATCTCTTCAAAAAAATAAAGgtactat---ttttcttaatttaatta---ttattatatttcctttttctttttatgggtttcaaaggactgatagttaaatttcctaccactgtcgtgtcaaatt------------------------

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 5
GGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagatagatttatgtaggctagccagaccttgtaaactcttatgttgactagatggtccttaaaatatctaagtttttattattattctgtatat-ttgagtatttgacctgtttgtttggtgttccag
 || ||||| ||||||||||| || ||  | ||||| || |||||||| |||||||| ||||||||||| || || || || || ||||| || ||||||||         || |  | | ||     |  || |    | ||   || |||   || ||       | ||||  | | |||||  | |    |    |||   || || |   |||              
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCGCTTCTTTGTGGCACTCTTCCTTTTGATGATGAAAACATTCCAAATCTCTTCAAGAAAATAAAGgta--------ttgttaatgtta-----attttat---ttatttaattaactgagtgatcagctgt-tgtctacatatatattaaaactgcccaggccttggacatatggctaattt--------------

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 5
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 5
GGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagatagatttatgtaggctagccagaccttgtaaactcttatgttgactagatggtccttaaaatatctaagtttttattattattctgtatatttgagtatttgacctgtttgtttggtgttccag
 || ||||| ||||||||||| ||||| || || ||||| || ||||| || ||||||||||||||||| || || |||||||| || || ||||||||||| | ||    |||      ||     | |  | | ||||  |   ||||        |  ||    ||| | | |||||  ||| |  ||     | | |   |||    |  |  ||| ||  |  ||
AGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgt-acattctattactcctcctctttcgtctatttgaactaatgc-ttga-------attttt----tatttta-tttttcgtatcacccttcgactgtaaccttttttttttctcttttcgtcctatag

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 5'ss of exon 5
GGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagatagatttatgtaggctagccagaccttgtaaactcttatgttgactagatggtccttaaaatatctaagtttttattattattctgtatatttgagtatttgacctgtttgtttggtgttccag
||| |||||||||||||| || || ||  | || ||||| ||||||||||||||||||||||||||||| || || |||||||| ||||| || ||||||||       ||||       |||     || |    |||| |||          |||  ||  |   || ||   | |  |||  | || | | |  ||     ||| |  | ||||||| |        
GGTGGATGTATGGAGCTGCGGTGTTATTTTGTACGCTCTTCTTTGTGGTACTCTTCCATTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATAAAGgt-------attt-------ctaaatttacttcactaactttta--------gcatgtgcc--agcttagctggatctgcattgctcttttttgtccttttactttttatttttttgtttagaa------

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|58667418|gb|CK056104.1|CK056104
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
EST: gi|29663426|gb|CB659701.1|CB659701
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGG
EST: gi|58666104|gb|CK054790.1|CK054790
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
EST: gi|58674982|gb|CK063669.1|CK063669
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
EST: gi|218482816|gb|FG952976.1|FG952976
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
EST: gi|218482252|gb|FG960526.1|FG960526
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
EST: gi|218502900|gb|FG954558.1|FG954558
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCACAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
EST: gi|2317303|gb|C22357.1|C22357
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
EST: gi|218484843|gb|FG952392.1|FG952392
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
EST: gi|29614995|gb|CB620008.1|CB620008
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTG
EST: gi|33381730|gb|CF197073.1|CF197073
EST:     CTCTTCCATTTGATGATGAGAATATCCCCANCCTATTCAAAAAGATAAAG                         GNTNGTATATATACTCTNNNNNGTCATTTATCTGCTCTGGCC
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCC
EST: gi|218488644|gb|FG955529.1|FG955529
EST:     CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAG                         GGTGGTATATATACTCTCC
genomic: CTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCC

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: 75 (upstream exon), 73 (downstream exon)
Score: 176

GGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataga ... ggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTGATCCCAAGGATGCTTGTTGTTGATCCAATGAAGAGAATCACAATTCGTG




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