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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGGTTCTCTCAGTGAGAGCAAAACTGGAGAAGGCATTGAGATGCTTGGGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaacttccctacaagataacttgtttgaactaaagaaaaaaggatttcagttattctatttcgtttctattttaaggtttatttttcgaacag...

Basic information

species Oryza sativa
transcript LOC_Os10g33275.2
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g33275.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G399212_T01 (Zea mays), 5'ss of exon 17
TGGTGGTTCTCTCAGTGAGAGCAAAACTGGAGAAGGCATTGAGATGCTTGGGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaacttccctacaagataacttgtttgaact----aaagaaaaaaggatttcagttattctatttcgtttctattttaaggtttatttttcgaacag
||||||||| || |||  |||||||||||||||||||||||||||||||||||| |||||||||||||| || |||| ||||| |||||||||||| |||||||  | | || | || ||| |||  |||| | ||||    ||| ||| ||    |||| || || | | |  ||| |  |  ||   || |||||  | |  
TGGTGGTTCGCTTAGTCCGAGCAAAACTGGAGAAGGCATTGAGATGCTTGGGGGTTATCTTCATTTCTCGGCTCCAAAGCGTACCATAGAGTTGATTCAGgtataaccagctccactccaatata--ttgtctcaactttgaaaaaaaataatatcttcaattgtt-tgtgttatttttgctaaaaaagttgtttttgtacct-

upper sequence: LOC_Os10g33275.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA10G10180.1 (Glycine max), 5'ss of exon 17
TGGTGGTTCTCTCAGTGAGAGCAAAACTGGAGAAGGCATTGAGATGCTTGGGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgta----tctctaacttccctacaagataacttgtttgaactaaagaaaaaaggatttcagttattctatttcgtttctattttaaggtttatttttcgaacag
|||||||  |||       ||||||| ||| || |||||||| |||||||| || || ||||||||||||||  |||   || |||| ||||| ||   ||||    || ||   | |  | | ||  ||| | |      |    | ||   | ||| |   ||     | |  ||| |    | |   |    |   ||   
TGGTGGTAATCTTGTCCCTAGCAAAAGTGGTGAGGGCATTGACATGCTTGGAGGTTACCTTCATTTCTCTGCTTCAAAAAGTGTCATTGAGTTAATAAGGgtaatgttccctctgtcctttcccagcaaacctatgctttgtctttataacttgttttaaaggatgtggctcc--ttcaaagcgaggaagtgcactcacaat--

upper sequence: LOC_Os10g33275.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA02G35240.1 (Glycine max), 5'ss of exon 18
TGGTGGTTCTCTCAGTGAGAGCAAAACTGGAGAAGGCATTGAGATGCTTGGGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgta------tctctaac--ttccctacaaga---taacttgtttgaactaaagaaaaaaggatttcagttattctatttcgtttctattttaaggtttatttttcgaacag
|||||||  |||       ||||||| ||| || |||||||| |||||||| || || ||||||||||||||  | |   || |||| ||||| ||   ||||       ||||| |  |||||  |||     | |    ||     || |    | | |  | |  | |  | |    ||   |     |  ||| ||           
TGGTGGTAATCTTGTCCCTAGCAAAAGTGGTGAGGGCATTGACATGCTTGGAGGTTACCTTCATTTCTCTGCTTCGAAAAGTGTCATCGAGTTAATAAGGgtaatgttccctctatcctttcccagcaaagctctgatgctttgtctttataagggatatggctcctttaaagcgaggaagtgcattcgcaatagttaat-----------

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|88272321|gb|CI386775.1|CI386775
EST:     GGGGGTATCTTCATTTCTCTGCACC-AGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|29681907|gb|CB678182.1|CB678182
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|86863896|gb|CI332875.1|CI332875
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|86869375|gb|CI339099.1|CI339099
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|89190185|gb|CI392235.1|CI392235
EST:     GGGGGTATGTTCATTTCTCTGCACC-AGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGAGTCGAGGAGCC
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGA-TCGAGGAGCC
EST: gi|88829519|gb|CI074389.1|CI074389
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|88253431|gb|CI352057.1|CI352057
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGCTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|88842850|gb|CI371750.1|CI371750
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|86864475|gb|CI334170.1|CI334170
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|3761879|gb|C99127.1|C99127
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|86887775|gb|CI319725.1|CI319725
EST:     GGCGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGCTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|88901940|gb|CI374548.1|CI374548
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|88431984|gb|CI560229.1|CI560229
EST:     GTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|88323608|gb|CI556239.1|CI556239
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|88266175|gb|CI377077.1|CI377077
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|86866355|gb|CI336954.1|CI336954
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|88491998|gb|CI429270.1|CI429270
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|88833760|gb|CI077241.1|CI077241
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|88418465|gb|CI548746.1|CI548746
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|88291326|gb|CI529916.1|CI529916
EST:     GGGGTATTCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGGCC
genomic: GGGGTA-TCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGA-GCC
EST: gi|27545909|gb|CA764270.2|CA764270
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|88492016|gb|CI429288.1|CI429288
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|86479957|gb|CI122590.1|CI122590
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|86873082|gb|CI328462.1|CI328462
EST:     GGGGCTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATT-GACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|88286808|gb|CI520118.1|CI520118
EST:     GGGGGTATGTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|88267195|gb|CI379130.1|CI379130
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|88286671|gb|CI517782.1|CI517782
EST:     GGGGGTATCTTCATTTCTCTGCACCAGGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|88460605|gb|CI534477.1|CI534477
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|29675438|gb|CB671713.1|CB671713
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCT
EST: gi|88292148|gb|CI534942.1|CI534942
EST:     ATCATAGAGTTGATCCAG                         AGATTAAGAGGTGGATTGGACAAACTCCTCCAGAGGAAGATCGANGAGCCT
genomic: ATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|88428949|gb|CI554665.1|CI554665
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|88268000|gb|CI378772.1|CI378772
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGATGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|25803109|gb|CA759070.1|CA759070
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|86833107|gb|CI333706.1|CI333706
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
EST: gi|88264916|gb|CI367567.1|CI367567
EST:     GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAG                         AGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT
genomic: GGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCT

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: 69 (upstream exon), 72 (downstream exon)
Score: 10

TGGTGGTTCTCTCAGTGAGAGCAAAACTGGAGAAGGCATTGAGATGCTTGGGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgtatctctaa ... tatttgacagAGATTAAGAGGTGAATTGGACAAACTCCTCCAGAGGAAGATCGAGGAGCCTGCACTTGACATATTTTCTGAAGGAAAAGGCGTTGTGGCGGCAGCAGTAG




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