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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTGgtaagctgatggagtttgctagttctttttctataataagtcatacagcaaactttttggttcaagctttcaatagaactggtagattgtttccctctat...

Basic information

species Oryza sativa
transcript LOC_Os03g60740.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g60740.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G068244_T01 (Zea mays), 5'ss of exon 4
CCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTGgtaagctgatggagtttgctagttctttttctataataagtcataca--gcaaactttttggttcaagctttcaatagaactggtagattgtttccctctat
| ||||||||||||||||||||||| ||||| |||||||| |||||||||||||||||||||||||| ||||||||| | || |||||||||||||||||||||| |   | || |||  | | |   | |  |  | ||| | |  | | |  |      |  |   ||  ||| | ||| || |              
CTAAAGCTGCTGGAGTGAAGCATATTGTGCTGGTGGGATCTATGGGAGGAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaa--aatttggctcttccataggcaactactattcacaaattgtagaagtgggatcttgattattgcatatatctgctatag-------------

upper sequence: LOC_Os03g60740.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA18G39930.2 (Glycine max), 5'ss of exon 4
CCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTGgtaagctgatggagtttgctagttctttttctataataagtcatacagcaaactttttggttcaagctt---tcaatagaactggtagattgtttccctctat----------------------------------------------------------------------------------------------
| || ||||||||||||||||| || ||| | || || || ||||| |||||| ||| |||||||||  |||||||| | || ||||| ||||||||||| || | |||   ||| ||     |  ||||| | ||  || | |   ||  || |    |     ||   | | |||| || | |  |  | |   |  |                                                                                               
CTAAGGCTGCTGGAGTGAAGCACATTGTGTTAGTAGGGTCTATGGGTGGAACAGATCTTAACCATCCTTTGAACAGCTTGGGTAATGGGAATATACTGgttag-taatgttttttcct----ttacttctaaactacctccttccataacattctgtcattgcttttatatgattagagcttgcaactcatcttaatgcaaaatgcaagtttggtgtaaatgcctaaatggatatgttttacttcccccatgccctttgatattcctcctttgataggaagaatgttgattgcag
















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|33818132|gb|CF334892.1|CF334892
EST:     GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTG                         GGTTTGGAAGCGCAAGTC
genomic: GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTGgtaagctgat ... tttgttatagG-TTTGGAAGCGCAAGTC
EST: gi|109711615|gb|CI013220.1|CI013220
EST:     AGGCAATGGCAATATACTG                         GTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
genomic: AGGCAATGGCAATATACTGgtaagctgat ... tttgttatagGTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
EST: gi|33818134|gb|CF334893.1|CF334893
EST:     AACAAATCCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTG                         GTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
genomic: AACAAAT-CCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTGgtaagctgat ... tttgttatagGTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
EST: gi|3762111|gb|C99359.1|C99359
EST:     GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTG                         GTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
genomic: GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTGgtaagctgat ... tttgttatagGTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
EST: gi|33686688|gb|CF314927.1|CF314927
EST:     AACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAANTATACTG                         GTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTA
genomic: AACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAA-TATACTGgtaagctgat ... tttgttatagGTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTA
EST: gi|32947908|gb|BP184480.1|BP184480
EST:     GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTG                         GTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
genomic: GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTGgtaagctgat ... tttgttatagGTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
EST: gi|163923266|gb|EG711075.1|EG711075
EST:     AACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTG                         GTTTGGAAGCGCAAGTCACAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
genomic: AACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTGgtaagctgat ... tttgttatagGTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
EST: gi|89189979|gb|CI013546.1|CI013546
EST:     GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTG                         GTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
genomic: GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTGgtaagctgat ... tttgttatagGTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
EST: gi|33821839|gb|CF336730.1|CF336730
EST:     CAATGGCAATATACTG                         GTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
genomic: CAATGGCAATATACTGgtaagctgat ... tttgttatagGTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
EST: gi|3762112|gb|C99360.1|C99360
EST:     GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTG                         GTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
genomic: GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTGgtaagctgat ... tttgttatagGTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
EST: gi|88847804|gb|CI005990.1|CI005990
EST:     GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTG                         GTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
genomic: GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTGgtaagctgat ... tttgttatagGTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
EST: gi|89198494|gb|CI007554.1|CI007554
EST:     GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTG                         GTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
genomic: GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTGgtaagctgat ... tttgttatagGTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
EST: gi|33817947|gb|CF334802.1|CF334802
EST:     GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTG                         GTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
genomic: GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTGgtaagctgat ... tttgttatagGTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
EST: gi|117234788|gb|CT847886.1|CT847886
EST:     GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTG                         GTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
genomic: GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTGgtaagctgat ... tttgttatagGTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
EST: gi|88239537|gb|CI240014.1|CI240014
EST:     CCACTGAACAGCCTAGGCAATGGCAATATACTG                         GTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
genomic: CCACTGAACAGCCTAGGCAATGGCAATATACTGgtaagctgat ... tttgttatagGTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
EST: gi|33660166|gb|CF291133.1|CF291133
EST:     CAATGGCAATATACTG                         GTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
genomic: CAATGGCAATATACTGgtaagctgat ... tttgttatagGTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
EST: gi|33821837|gb|CF336729.1|CF336729
EST:     GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTG                         GGGTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAG
genomic: GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTGgtaagctgat ... tttgttatagG--TTTGGAAGCGCAAGTCAGAACAGTATTTGGCAG
EST: gi|88227808|gb|CI227288.1|CI227288
EST:     GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTG                         GTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
genomic: GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTGgtaagctgat ... tttgttatagGTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
EST: gi|42592251|gb|CK738737.1|CK738737
EST:     GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTG                         GTTTGGAAGCGCAAGTCAGAACAGTATTTGGGCAAACGGTGGAGTCCCTTA
genomic: GAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTGgtaagctgat ... tttgttatagGTTTGGAAGCGCAAGTCAGAACAGTATTTGG-CAGACAGTGGAGTCCCTTA

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), 37 (downstream exon)
Score: 77

CCAAAGCTGCTGGAGTGAAGCATATCGTGCTTGTGGGATCCATGGGAGGAACAAATCCTAACCATCCACTGAACAGCCTAGGCAATGGCAATATACTGgtaagctgat ... tttgttatagGTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAG




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