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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACAACCACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATATTTCACGgtatgcactcaactgtggtgacagagggatcctttctaatattgacgtaattttccatgctctttttttgtggtttcatagtcaacatctaggtcactgt...

Basic information

species Oryza sativa
transcript LOC_Os12g40830.3
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g40830.3 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G069758_T01 (Zea mays), 5'ss of exon 10
GAACAACCACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATATTTCACGgtatgcactcaact----gtggtgacagagggatcctttctaatattg-acgtaattttccatgctctttttttgtggtttcatagtcaacatctaggtcactgt
|||||||  |||||||||||||||||||||||||| |||||||||||||||||||||||||   |  | ||     |  |  |    | | | | |  |||   |   | | |     ||    || |||| | ||    |  |    ||    ||      
GAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACGgtatatccatatctctttattctttcgctagaaacttctagaatggagtgtggagtacggaatatgattgttttattgtagattgattcttataggagtt-----

upper sequence: LOC_Os12g40830.3 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv14s0006g01660.t01 (Vitis vinifera), 5'ss of exon 10
GAACAACCACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATATTTCACGgtatgca--------ctcaactgtggtgacagagggatcctttctaatattgacgtaattttccatgctctttttt-tgtggtttcatagtcaacatctaggtcactgt
|  ||  | || || ||||| ||||||| ||| ||||| || ||||||||||||||||||||||        || |    |       | ||||   ||     | ||    |    |  || | |||| ||| | |  |   ||   |    | |          
GGTCATTCTCCTGACCAATTCAAGATTGTGATGCCCAAAATTCCTGCATATTTCACGgtatgcatattcttccttattcctcccacttgtgggacttttatggttgtttctatgggatggcaagatcttatttatatattaaaattacctttttttg---------
















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|568331|gb|D39176.1|D39176
EST:     CACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATATTTCACG                         GGGCACTGGAGATTTAACAACTG
genomic: CACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATATTTCACGgtatgcactc ... tgctttgcagGG-CACTGGAGATTTAACAACTG
EST: gi|427643|gb|D23776.1|D23776
EST:     CACCAGAACAATTTAAGATTGNGATACCCAAGATACCTGCATATTTCACG                         GGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGNGTAAT
genomic: CACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATATTTCACGgtatgcactc ... tgctttgcagGGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAAT
EST: gi|86885325|gb|CI317085.1|CI317085
EST:     ATACCTGCATATTTCACG                         GGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAAT
genomic: ATACCTGCATATTTCACGgtatgcactc ... tgctttgcagGGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAAT
EST: gi|13165352|gb|AU174149.1|AU174149
EST:     CACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATATTTCACG                         GGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAAT
genomic: CACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATATTTCACGgtatgcactc ... tgctttgcagGGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAAT
EST: gi|89185094|gb|CI049640.1|CI049640
EST:     CACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATATTTCACG                         GGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAAT
genomic: CACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATATTTCACGgtatgcactc ... tgctttgcagGGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAAT
EST: gi|88543303|gb|CI473300.1|CI473300
EST:     TTAAGATTGAGATACCCAAGATACCTGCATATTTCACG                         GGCACTGGAGATTTAACAACTGCCCTTTTACTAGGATGGAGTAAT
genomic: TTAAGATTGAGATACCCAAGATACCTGCATATTTCACGgtatgcactc ... tgctttgcagGGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAAT

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: 57 (upstream exon), 45 (downstream exon)
Score: 30

GAACAACCACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATATTTCACGgtatgcactc ... tgctttgcagGGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAAT




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