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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCTTTGGCCTAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGGgtatgatatggcaaactttgttcaggttaactctgttgataactctgaattggcatctaaattctcgcttttcttttgcattggttgtgcccgtgtacag

Basic information

species Oryza sativa
transcript LOC_Os12g02390.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g02390.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G389362_T01 (Zea mays), 5'ss of exon 12
TGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCTTTGGCCTAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGGgta--tgatatg-gcaaactttgttcaggttaact--ctgttgataactctgaattggcatctaaattctcgcttttcttttgcattggttgtgcccgtgtacag
|| |||| |||| | ||| |||  |||||||||||| |||||||||||||| || | ||| ||  |||||||||| || || |||||||||||||||||||||  |  |||  ||  ||  | |  | ||| | |  ||  ||||||||| |   ||||||||||        | |  | ||||||||  | ||||    |||||
TGGAGCATCAGAAGCAGGTTGGGGCTTCTTGTGGGTCATCTTCTTTGGCCTTGTTGCAGCAGGAGTTGCAGGATATGCTGTGTACAAGTACAGGATCCGGgtaagtagtatctgctgacact-tgtatgttcattaccttctgataactcggg--tggcatctaa-------ttctgttcttgcattgcctatgcc----tacag

upper sequence: LOC_Os12g02390.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G347541_T02 (Zea mays), 5'ss of exon 5
TGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCTTTGGCCTAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGGgtatgatat-ggcaaactttg-----ttcaggttaact--ctgttgataactctgaattggcatctaaattctcgcttttcttttgcattggttgtgcccgtgt--acag
 | |||| |||| |  || |||  |||| |||||||  || |||| ||||| || | ||| || |||||||| ||||| || ||||||||||||||||||||| ||||| ||||  || |      |    ||| | |  ||  ||||  |||          |||   ||  ||  |   | |     ||  | |||||||||   |||
CGGAGCATCAGAAGCCGGCTGGGGCTTCCTGTGGGTCGTCGTCTTCGGCCTCGTCGCAGCAGGAATTGCAGGGTACGCGGTGTACAAGTACAGGATCCGGgtaagatataggcagcctgtaatgcttctttgttcattgccttctgatggctcgctcgctcactctgggttggcgtctgattctgttcctgcatttgcccgtgtctgcag
















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|86598375|gb|CI354992.1|CI354992
EST:     TAGTGGTAGCCGGCATTTCAGGATACCCAGTATACAAGTACAGGATCCGG                         AGGTACATGGATTCAGAGATCCGCCCCATCATGGCCCAGTACATGCCCCTG
genomic: TAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGGgtatgatatg ... ccgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
EST: gi|58673963|gb|CK062649.1|CK062649
EST:     TAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGG                         AGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
genomic: TAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGGgtatgatatg ... ccgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
EST: gi|88955756|gb|CI092045.1|CI092045
EST:     TAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGG                         AGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
genomic: TAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGGgtatgatatg ... ccgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
EST: gi|86850762|gb|CI338738.1|CI338738
EST:     TAGTGGTAGCCGGCATTGCA-GATACGCAGTATACAAGTACAGGATCCGG                         AGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
genomic: TAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGGgtatgatatg ... ccgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
EST: gi|2312600|gb|C28755.1|C28755
EST:     TAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGG                         AGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
genomic: TAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGGgtatgatatg ... ccgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
EST: gi|88837810|gb|CI079170.1|CI079170
EST:     TAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGG                         TGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
genomic: TAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGGgtatgatatg ... ccgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
EST: gi|88960134|gb|CI382012.1|CI382012
EST:     TAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGG                         AGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
genomic: TAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGGgtatgatatg ... ccgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
EST: gi|86415054|gb|CI069457.1|CI069457
EST:     TAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGG                         AGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
genomic: TAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGGgtatgatatg ... ccgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
EST: gi|86494648|gb|CI137281.1|CI137281
EST:     TAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGG                         AGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCNTG
genomic: TAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGGgtatgatatg ... ccgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
EST: gi|86842050|gb|CI338421.1|CI338421
EST:     TAGTGGTAGCCGGCATTCCAG-ATACCCAGTATACAAGTACAG-ATCCGG                         AGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
genomic: TAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGGgtatgatatg ... ccgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG

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: 60 (upstream exon), 71 (downstream exon)
Score: 9

TGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCTTTGGCCTAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAGGATCCGGgtatgatatg ... ccgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTGGACAACCAAGGAGATGTTCCCAATCATTCTCACCATATCGAGCTATGAA




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