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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTCTCAAGGAAAAGTATCACTCCCCTAAAGGATATAGGAGTGAGTGCAAGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAGgtactgtgattcttgcatttatcctcactttgtactctctttcaacttgttgatgcttatgtattatcctacagcag

Basic information

species Oryza sativa
transcript LOC_Os04g35700.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g35700.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G140726_T01 (Zea mays), 5'ss of exon 10
------AGTTCTCAAGGAAAAGTATCACTCCCCTAAAGGATATAGGAGTGAGTGCAAGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAGgtactgtgattcttgcatttatcctcactttgtactctctttcaacttgttgatgcttatgtattatcctacagcag
       |   ||  |||||| ||| ||||| || |||||||| ||| || |    ||||||||||| |||||||||||  | ||||||||||||||||      |||| |     |  | |   || | ||  | | |  | |||  ||| |  |   ||   |||| || |  || |||||
GGGAGTTGCCATCTCGGAAAATTATAACTCCTCTGAAGGATATTGGACTGGGCATGAGAGATTTTACTGGATTTTCCACTACTGTTCCTTCACCACACA------Ggtatt----ctactaccactaccatccttgtatcgtttctcacaattc-tgactgacaatgt-ttgtggtatagcag
















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|218492792|gb|FG953621.1|FG953621
EST:     AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAG                         C
genomic: AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAGgtactgtgat ... cctacagcag-
EST: gi|218492792|gb|FG953621.1|FG953621
EST:     AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAG                         C
genomic: AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAGgtactgtgat ... cctacagcag-
EST: gi|218492792|gb|FG953621.1|FG953621
EST:     AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAG                         C
genomic: AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAGgtactgtgat ... cctacagcag-
EST: gi|218492792|gb|FG953621.1|FG953621
EST:     AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAG                         C
genomic: AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAGgtactgtgat ... cctacagcag-
EST: gi|29622196|gb|CB627207.1|CB627207
EST:     AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAG                         TCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
genomic: AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAGgtactgtgat ... cctacagcagTCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
EST: gi|29629685|gb|CB634694.1|CB634694
EST:     AGAGATTTAACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAG                         TCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
genomic: AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAGgtactgtgat ... cctacagcagTCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
EST: gi|218489615|gb|FG967806.1|FG967806
EST:     AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAG                         TCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
genomic: AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAGgtactgtgat ... cctacagcagTCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
EST: gi|29666846|gb|CB663121.1|CB663121
EST:     AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAG                         TCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
genomic: AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAGgtactgtgat ... cctacagcagTCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
EST: gi|313081071|gb|HO213657.1|HO213657
EST:     AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAG                         TCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
genomic: AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAGgtactgtgat ... cctacagcagTCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
EST: gi|58668178|gb|CK056864.1|CK056864
EST:     AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGACAG                         TCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
genomic: AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAGgtactgtgat ... cctacagcagTCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
EST: gi|109974311|gb|DT806838.1|DT806838
EST:     GAGATTTT-CCGGGATTTTCCACAGCCGTTCTTTCACCACACACCGCCAG                         TCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
genomic: GAGATTTTACCGG-ATTTTCCACAGCCGTTCCTTCACCACACACCGCCAGgtactgtgat ... cctacagcagTCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
EST: gi|29628152|gb|CB633163.1|CB633163
EST:     AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAG                         TCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
genomic: AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAGgtactgtgat ... cctacagcagTCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
EST: gi|29629744|gb|CB634753.1|CB634753
EST:     AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAG                         TCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
genomic: AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAGgtactgtgat ... cctacagcagTCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
EST: gi|29666845|gb|CB663120.1|CB663120
EST:     AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAG                         TCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
genomic: AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAGgtactgtgat ... cctacagcagTCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
EST: gi|29639138|gb|CB644147.1|CB644147
EST:     AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAG                         TCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC
genomic: AGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAGgtactgtgat ... cctacagcagTCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTC

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: 73 (upstream exon), 55 (downstream exon)
Score: 13

AGTTCTCAAGGAAAAGTATCACTCCCCTAAAGGATATAGGAGTGAGTGCAAGAGATTTTACCGGATTTTCCACAGCCGTTCCTTCACCACACACCGCCAGgtactgtgat ... cctacagcagTCCTATTTCCGTTGTGAGAACAAACATGTCTCTACCGGTGTCCCCATGCTCAAGCCCATTGCGGCAGTTTAAGCAATCCAACTGGAGCTGCCTGCCATCC




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