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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACGCCAACGCGCGCCGCGACGACGCCGACCTCCCGCCCGTCGCCAAGCGCGTCGGGGACCACGTCTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTGgtcagtgcgttgccgcctccccgatctgggcgcggtttgggtcggagatctctcgcctgctgctcaactgctgactagttttcttctgtatttgattaattgaattag

Basic information

species Oryza sativa
transcript LOC_Os04g20230.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g20230.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G028730_T02 (Zea mays), 5'ss of exon 1
CCACGCCAACGCGCGCCGCGACGACGCCGACCTCCCGCCCGTCGCCAAGCGCGTCGGGGACCACGTCTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTGgtcag-tgcgttgccgcctccccgatctgggcgc-ggtttgggtcggag-atctctcgcctgctgctcaactgctgactagttttcttctgtatttgattaattgaattag
 ||||||||| ||||| |||||||| |||| |||||||| ||||||||||||||||| |||||| |||||||  ||||||||||| |||| ||  |  |||| || | |||| |    ||     | ||  | |  || || |  |  | |  ||||  ||     | |     ||| |||                              
TCACGCCAACCCGCGCTGCGACGACACCGAGCTCCCGCCAGTCGCCAAGCGCGTCGGAGACCACATCTTCCGATACTTCCCCCGCTCCGCGGTGTTGTTGgtgagctacgtttc--tttcgttattttgatctccagtctgcgcggatgcagatctcatctttctttaattgattgattag------------------------------
















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|88832118|gb|CI014677.1|CI014677
EST:     GCGTCGGGGACCACGTCTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTG                         CTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
genomic: GCGTCGGGGACCACGTCTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTGgtcagtgcgt ... attgaattagCTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
EST: gi|87034371|gb|CI188995.1|CI188995
EST:     AACTTCCCCCGCGCCGCCGTACTCCTG                         CTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
genomic: AACTTCCCCCGCGCCGCCGTACTCCTGgtcagtgcgt ... attgaattagCTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
EST: gi|87029911|gb|CI267924.1|CI267924
EST:     GCGTCGGGGACCACGTCTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTG                         CTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
genomic: GCGTCGGGGACCACGTCTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTGgtcagtgcgt ... attgaattagCTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
EST: gi|86511407|gb|CI154040.1|CI154040
EST:     GCGTCGGGGACCACGTCTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTG                         CTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
genomic: GCGTCGGGGACCACGTCTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTGgtcagtgcgt ... attgaattagCTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
EST: gi|86511306|gb|CI153939.1|CI153939
EST:     TTCCGCAACTTCCCCCGCGCCGCCGTACTCCTG                         CTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
genomic: TTCCGCAACTTCCCCCGCGCCGCCGTACTCCTGgtcagtgcgt ... attgaattagCTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
EST: gi|86595452|gb|CI264549.1|CI264549
EST:     GCGTCGGGGACCACGTCTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTG                         CTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
genomic: GCGTCGGGGACCACGTCTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTGgtcagtgcgt ... attgaattagCTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
EST: gi|86505090|gb|CI147723.1|CI147723
EST:     CTTCCCCCGCGCCGCCGTACTCCTG                         CTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
genomic: CTTCCCCCGCGCCGCCGTACTCCTGgtcagtgcgt ... attgaattagCTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
EST: gi|88848172|gb|CI086694.1|CI086694
EST:     CTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTG                         CTTGATAACAAGAGGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
genomic: CTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTGgtcagtgcgt ... attgaattagCTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
EST: gi|87009322|gb|CI313795.1|CI313795
EST:     GGACCACGTCTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTG                         CTTGATGACAAGAAGCTGGAGGAGGCAGTCAA-GGGAAGAGTCGCGAGCCA
genomic: GGACCACGTCTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTGgtcagtgcgt ... attgaattagCTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
EST: gi|88205861|gb|CI205710.1|CI205710
EST:     CTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTG                         CTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
genomic: CTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTGgtcagtgcgt ... attgaattagCTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
EST: gi|86428529|gb|CI075210.1|CI075210
EST:     ACGTCTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTG                         CTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
genomic: ACGTCTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTGgtcagtgcgt ... attgaattagCTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
EST: gi|87034259|gb|CI188883.1|CI188883
EST:     GCGTCGGGGACCACGTCTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTG                         CTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA
genomic: GCGTCGGGGACCACGTCTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTGgtcagtgcgt ... attgaattagCTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCA

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: 74 (upstream exon), 74 (downstream exon)
Score: 58

CCACGCCAACGCGCGCCGCGACGACGCCGACCTCCCGCCCGTCGCCAAGCGCGTCGGGGACCACGTCTTCCGCAACTTCCCCCGCGCCGCCGTACTCCTGgtcagtgcgt ... attgaattagCTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAG




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