Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGCGCTCCGAGGGCGCCGTCGCCGGGGCCGTCGACTTCCGCGGCCGCCCGGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaatctccccctcctccccgaaccccaactcccgaggatcgattgagtgaaattttgtggattttggatgtgaaaag

Basic information

species Oryza sativa
transcript LOC_Os01g65100.3
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65100.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G400602_T01 (Zea mays), 5'ss of exon 1
CCGCGCTCCGAGGGCGCCGTCGCCGGGGCCGTCGACTTCCGCGGCCGCCCGGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacg-----cccaatctccccctcctccccgaaccccaactcccgaggatcgatt--gagtgaaat--tttgtggattttggatgtgaaaag
||  ||||||| |||||||||||||| || || ||||||||||| ||||| || |||||  ||  ||||||||| ||||||||||| ||||||||||||||||||     |||  ||  | |      | ||  | |  |||   | ||  ||     | ||  | |  |     |   | ||||| |   ||
CCCTGCTCCGACGGCGCCGTCGCCGGCGCGGTGGACTTCCGCGGGCGCCCCGCGTCCCGGTCCGGCACCGGCCGATGGTCCGCCGCGATGTTCGTCCTCGgtacggcgccccctgtcctcgctgggcacgcgcgcacacactgatgcggcgcgggccggggttgactaatcgagaggggtcggatgggtgcag
















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|88388197|gb|CI627736.1|CI627736
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|88410323|gb|CI575921.1|CI575921
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|87023816|gb|CI288169.1|CI288169
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|88354398|gb|CI624788.1|CI624788
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|88309678|gb|CI656419.1|CI656419
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGNGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|88765227|gb|CI774321.1|CI774321
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|86888738|gb|CI307796.1|CI307796
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|86901070|gb|CI306259.1|CI306259
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|88370001|gb|CI680683.1|CI680683
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTTAC-ACGGCGTGTCGGCGAACCTG
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGT-ACCACGGCGTGTCGGCGAACCTG
EST: gi|88426172|gb|CI574055.1|CI574055
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCAAGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|88410871|gb|CI578677.1|CI578677
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGAGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|88326976|gb|CI676089.1|CI676089
EST:     GGCCTCCCGCGCCTCCACCGGCCGNTGGTCCGCCGTAATGTTCGTNCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACTACGGTGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA

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: 18 (upstream exon), 73 (downstream exon)
Score: 4

CCGCGCTCCGAGGGCGCCGTCGCCGGGGCCGTCGACTTCCGCGGCCGCCCGGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGATCAGCTACCTGACGGGACCGCTGGGGGAGTCGACGGCGGGGGCGGCGGC




<











<


<