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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATTGGTGCAGGCCTGGAATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAAgtatgaattctatgagcaccagagcatcctctgtatttctgttgttctctggtgatgccttgtaacaccacgtactttgtag

Basic information

species Oryza sativa
transcript LOC_Os02g57260.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57260.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G848768_T02 (Zea mays), 5'ss of exon 6
GGATTGGTGCAGGCCTGGAATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAAgtatgaattctatgagcaccagagcatcctctgtatttctgttgttctctggtgatg-----ccttgtaacaccacgtactttgtag------
|||||||||| ||  |||||||||||||  ||||| | || | ||||||||||||||| ||||| |||||| | ||| ||    ||    |   |    |   ||| |  | ||  |     | |      || |||||||    | || | |        
GGATTGGTGCTGGTTTGGAATCCATGTCCATAAATTCCATTGCTTGGGAAGGACAAGTTAACCCAAAAgtaaggattataaccacaatgtaaattgaaatagttttttcctttttacacaaaaaggaaactctcgtaacacatttttctctctccttgcag
















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|29661674|gb|CB657949.1|CB657949
EST:     AATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAA                         GTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
genomic: AATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAAgtatgaattc ... tactttgtagGTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
EST: gi|33793905|gb|CF322841.1|CF322841
EST:     AATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAA                         GTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
genomic: AATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAAgtatgaattc ... tactttgtagGTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
EST: gi|29664436|gb|CB660711.1|CB660711
EST:     AATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAA                         GTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
genomic: AATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAAgtatgaattc ... tactttgtagGTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
EST: gi|218485684|gb|FG959002.1|FG959002
EST:     AATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAA                         GTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
genomic: AATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAAgtatgaattc ... tactttgtagGTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
EST: gi|29687731|gb|CB684006.1|CB684006
EST:     AATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAA                         GTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
genomic: AATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAAgtatgaattc ... tactttgtagGTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
EST: gi|218500667|gb|FG957553.1|FG957553
EST:     AATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAA                         GTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
genomic: AATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAAgtatgaattc ... tactttgtagGTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
EST: gi|38471798|gb|CF955929.1|CF955929
EST:     AATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAA                         GTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
genomic: AATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAAgtatgaattc ... tactttgtagGTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
EST: gi|38565849|gb|CK085302.1|CK085302
EST:     AATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAA                         GTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
genomic: AATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAAgtatgaattc ... tactttgtagGTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
EST: gi|29667870|gb|CB664145.1|CB664145
EST:     AATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAA                         GTAAATGAAGTCCACAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
genomic: AATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAAgtatgaattc ... tactttgtagGTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
EST: gi|33681865|gb|CF310104.1|CF310104
EST:     ATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAA                         GTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
genomic: ATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAAgtatgaattc ... tactttgtagGTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
EST: gi|58606960|gb|CK034993.1|CK034993
EST:     AATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAA                         GTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG
genomic: AATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAAgtatgaattc ... tactttgtagGTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACG

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: 75 (upstream exon), 69 (downstream exon)
Score: 125

GGATTGGTGCAGGCCTGGAATCCATGTCAGTAAATGCTATGGGTTGGGAAGGACAAGTAAACCCTAAAgtatgaattc ... tactttgtagGTAAATGAAGTCCAGAAAGCACAGGATTGTCTTTTGCCCATGGGGATAACGTCCGAAAATGTTGCGCACCGATATGGTGTAACAAGACAAGAGCAGGATC




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