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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttagagtgttacctgataattagatccttttcctaatagctattgcagctgaactttatgctatctgatttagtcccccccccccttcttattactgtgctatcttttgtagatctgatataaatcctaggcgattacacatcacactcaaacaaaatctaatgcttcaagagtttccttgcagCAAAAAAATGGGGATAAATATATCCCATATTGGCCAGCTGCACTATATACAGCTGTGCCTAGTCGCTCATTCTTCCCAAGGGGATTTCTATGGGATGAGG

Basic information

species Oryza sativa
transcript LOC_Os01g69210.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g69210.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G126468_T01 (Zea mays), 3'ss of exon 9
gtaagttttagagtgttacctgataattagatccttttcctaatagctattgcagctgaactttatgctatctgatttagtcccccccccccttcttattactgtgct-atcttttgtagatctgatataaatcctaggc-gattacacatcacactcaaacaaaatctaatgcttcaagagtttccttgcagCAAAAAAATGGGGATAAATATATCCCATATTGGCCAGCTGCACTATATACAGCTGTGCCTAGTCGCTCATTCTTCCCAAGGGGATTTCTATGGGATGAGG
                                                                                           | | |||||  | | || |||| | |||  |    | | | ||||| || ||||||   ||||   ||| |||||  ||||||||  |   ||  ||  |||||||||||||||||||| || ||  |||||||||| |||||| ||||||||||||| || || ||||| |||||||||||||||||||| ||||||||||
-------------------------------------------------------------------------------------------cgttttatttttatactgatctgtagtacgttgcttctgattcctaagctgattacgagtcactggcaaccaaaacttaatgctt--atttttctctgccagCAAAAAAATGGGGATAAGTACATTTCATATTGGCCTGCTGCATTATATACAGCTGTCCCCAGCCGCTCTTTCTTCCCAAGGGGATTTCTGTGGGATGAGG

upper sequence: LOC_Os01g69210.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv01s0010g03300.t01 (Vitis vinifera), 3'ss of exon 9
gtaagttttagagtgttacctgataattagatccttttcctaatagctattgcagctgaactttatgctatctgatttagtcccccccccccttcttattactgtgctatcttttgtagatctgatataaatcctaggcgattacacatcacactcaaacaaaatctaatgcttcaagagtttc-cttgcagCAAAAAAATGGGGATAAATATATCCCATATTGGCCAGCTGCACTATATACAGCTGTGCCTAGTCGCTCATTCTTCCCAAGGGGATTTCTATGGGATGAGG
                                                                                            | ||  | |  |||||||| ||| |  |  ||  || ||      || || | |  |     ||  ||||| ||  |   |     | |||| |||||||   || | |   ||||| | |||  |||||||||| |||| ||| || |||||||| || ||||| || ||||| |||||||||||| |||||||||| |
--------------------------------------------------------------------------------------ggtttttactggtgaaggtgctatcctttat--acttgtcatcaact----gccatcaaatttggacatctgacaaagtcatacagtgggtcattttctcttgcagTTTAAGAGTCATGATAATTTTATTTCATATTGGCCGGCTGAACTTTACACAGCTGTTCCAAGTCGATCCTTCTTTCCAAGGGGATTTTTATGGGATGAAG
















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|58672225|gb|CK060911.1|CK060911
EST:     TTGGCTATTTCTATGGGCAGTCAAAAATTGCACTTCCAAAAGGTTTTACA                         CNNNNNNNTGGGGATAAATATATCCCATATTGGCCAGCTGCACTATATACA
genomic: TTGGCTATTTCTATGGGCAGTCAAAAATTGCACTTCCAAAAGGTTTTACAgtaagtttta ... ttccttgcagCAAAAAAATGGGGATAAATATATCCCATATTGGCCAGCTGCACTATATACA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcgattacacatcacactcaaacaaaatctaatgcttcaagagtttccttgcagCAAAAAAATGGGGATAAATATATCCCATATTGGCCAGCTGCACTATATACAGCTGTGCCTAGTCGCTCATTCTTCCCAAGGGGATTTCTATGGGATGAGG
                           atctaat  putative branch site (score: 3)
                                            tttccttgc  putative PPT
                    aaacaaaatctaat  TA-rich tract