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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accaacctagtcaatttgttatgctgtctttttaaatatcttgatatttttcacttcaggatgaagaaactaactactggttgttatatgctattggcagAAAAATAGTTGGAAGAACCTATTTTCATACATAGGGCCCGGATTTCTTGTCTCTATTGCGTATATTGATCCTGGAAATT

Basic information

species Oryza sativa
transcript LOC_Os06g46310.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G069198_T04 (Zea mays), 3'ss of exon 2
accaacctagtcaatttgttatgctgtctttttaaatatcttgatatttttcacttcaggatga--agaaactaactactggttgttatatgctattggcagAAAAATAGTTGGAAGAACCTATTTTCATACATAGGGCCCGGATTTCTTGTCTCTATTGCGTATATTGATCCTGGAAATT
|   |  || | |  ||| | | ||  |||||   || ||  ||| || | | |||||  ||||  |||||||||||| ||  ||  ||||    ||| |||||||| |||||||||||| |||| |||||||||||||| |||||||| ||||| ||||| ||||||||||||||||| |
aatgatatacttagattgctctactaactttt-gtatctccagatcttatgc-cttcataatgatgagaaactaactattgcctgacatatcactttgacagAAAAACAGTTGGAAGAACTTATTCTCATACATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACT

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G15960.1 (Arabidopsis thaliana), 3'ss of exon 1
-accaacctagtcaatttgttatg------ctgtctttttaaatatcttgatatttttcacttcaggatgaagaaactaactactggttgttatatgc-tattggcagAAAAATAGTTGGAAGAACCTATTTTCATACATAGGGCCCGGATTTCTTGTCTCTATTGCGTATATTGATCCTGGAAATT
 |  ||  |  | | |   | | |        | |||  ||| ||      | ||||| ||||  || |        |   |  | |||| ||||| | ||   ||||||||| || ||||| ||| | || |||||| |||| || |||||||||||||| ||||| || |||||||||||||| |
catgaatttgattactgcctaaagggttgatagacttcataagtacaagagtgtttttgacttgtggtt--------ttgatgtttgttgctatatacataactgcagAAAAAGAGCTGGAAAAACTTCTTCTCATACTTAGGCCCTGGATTTCTTGTCTCAATTGCTTACATTGATCCTGGAAACT

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv09s0070g00210.t01 (Vitis vinifera), 3'ss of exon 2
accaacctagtcaatttgttatgctgtctttttaaatatc----ttgatatttttcacttcaggatgaagaaactaactactggttgttatatg--ctattg-gcagAAAAATAGTTGGAAGAACCTATTTTCATACATAGGGCCCGGATTTCTTGTCTCTATTGCGTATATTGATCCTGGAAATT
       || || |   | ||||||||| |  || ||        ||| |||  | |||| | | |||| |   | | |  |||   ||| |||   ||| | |||||  || || ||||| ||| ||||| |||| || || || || |||||||| |||||||| |||||||||||||||||||
---ggtttactcca--ggctatgctgtcataatacatgctggaactgagattagttactttatg-tgaataccttgattgatggcc-ttaaatgatttatcgtgcagAGGAAAAGCTGGAAAAACTTATTTGCATATATGGGTCCTGGGTTTCTTGTGTCTATTGCATATATTGATCCTGGAAATT

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|33653430|gb|CF276044.1|CF276044
EST:     GCACTCCTCTTATTGACAGCATAGATGTTGATCAGATTGTTATTCCAGAG                         AAAAATAGTTGGAAGAACCTATTTTCATACATAGGGCCCGGATTTCTTGTC
genomic: GCACTCCTCTTATTGACAGCATAGATGTTGATCAGATTGTTATTCCAGAGgtatgttgta ... ctattggcagAAAAATAGTTGGAAGAACCTATTTTCATACATAGGGCCCGGATTTCTTGTC
EST: gi|88721773|gb|CI745072.1|CI745072
EST:     GCACTCCTCTTATTGACAGCATAGATGTTGATCAGATTGTTATTCCAGAG                         AAAAATAGTTGGAAGAACCTATTTTCATACATAGGGCCCGGATTTCTTGTC
genomic: GCACTCCTCTTATTGACAGCATAGATGTTGATCAGATTGTTATTCCAGAGgtatgttgta ... ctattggcagAAAAATAGTTGGAAGAACCTATTTTCATACATAGGGCCCGGATTTCTTGTC
EST: gi|88692251|gb|CI735826.1|CI735826
EST:     GCACTCCTCTTATTGACAGCATAGATGTTGATCAGATTGTTATTCCAGAG                         AAAAATAGTTGGAAGAACCTATTTTCATACATAGGGCCCGGATTTCTTGTC
genomic: GCACTCCTCTTATTGACAGCATAGATGTTGATCAGATTGTTATTCCAGAGgtatgttgta ... ctattggcagAAAAATAGTTGGAAGAACCTATTTTCATACATAGGGCCCGGATTTCTTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttcacttcaggatgaagaaactaactactggttgttatatgctattggcagAAAAATAGTTGGAAGAACCTATTTTCATACATAGGGCCCGGATTTCTTGTCTCTATTGCGTATATTGATCCTGGAAATT
                      aactaac  putative branch site (score: 1)
                                   ttgttatat  TA-rich tract