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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcttgattgctttacatgtgctcccttctgttattgctcatgcagttacactgatctcatgttattttccttgtagGTTGGCATGTCTCTTGCACAAATAGGAGAGTTTGCTTTTGTTCTTCTAAGCCGTGCTTCAAGCATCCATCTGATTGAG

Basic information

species Oryza sativa
transcript LOC_Os06g36590.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36590.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G171031_T01 (Zea mays), 3'ss of exon 16
gtaagtcttgattgc-------tttacatgtgctcccttctgttattgctcatgcagttacactgatctcatgttattttccttgtagGTTGGCATGTCTCTTGCACAAATAGGAGAGTTTGCTTTTGTTCTTCTAAGCCGTGCTTCAAGCATCCATCTGATTGAG
||||||||   || |       | |  |||  ||| | ||||    ||||| |  | | ||| | | |   |    |||||    ||||| ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||| || |||
gtaagtctgtttttcatgtctttctgaatgcactcacatctgccggtgctcttaaaatcacattaaccgtgt----ttttctccatagGTCGGCATGTCTCTTGCACAAATAGGAGAGTTTGCTTTTGTTCTCCTAAGCCGTGCTTCAAGTATCCATCTCATCGAG

upper sequence: LOC_Os06g36590.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G169114_T02 (Zea mays), 3'ss of exon 15
gtaagtcttg------attgctttacatgtgctcccttctgttattgctcatgcagttacactgatctcatgttattttccttgtagGTTGGCATGTCTCTTGCACAAATAGGAGAGTTTGCTTTTGTTCTTCTAAGCCGTGCTTCAAGCATCCATCTGATTGAG
||||||| |       ||     |  |||  ||| | ||||  | |||||||  | | ||| | | |   |    || |||    |||| |||||||| ||||||||||||||||||||||||||||||||  |||||||||||||||| || ||||| || |||
gtaagtcctttttcatatcttccttaatgcactcacatctgccagtgctcataaaatcacattaaccgtgt----ttgtccccacagGTCGGCATGTCACTTGCACAAATAGGAGAGTTTGCTTTTGTTCTCTTAAGCCGTGCTTCAAGTATTCATCTAATCGAG

upper sequence: LOC_Os06g36590.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv11s0016g02400.t01 (Vitis vinifera), 3'ss of exon 16
gtaagtcttgattgctttacatgt--------gctcccttctgttattgctcatgcagttacactgat-------ctcatgttattttccttgt--agGTTGGCATGTCTCTTGCACAAATAGGAGAGTTTGCTTTTGTTCTTCTAAGCCGTGCTTCAAGCATCCATCTGATTGAG
|||||  ||   ||   |||   |        ||| | ||   |  |    ||| || |  || |||        || | || |||   | |||  ||||||| |||||||| |||||||| || |||||||||||||||||||||||||||||||| |   | |||||  |||||
gtaagattttgctgaactaccaatacggttaagctgcattgcatcttattccatacattaccattgacagaggaccttaggtgattccacatgtgtagGTTGGAATGTCTCTGGCACAAATTGGGGAGTTTGCTTTTGTTCTTCTAAGCCGTGCTTCTAATCTTCATCTAGTTGAG

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|11544417|gb|BF475235.1|BF475235
EST:     TTGCTGTTGTCGTTAAAGGGTTTGGCTATAGCAACAAAACATCTCTTCTT                         GTTGGCATGTCTCTTGCACAAATAGGAGAGTTTGCTTTTGTTCTTCTAAGC
genomic: TTGCTGTTGTCGTTAAAGGGTTTGGCTATAGCAACAAAACATCTCTTCTTgtaagtcttg ... ttccttgtagGTTGGCATGTCTCTTGCACAAATAGGAGAGTTTGCTTTTGTTCTTCTAAGC
EST: gi|58612420|gb|CK040132.1|CK040132
EST:     TTGCTGTTGTCGTTAAAGGGTTTGGCTATAGCAACAAAACATCTCTTCTT                         GTTGGCATGTCTCTTGCACAAATAGGAGAGTTTGCTTTTGTTCTTCTAAGC
genomic: TTGCTGTTGTCGTTAAAGGGTTTGGCTATAGCAACAAAACATCTCTTCTTgtaagtcttg ... ttccttgtagGTTGGCATGTCTCTTGCACAAATAGGAGAGTTTGCTTTTGTTCTTCTAAGC
EST: gi|218489725|gb|FG964366.1|FG964366
EST:     TTGCTGTTGTCGTTAAAGGGTTTGGCTATAGCAACAAAACATCTCTTCTT                         GTTGGCATGTCTCTTGCACAAATAGGAGAGTTTGCTTTTGTTCTTCTAAGC
genomic: TTGCTGTTGTCGTTAAAGGGTTTGGCTATAGCAACAAAACATCTCTTCTTgtaagtcttg ... ttccttgtagGTTGGCATGTCTCTTGCACAAATAGGAGAGTTTGCTTTTGTTCTTCTAAGC

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), 53 (downstream exon)
Score: 9

TATACTCCTTGCAGCTGTGATTTTGGTGATAACTGTAAAGACGTTTATTGTTGCTGTTGTCGTTAAAGGGTTTGGCTATAGCAACAAAACATCTCTTCTTgtaagtcttg ... ttccttgtagGTTGGCATGTCTCTTGCACAAATAGGAGAGTTTGCTTTTGTTCTTCTAAGCCGTGCTTCAAGCATCCATCTGATTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcccttctgttattgctcatgcagttacactgatctcatgttattttccttgtagGTTGGCATGTCTCTTGCACAAATAGGAGAGTTTGCTTTTGTTCTTCTAAGCCGTGCTTCAAGCATCCATCTGATTGAG
                           cactgat  putative branch site (score: 9)
                                        ttattttcctt  putative PPT
                                     atgttatttt  TA-rich tract