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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatcatctctatctggcttgattgcaactcttgtttcttgatctgttactacattttatcctaaagagttttgatgtgttggttttcacttttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGCAATTGACACCTCTGCTTCTCCTCCTTGTGCATGCAGCTAAGCTCTCATG

Basic information

species Oryza sativa
transcript LOC_Os08g42420.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42420.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G085330_T01 (Zea mays), 3'ss of exon 1
tatcatctctatctggcttgattgcaactcttgtttcttgatctg---ttactacattttatcctaa-agagttttgatgtgttggttttcacttttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGCAATTGACACCTCTGCTTCTCCTCCTTGTGCATGCAGCTAAGCTCTCATG
  |  | ||| |  |   || | | |  |  |||  | || ||     || || ||  | |    |  |    |||  ||||      | ||  |||||| |||||| | ||||| |||||||||||||| |||||||||||||||||||||                                                    
--ttgt-tctgttagatctg-tagaatttagtgtggcatgctccaactttgctgcagctgagtggagcatgactttagtgtggcatgctccaactttgttgcagCTGAGAGTGGAGCATGACTTCCCTGCCGATCCCAAGTACTTCGACATA----------------------------------------------------

upper sequence: LOC_Os08g42420.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G138425_T04 (Zea mays), 3'ss of exon 2
tatcatc-tctatctggcttgattgcaactcttgtttcttgatctgttactacattttatcctaaagagttttgatgtgttggttttcacttttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGCAATTGACACCTCTGCTTCTCCTCCTTGTGCATGCAGCTAAGCTCTCATG-
| | ||   ||||  |  |  ||    ||| ||  ||     | | ||  |   || ||           ||| ||||| | | |||||  |||||| |||||||| ||||| ||||| ||||| || |||||||||||||| ||||||||||| |||    |  ||| || | ||      ||     |  |     ||| 
tctaatagcctatacgtgtctatca-gactgttccttgactgtttcttgttctgttataaatccgtagaatttaatgtgataggtttcatctttgttgcagCTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGCAACTGATGGTTGCGCTGCTGCACCGGACA-ATAATAATCTGTAAATATGT
















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|29641164|gb|CB646171.1|CB646171
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|29674774|gb|CB671049.1|CB671049
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|218482597|gb|FG970654.1|FG970654
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|7332528|gb|AU085874.1|AU085874
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|86827407|gb|CI272815.1|CI272815
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|29631101|gb|CB636110.1|CB636110
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|86852808|gb|CI323117.1|CI323117
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|87014026|gb|CI273216.1|CI273216
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|29632036|gb|CB637045.1|CB637045
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|86478112|gb|CI120745.1|CI120745
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|33683476|gb|CF311715.1|CF311715
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|87038959|gb|CI193581.1|CI193581
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|33380551|gb|CF195894.1|CF195894
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|29645251|gb|CB650258.1|CB650258
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|29642943|gb|CB647950.1|CB647950
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|86597710|gb|CI274701.1|CI274701
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|29645905|gb|CB650912.1|CB650912
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|86875607|gb|CI323948.1|CI323948
EST:     TCTTAGAGATTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: TCTTAGAG-TTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|86858202|gb|CI271104.1|CI271104
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|29639665|gb|CB644674.1|CB644674
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|29639196|gb|CB644205.1|CB644205
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC

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: 74 (upstream exon), 72 (downstream exon)
Score: 65

TGATAGTAATGCCGCGAAAGAGGACGATCGCAGATTCTACCTTTATAATGATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgcaccc ... tttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGCAATTGACACCTCTGCTTCTCCTCCTTGTGCATGCAGCTAAGCTCTCATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactacattttatcctaaagagttttgatgtgttggttttcacttttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGCAATTGACACCTCTGCTTCTCCTCCTTGTGCATGCAGCTAAGCTCTCATG
                                     ttttcacttttgtttc  CT-rich tract
     acattttat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatcatctctatctggcttgattgcaactcttgtttcttgatctgttactacattttatcctaaagagttttgatgtgttggttttcacttttgtttcagCTGCGTGTGGAACATGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGCAATTGACACCTCTGCTTCTCCTCCTTGTGCATGCAGCTAAGCTCTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT