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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatatcaatttcaaatttttgaatcatccattgcaaaaaatacaaaaaaaggtgtattagtattagatgacatgataacaaataatatacctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGCAATACGGCCTATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACA

Basic information

species Oryza sativa
transcript LOC_Os11g29370.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g29370.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G574782_T01 (Zea mays), 3'ss of exon 9
aatatcaatttcaaatttttga-atcatccattgcaaaaaatacaaaaaaaggtgtattagtattagatgacatgataacaaataat--atacctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGCAATACGGCCTATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACA
 ||   | ||           | | ||| |||| |  |   |   || |  | || | | |||||   |  ||||||   || | ||  |||| ||  | ||||||||||||||||||||||| ||  | || || ||||||||  |||||||||||||  | || ||||| |||||| | | ||| ||||| |  ||||| |
-attctagttaagttagcacaacaacatgcattcctcagtgtgttaagagtg-tgcaatcgtatttt-tctcatgatgcaaagttatgaatacttgtgattagGTCTACATATACTCAAGTGGAAGTAGAGAAGCACAAAGGCTTCTATTTGGCAATACAACATACGGTGACCTGCGAAAGTTCCTGTGTGGGTATTTTGATA
















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|86877415|gb|CI312773.1|CI312773
EST:     TCGATGATGTCCCCGAGGCGCTANAGCACTGGCATGCTAGTGGCATGAAG                         GTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
genomic: TCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAGgtatctcttt ... ctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
EST: gi|86522174|gb|CI162380.1|CI162380
EST:     CTAGTGGCATGAAG                         GTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
genomic: CTAGTGGCATGAAGgtatctcttt ... ctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
EST: gi|89183965|gb|CI046530.1|CI046530
EST:     TGGCATGCTAGTGGCATGAAG                         GTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
genomic: TGGCATGCTAGTGGCATGAAGgtatctcttt ... ctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
EST: gi|33683943|gb|CF312182.1|CF312182
EST:     TCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAG                         GTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
genomic: TCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAGgtatctcttt ... ctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
EST: gi|25806482|gb|CA762443.1|CA762443
EST:     TCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAG                         GTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
genomic: TCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAGgtatctcttt ... ctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
EST: gi|29686093|gb|CB682368.1|CB682368
EST:     TCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAG                         GTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
genomic: TCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAGgtatctcttt ... ctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
EST: gi|4716001|gb|AU057117.1|AU057117
EST:     TCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAG                         GTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
genomic: TCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAGgtatctcttt ... ctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
EST: gi|9884555|gb|BE607388.1|BE607388
EST:     GTGGCATGAAG                         GTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
genomic: GTGGCATGAAGgtatctcttt ... ctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
EST: gi|86522877|gb|CI163083.1|CI163083
EST:     CCCCGAGGCGCTAAAGCACGGGCATGCTAGTGGCATGAAG                         GTCTACAGAGACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
genomic: CCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAGgtatctcttt ... ctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
EST: gi|29671700|gb|CB667975.1|CB667975
EST:     TCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAG                         GTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
genomic: TCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAGgtatctcttt ... ctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
EST: gi|11173109|gb|AU164617.1|AU164617
EST:     TCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAG                         GTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
genomic: TCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAGgtatctcttt ... ctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
EST: gi|29615092|gb|CB620105.1|CB620105
EST:     TCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAG                         GTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
genomic: TCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAGgtatctcttt ... ctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
EST: gi|88962224|gb|CI097377.1|CI097377
EST:     GTGGCATGAAG                         GTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
genomic: GTGGCATGAAGgtatctcttt ... ctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
EST: gi|427846|gb|D23987.1|D23987
EST:     TCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAG                         GTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAAGGCTATTATTTGG
genomic: TCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAGgtatctcttt ... ctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAA-GGCTATTATTTGG
EST: gi|3767686|gb|AU031713.1|AU031713
EST:     GCACTGGCATGCTAGTGGCATGAAG                         GTCTACATATACTCAAGTGNCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
genomic: GCACTGGCATGCTAGTGGCATGAAGgtatctcttt ... ctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
EST: gi|58590134|gb|CF988442.1|CF988442
EST:     TCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAG                         GTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC
genomic: TCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAGgtatctcttt ... ctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGC

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), 73 (downstream exon)
Score: 127

CCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTTTTCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGAAGgtatctcttt ... ctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGCAATACGGCCTATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaggtgtattagtattagatgacatgataacaaataatatacctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGCAATACGGCCTATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACA
                           tgataac  putative branch site (score: 127)
                          atgataacaaataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatatcaatttcaaatttttgaatcatccattgcaaaaaatacaaaaaaaggtgtattagtattagatgacatgataacaaataatatacctgcaaatagGTCTACATATACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGCAATACGGCCTATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACA

- - - - - - - - - -tgaatca
- - - - - - - - - - - - - - cattgca
- - - - - - - - - - - - - - - - -caaaaaa
- - - - - - - - - - - - - - - - - -aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaaata