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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatgtatgccatctttcagtatcctcttttacctgaaaaggagtcgactttcccataatttgtttttacattctagagtgtcgttttatcttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG

Basic information

species Oryza sativa
transcript LOC_Os02g02690.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02690.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G068277_T01 (Zea mays), 3'ss of exon 7
caatgtatgccatctttcagtatcctcttttacctgaaaaggagtcgactttccca-taatttgtt--tttacattctagagtgtcgttttatcttg-caccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG
| ||   ||||||||    | ||  ||  |   |||||||| | ||      |||| |  |  |     | ||  | |    ||  | ||  |||||    |||||||| |||||||| |||||||| |||||||||||||  || ||||| ||||| ||||| ||||| ||||||||||||
ccatac-tgccatctcaaggaatattccgt---ctgaaaagaactcatggaacccaatgttccgccagctaactgtttgctctgatgattgttcttggtgtcagGTTTCGCGGTTGCGTGAGTACCAGGGTGTAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG

upper sequence: LOC_Os02g02690.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA18G11000.1 (Glycine max), 3'ss of exon 11
caatgtatgccatctttcagtatcctcttttacctgaaaaggagtcgact-ttcccataatttgtttttacattctagagtgtcgttttatc-ttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG
 |  |  |   || | | | | | ||| ||    ||        || | |  | | || |||  |  |     | |    | |  ||| | | |||  ||||||| | || ||||| |||||||| ||||| ||||| ||||||||    ||||||||||| |||||||| |||||  ||
-agagcttaa-atttatgattgttctcattatgatgtcctttcctccattacttcaatcattcatcatgtttgtgttagttatattttgacccttgtgccagGTTACCCGCTTGCGTGAGTACCAGGGTGTTGATCCTCACTTTGACAACATTGCAAGGCAGTACCATGACATTGTGCAG

upper sequence: LOC_Os02g02690.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv19s0090g00440.t01 (Vitis vinifera), 3'ss of exon 11
--caatgtatgcc-atctttcagtatcctcttttacctgaaaaggagtcgactttcccataatttgtttttacattctagagtgtcgttttatcttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG
  ||||   |||| ||    |   | ||| |    ||||  |      |  |   || |     |   |  | ||  ||   | ||| |||   ||| |||||||  ||||  |  | |||||||||||||| ||||| |||||||||  |||||||||||| || || || |||||||||
atcaattcctgcccattgcactacaacctttacaccctgccacaattgcatcccaccaaccccattactgaatatcttaccctttcgattt---ttgtaccagGTGACACGCCTTAGAGAGTACCAAGGTGTTGATCCTCACTTTGATACAATTGCAAGGCAGTATCACGAAATTGTAAAG

upper sequence: LOC_Os02g02690.1 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S105_58V6.1 (Physcomitrella patens), 3'ss of exon 11
caatgtatgccat-ctttcagtatcctcttttacctgaaaaggagtcgactttcccataatttgtttttacattctagagtgtcgttttatcttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG
   | | ||  |  |   | |||   ||    |     |||    ||   | |    ||| |   ||| |        | | | |||   | ||     ||||  || |  | || ||||||||||| |||||||   ||||||||| |||||| |||| |||||||||  ||||||  
ttgtatgtgagaggccccctgtaat-tcacacattctgaaatttttctcttgttatttaagtgagtttaaacgaagctattcttgttgatttttcttgtagGTAACAAGACTCCGTGAGTACCAAGGAGTAGATCAGGACTTTGATGAAATTGCTAGGCGATACCATGACCTTGTAACT

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|88247791|gb|CI247640.1|CI247640
EST:     AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|89182448|gb|CI113817.1|CI113817
EST:     AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|88481854|gb|CI419125.1|CI419125
EST:     AATATTTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|86428585|gb|CI075266.1|CI075266
EST:     AANATTTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|88481007|gb|CI418278.1|CI418278
EST:     AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|86491300|gb|CI133933.1|CI133933
EST:     AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|163917926|gb|EG714758.1|EG714758
EST:     AATATCTAGTAGAGGCCACAAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAA
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAA
EST: gi|86426334|gb|CI071431.1|CI071431
EST:     AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGTGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|86505602|gb|CI148235.1|CI148235
EST:     AATATCTAGTAGAGCCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|88248278|gb|CI248127.1|CI248127
EST:     AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|86501777|gb|CI144410.1|CI144410
EST:     AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|88227499|gb|CI226979.1|CI226979
EST:     AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|88514227|gb|CI441733.1|CI441733
EST:     AATATTTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|88477822|gb|CI415093.1|CI415093
EST:     AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|88990699|gb|CI108086.1|CI108086
EST:     AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|396941424|gb|HO188633.1|HO188633
EST:     AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACCGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|88245688|gb|CI245537.1|CI245537
EST:     AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|88974820|gb|CI023114.1|CI023114
EST:     AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|94362670|gb|CI052789.1|CI052789
EST:     AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGGGGGCAAGGTGTAGATCCACACTTTGATGTAAT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGA-GTACCAAGGTGTAGATCCACACTTTGATGTAAT
EST: gi|86539112|gb|CI179318.1|CI179318
EST:     AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|89167956|gb|CI109160.1|CI109160
EST:     AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|163926568|gb|EG712432.1|EG712432
EST:     AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|88221660|gb|CI221616.1|CI221616
EST:     AATATGTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|88281120|gb|CI402318.1|CI402318
EST:     AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|86503019|gb|CI145652.1|CI145652
EST:     AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
EST: gi|86426368|gb|CI071465.1|CI071465
EST:     AANATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCG                         GTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT
genomic: AATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATT

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: 64 (upstream exon), 48 (downstream exon)
Score: 6

GAAATATCTAGTAGAGGCCACGAAAGAAGCATCCAATTCTTATACTGAAGCGgtatgataca ... cttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgactttcccataatttgtttttacattctagagtgtcgttttatcttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG
                                       ttttatctt  CT-rich tract
          ataatttgtttttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatgtatgccatctttcagtatcctcttttacctgaaaaggagtcgactttcccataatttgtttttacattctagagtgtcgttttatcttgcaccagGTTTCACGGTTGCGCGAGTACCAAGGTGTAGATCCACACTTTGATGTAATTGCAAGGCAATACCATGAGATTGTAAAG

- -tgtatgc
- - - - - - - - - - - - - - - -acctgaa