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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctcatattgttcgatagattcagtgccgctaatcagtagaaaacacaatcctgctcttggagatgcatgtaacttttctatatcctctcggtgttgtagATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCAGGGAGCACTTACCGCACCAGAGATGAAATTGCAGGCATAAGACAG

Basic information

species Oryza sativa
transcript LOC_Os06g13720.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G027627_T01 (Zea mays), 3'ss of exon 3
---gctcatattgttcgatagattcagtgccgctaatcagtagaaaacacaatcctgctcttggagatgcatgtaactttt-ctatatcctctcggtgttgtagATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCAGGGAGCACTTACCGCACCAGAGATGAAATTGCAGGCATAAGACAG
    | | ||   |     ||  |      || |  |  ||   |  |   |   |  ||||  ||||||   | ||      | ||| |  |   ||||  |||| ||||||||||||||||||||||||||||| ||||| |||||||||||||| ||||| |||||||| || ||||| || || |||||||| |||
aggacccttaaactagacgaggcttgacatcggt--tttgtg--attccagactttcttcttaaagatgctgatcaccacggttctattcgttttatgtttcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAG

upper sequence: LOC_Os06g13720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 3
gctcatattgttcgatagattcagtgccgctaatcagtagaaaacacaatcc-tgctcttggagatgcatgtaacttttctatatcctct-cggtgttgt--agATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCAGGGAGCACTTACCGCACCAGAGATGAAATTGCAGGCATAAGACAG
  | ||  |    |  |  ||  ||     | ||    |   | || | |   | ||||   ||||     | | || ||||| |  |      |  |||  |||||||||| |||||||| ||||||||||| |||||||||||||| ||||| || ||||| ||||| ||  | ||||||||| | ||  | ||||||
-tttatcatagctgtcat-ttgtgtagttttgattg--aattatcatagtttattctctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCTGGCAGCACATACCGGACACGTGATGAAATTTCTGGTGTGAGACAG

upper sequence: LOC_Os06g13720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 3
---------------gctcatattgttcgatagattc----agtgccgctaatcagtagaaaacacaatcctgctcttggagatgcatgtaact--tttctatatcctctcggtgttgt--agATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCAGGGAGCACTTACCGCACCAGAGATGAAATTGCAGGCATAAGACAG
                ||||| |      |||  ||     | |     ||     ||| ||  |   |  |  |||  |  ||   | ||| |  ||||| |||| |     | ||||  |||||||||| |||||||| ||||||||||| || ||||| ||||| ||||| || ||||| ||||| ||  | ||||| ||| | ||  | ||||||
gtaagtaaattaacctctcatttgtacttatattttttaagaatttttttagcttttaggaatgattcttttattctctgttatat-tataattgatttctctatcttaattattttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTGAGACAG

upper sequence: LOC_Os06g13720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA01G04470.2 (Glycine max), 3'ss of exon 1
gctcatattgttcgatagattcagtgccgctaatc---agtagaaaacacaatcctgctcttggagatgcatgtaacttttctatatcctct-cggtgttgt--agATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCAGGGAGCACTTACCGCACCAGAGATGAAATTGCAGGCATAAGACAG
      ||| |   |||| |    |     || |    | || |  |   ||   |  |||   ||||     | | || ||||| |  |      |  |||  |||||||||| |||||||| ||||||||||| |||||||||||||| ||||  || ||||| ||||| ||  | ||||||||| | ||  | ||||||
------attttaacatagctgtcatttgtgtagttttgattaaattatcaaagtttattctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCATGGCAGCACATACCGTACACGTGATGAAATTTCTGGTGTGAGACAG

upper sequence: LOC_Os06g13720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G17240.1 (Glycine max), 3'ss of exon 3
-------------------------gctcatattgttcgatagattcagtgccgctaatcagtagaaaacacaatcctgctcttggagatgcatgtaact--tttctatatcctctcggtgttgt--agATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCAGGGAGCACTTACCGCACCAGAGATGAAATTGCAGGCATAAGACAG
                          || |||||  |   || |||   ||    ||     ||| ||  |   |  |  |||  |  ||   |  || |  ||||| |||| |     | ||||  ||||||| ||||||||||| ||||||||||| || ||||| ||||| ||||| || ||||| ||||| ||  | ||||| ||| | ||  ||||||||
gtaagtaaatttacttcttttttgtacttatatttct---taaatt---tgtgtttagattttaggaatgattcttttattctctgttatat-tacaattgatttctctatcttaattattttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTAAGACAG

upper sequence: LOC_Os06g13720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G24180.1 (Arabidopsis thaliana), 3'ss of exon 3
--gctcatattgttcgatagattcagtgccgctaatcagtagaaaacacaatcctgctcttggagatgcatgtaacttttctatatcctctcggtgttgtagATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCAGGGAGCACTTACCGCACCAGAGATGAAATTGCAGGCATAAGACAG
  |   ||    |   ||||  |         |  |   |  | ||  || ||     || |    |      ||| |  |  |  | |     |   | |||| |||||||||||||| |||||||||||||| ||||||||||| || ||||| ||||||||||| ||  | ||||||||  | ||| | ||||||
ttgtgaattcaatcacatagcgttgacatttatcgtatttttataatccattctctacctagtgattatgaccaacataccattgccatt--atttgcgcagATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAG

upper sequence: LOC_Os06g13720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 3
gctcatattgttcgatagattcagtgccgctaatcagtagaaaacaca-atcctgctcttggagatgcat----gtaacttttctatatcctctcggtgttgtagATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCAGGGAGCACTTACCGCACCAGAGATGAAATTGCAGGCATAAGACAG
   |||||   |   ||| ||  ||  | | | | | |           || ||   ||   | ||| ||    | | | ||  || ||| | ||     |  ||||||||||||||||||| ||||| |||||||| ||||| ||||| ||||| |||||||| ||||| ||| ||||||| ||  | ||  | || |||
---catataagt-agtagctttggtttc-caatttattttcctgtgtttattctttcctatcatatggattacagaagcattaatacatcgtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG

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|86594846|gb|CI258100.1|CI258100
EST:     AACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATT                         ATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCA
genomic: AACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATTgtaagtgaat ... ggtgttgtagATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCA
EST: gi|218481294|gb|FG969686.1|FG969686
EST:     AACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATT                         ATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCA
genomic: AACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATTgtaagtgaat ... ggtgttgtagATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCA
EST: gi|218498886|gb|FG966541.1|FG966541
EST:     AACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATT                         ATTCTTGAGATGGACACCTACAGATAC-ACGGACACTCTATGT
genomic: AACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATTgtaagtgaat ... ggtgttgtagATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGT
EST: gi|88974166|gb|CI002785.1|CI002785
EST:     TGCTCTTGAAAATGGACCGATT                         ATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCA
genomic: TGCTCTTGAAAATGGACCGATTgtaagtgaat ... ggtgttgtagATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCA
EST: gi|218483908|gb|FG949227.1|FG949227
EST:     AACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATT                         ATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCA
genomic: AACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATTgtaagtgaat ... ggtgttgtagATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCA
EST: gi|218486487|gb|FG956233.1|FG956233
EST:     AACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATT                         ATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCA
genomic: AACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATTgtaagtgaat ... ggtgttgtagATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCA
EST: gi|218483530|gb|FG955438.1|FG955438
EST:     AACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATT                         ATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCA
genomic: AACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATTgtaagtgaat ... ggtgttgtagATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCA
EST: gi|218494530|gb|FG953442.1|FG953442
EST:     AACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATT                         ATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCA
genomic: AACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATTgtaagtgaat ... ggtgttgtagATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCA
EST: gi|218478459|gb|FG951913.1|FG951913
EST:     AACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTG-AAATGGACCGATT                         ATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCA
genomic: AACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATTgtaagtgaat ... ggtgttgtagATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCA

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: 72 (upstream exon), 63 (downstream exon)
Score: 17

GTCGATGGTATGGATGTTCTTGCAGTCAAACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATTgtaagtgaat ... ggtgttgtagATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCAGGGAGCACTTACCGCACCAGAGATGAAATTGCAGGCATAAGACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaatcctgctcttggagatgcatgtaacttttctatatcctctcggtgttgtagATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCAGGGAGCACTTACCGCACCAGAGATGAAATTGCAGGCATAAGACAG
                      atgtaac  putative branch site (score: 17)
                                      tcctctcg  putative PPT
                         taacttttctatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctcatattgttcgatagattcagtgccgctaatcagtagaaaacacaatcctgctcttggagatgcatgtaacttttctatatcctctcggtgttgtagATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCAGGGAGCACTTACCGCACCAGAGATGAAATTGCAGGCATAAGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - -gtgccgc
- - - - - - - - - - - - - - - - - - - - - -acacaat
- - - - - - - - - - - - - - - - - - - - - - - - - cctgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatgt