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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacaattcttcatcttgagttaaattaataatggttgatgagcctacatcatctgaagacaagattcatgtatcaacatgttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCA

Basic information

species Oryza sativa
transcript LOC_Os09g36450.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g36450.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G852968_T02 (Zea mays), 3'ss of exon 6
gtgacaattcttcatcttgag-ttaaattaataatggtt-----gatgagccta-----catcatctgaagacaagat--tcatgtat---caacatgt---tgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCA
|||| | |||||||||||  | ||   || ||    |||     || ||   |      |||    | |     || |  | ||| ||   ||||||||   ||||| |||| |||||| |||||||||| ||||| || ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| |||||||||||
gtgaaatttcttcatcttaggattttttttatgggcgttctagagaagaagttgggaggcattgatttagcttgaggtgttgatgcatgcgcaacatgtatctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAGCAAGCCCAGGAAGTTCA

upper sequence: LOC_Os09g36450.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G002807_T01 (Zea mays), 3'ss of exon 6
gtgacaatt-cttcatcttgagttaaattaataatgg-----ttgatgagcctaca----------tcatctgaagacaagattcatgtatcaacatgt---tgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCA
|||| | || ||||||||| ||  |  ||  || |||     | ||  ||  |  |          | |||||| |    ||| ||| |  ||||||||   ||| | |||| |||||| |||||||||| ||||| ||||||||||| |||||||||||||||||||||||||| ||||||||||||||||| ||||| |||||||||||
gtgaaactttcttcatcttaagaaacttttttattggcattctagagaagtttgtaggcattgatttaatctgaggtgttgatgcatatg-caacatgtatctgcctgcagATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAACAAGCCCAGGAAGTTCA

upper sequence: LOC_Os09g36450.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA03G34300.1 (Glycine max), 3'ss of exon 6
------------------gtgacaattcttcatcttgagttaaattaataatggttgatgagcct--acatcatctgaagacaagattcatg-tatcaa-catgt-tgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCA
                     |  ||  | ||| |  |||  | ||  |   |    |  |  ||  | |   | ||  ||     | |||   ||| | | ||| ||  | |||||    || | |  ||||   |  | || ||||||||||| ||||| ||||| |||||||| || ||||| || |||||  | |||||||||||||| ||
gtaggtgcaagctatatttctaatataatccatttaaagtccattttctttggaaaaaacaaactggagagggtttgctgattgcttgcataacatccatcgtgtctgtatgcagACGCAGTTGCTAGTTGGGACAACATTGTTATTGCATATGAACCTGTATGGGCCATTGGAACGGGCAAAGTGGCCACTCCCCAACAAGCTCAGGAAGTACA

upper sequence: LOC_Os09g36450.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA19G36990.2 (Glycine max), 3'ss of exon 6
-------------------------------gtgacaattcttcatcttgagttaaattaataatggttgatgagcctacatcatctgaagacaagattcatgtatcaacatgttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCA
                                | | ||||| |  ||||   || | |||  |       | | |     ||    ||       |  | |  |         ||  || ||||     || | | |||||   |  | || ||||||||||| ||||| |||||||||||||| || ||||| || |||||  |||||||||||||||| ||
gtagtggaagttatgtttcttatataatccatttaaaattcgttttctt---ttgatttagaagaaacaaaaggggaaggatttggtggttgattgcattacatcgtttgccattatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGGCTATTGGAACGGGCAAAGTGGCCACTCCCCAGCAAGCTCAGGAAGTACA

upper sequence: LOC_Os09g36450.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G06740.1 (Glycine max), 3'ss of exon 6
-----gtgacaat--tcttcatcttgagttaaattaataatggttgatgagcctacatcatctgaagacaagatt-catgtatca-acatgttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCA
      ||| | |  | ||| | ||  ||  |   || ||  |  |  | |  |   |   |    ||    ||  |||   | |      ||   | ||||     |  |||  ||||   || |||| ||||||||||||||||| ||||| |||||||| || ||||| || || || |||||||| |||||||| ||
tttatttgaaagtcattttctttttaggtggagaaaagaaaagaagg-gggagtgggttgccgattgattccataacatcctttatgtccattatatgcagATGTAGTGCCAAGTTGGGATAATATAGTTATTGCATATGAGCCTGTATGGGCAATTGGAACTGGCAAAGTGGCCACACCCGAGCAAGCCCAGGAAGTCCA

upper sequence: LOC_Os09g36450.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 6
-------gtgacaattcttcatcttgagttaaattaataatggttg-atgagcctacatcatctgaagacaagattcatgtatcaacatgttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCA
       |  |    ||||| | ||  ||  |   || ||| |  | | |||   | | ||  |     | | |      | |       ||   | ||||     |  |||  ||||   || |||| ||||||||||||||||| ||||| |||||||| || ||||| || || || |||||||| |||||||| ||
ttcattagaaagtcatcttctttttaggtggagaaaagaataggagcaagaggggatagcagattgtttccataacatcctttatgtccattatgtgcagATGCAGTGCCAAGTTGGGATAATATAGTTATTGCATATGAGCCTGTATGGGCAATTGGAACTGGCAAAGTGGCCACACCCGAGCAAGCCCAGGAAGTCCA

upper sequence: LOC_Os09g36450.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 6
-------------gtgacaat-tcttcatcttgagttaaattaataatggttgatgagcctacatcatctgaa---gacaagattcatgtatcaacatgttgcttt---------cagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCA
              |||   | ||||  || ||   |  | |     |   || |   | |     |   |||   |   |   |  |||| || |    |  ||          ||||   | |  | |  ||||  |||||||| |||||||||||||| ||||||||||||||||| || ||||| || || ||   ||| || |||||||| ||
gcaagttctcttgctgatgttctctttctcatggaatgtactgtcgttttgtggtcctcttgtgaaaagagaacttgttgactcttttgtaacatcgctcttgttcaatcatgcgcagATGCTGTACCCAGTTGGGATGATGTAGTTATTGCATATGAGCCGGTTTGGGCTATTGGAACTGGTAAAGTGGCCACACCCCTGCAGGCACAGGAAGTACA

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|29645954|gb|CB650961.1|CB650961
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         ACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... ttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
EST: gi|38480252|gb|CF964341.1|CF964341
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         ACAGTATTACAAACTGGGCGGATGTAGTAATTGCATA
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... ttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATA
EST: gi|29678932|gb|CB675207.1|CB675207
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         ACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... ttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
EST: gi|29641345|gb|CB646352.1|CB646352
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         ACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... ttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
EST: gi|29667622|gb|CB663897.1|CB663897
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         ACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... ttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
EST: gi|33381301|gb|CF196644.1|CF196644
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         ACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... ttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
EST: gi|33682001|gb|CF310240.1|CF310240
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         ACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... ttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
EST: gi|29638544|gb|CB643553.1|CB643553
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         ACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... ttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
EST: gi|87020131|gb|CI277863.1|CI277863
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTT---G                         -CAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... ttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
EST: gi|86902043|gb|CI300282.1|CI300282
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         ACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... ttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
EST: gi|29637218|gb|CB642227.1|CB642227
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         ACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... ttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
EST: gi|29628219|gb|CB633230.1|CB633230
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         ACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... ttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
EST: gi|86505521|gb|CI148154.1|CI148154
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         ACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... ttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGG

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), 70 (downstream exon)
Score: 70

CAAAATGTAAAGGTTATTGCCTGCATAGGGGAGCTGTTGGAAGAGAGAGAAGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... ttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgagcctacatcatctgaagacaagattcatgtatcaacatgttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCA
 ggttgat  putative branch site (score: 70)
                                             ttgctttc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgacaattcttcatcttgagttaaattaataatggttgatgagcctacatcatctgaagacaagattcatgtatcaacatgttgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA