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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatctgtttgttggaatccatgctaaattgttattttgtttttgcatgttatgcttcccagtttggtcatttataaactttttatataacttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATTCTAGTGAACATTTTTGGTGGTATCATGAAATGTGATGTGATAGCAAGTG

Basic information

species Oryza sativa
transcript LOC_Os02g40830.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 9
----------------------------------aatctgtttgttggaatccatgctaaatt-----gttattttgtttttgcatgttatgcttcc-----cagtttggtcatttataaacttt---ttatataacttgtattc-----agGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATTCTAGTGAACATTTTTGGTGGTATCATGAAATGTGATGTGATAGCAAGTG
                                    | ||    |    ||||||| ||||       |  ||||||   ||| |  |||   | ||     |   |  | | || | |    ||   || || || || |||||     ||||||||||||| ||||||||  ||||||| ||||||||||||||||| ||||||||||||||||||||||| || |||||||||||||||||||||||||
gtataaattggttgccgttttagcgttacttgaatgtttgaccttctctatccatgttaaaccctgacgccattttgacattgtagcttaatttgccgcaggcgcatatgcctttgacagtgcttatcttgtaaaatttctattctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTG

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA13G18730.1 (Glycine max), 3'ss of exon 9
aatctgtttgttggaatccatgctaaattgttattttgtttttgca-tgttatgcttcccagtttggtcatttataaactttttatataact-tgtat-tcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATTCTAGTGAACATTTTTGGTGGTATCATGAAATGTGATGTGATAGCAAGTG
||  | | | ||  | |      | | || ||  |   ||  | || || | | | |   |   || |  ||| |  || ||| ||  || | ||||  |||||| || || |||||||| || |||||| | ||||| | ||||||||| ||| | || ||||||||||| ||||| ||||| |||||||| ||||||||||
aagat-tatattaaatttttcttttagtttttgctagattccttcaatgatctacatgttatgatgtt--tttgttcacatttaatgcaattatgtaaatcagGTGGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGGGGTATAATGAAGTGTGATGTTATAGCAAGTG

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 9
aatctgtttgttggaatccatgctaaattgttattttgtttttgcatgttatgcttccca-gtt-tggt-catttataaactttttatataact-tgtat-tcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATTCTAGTGAACATTTTTGGTGGTATCATGAAATGTGATGTGATAGCAAGTG
|   | |   ||  ||   |   |  || ||| |||  |   | | | | ||| |  ||| ||| || |   ||| |  |  ||| ||  || | ||||  ||||||||| || |||||||| || |||||| | ||||| | ||||||||| ||| | || ||||||||||||||||| ||||| |||||||| ||||||||||
agattat--attaaaa---aaattgtatagttttttcctagatacctttaatgttctccatgttatgatgtttttgttcatatttaatgcaattatgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGTGGTATAATGAAGTGTGATGTTATAGCAAGTG

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 9
aatctgtttgttggaatccatgctaaattgttattttgtttttgcatgttatgcttcccagtttggtcatttataaactttttatataacttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATTCTAGTGAACATTTTTGGTGGTATCATGAAATGTGATGTGATAGCAAGTG
           |  ||   |  ||   || ||  ||   |||||    | ||       |         || ||| |  ||   | |  |    | | |||| |||||||| ||||||||  |||| || || |||| |||||| || ||  | |||||||| |||||||| || ||||||||||||||||| || ||||
----------gtaaaaggaac-cttctttctttcttcacttttgggaatcattggaatgaaaaccaattttaatagaggtt---tgtgtcaaaaaataagGTGGTGGAAGCGTTTAAGATACTGACATCGGACGATAAAGTGAAAGCAATCTTGGTGAACATATTTGGTGGGATAATGAAATGTGATGTGATTGCTAGTG

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 9
----aatctgtttgttggaatc-catgctaaattgttattttgtttttgcatgttatgcttcccagtttggtcatttataaactttttatataacttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATTCTAGTGAACATTTTTGGTGGTATCATGAAATGTGATGTGATAGCAAGTG
      ||| | | |   | |      || || |   | |    ||     ||||||   |     | |    |||||| || || ||| || |  || |  ||||| ||||||||||| || || |||||| | |||||||  || || || ||| |||||||||||||||| || || |||||||||||  | ||||||||||
tcttgctctttctctcacattgatgcacttaaatacaactcaagttac-tgtgttataaataaagatata--tatttattaa-ttcttaaattatgtgaaa-cagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATTTTAGTGAACATTTTTGGAGGAATAATGAAATGTGACATAATAGCAAGTG

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 9
aatctgtttgttggaat-ccat-gcta-aattgttattttgtttttgcatgtta-tgcttcccagtttggtcatttataaactttttatataacttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATTCTAGTGAACATTTTTGGTGGTATCATGAAATGTGATGTGATAGCAAGTG
   |  | |  |  | | |||| |||  | |||||  | |  |   |||  |   || |       ||| |  || |   || ||  ||||  |   | | |||||||||||||| ||||| ||| ||||||||||    |||||||| |||||||| ||||||||||||||||| |||||||| |||||||| || ||   ||
---ccatgtaatcaactaccatagctgtagttgttgctgttgtgaagcaattgggtggtatgttcgttgatagttaaccgaccttg-atatgtcgcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTG

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|58589675|gb|CF987983.1|CF987983
EST:     GTACGCCTGCCAATTTTCTTGAT-TTGGTGGAAGTGCATCAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|89193215|gb|CI050513.1|CI050513
EST:     GTGGAAGTGCATCAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: GTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|88837352|gb|CI078712.1|CI078712
EST:     GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|33688589|gb|CF316828.1|CF316828
EST:     GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|218478127|gb|FG953382.1|FG953382
EST:     GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|7378380|gb|AU088651.1|AU088651
EST:     GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|88906319|gb|CI375391.1|CI375391
EST:     GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGGCAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|163921201|gb|EG714126.1|EG714126
EST:     GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGA
genomic: GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGA
EST: gi|88994236|gb|CI116200.1|CI116200
EST:     AGTGCATCAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: AGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|86841053|gb|CI342839.1|CI342839
EST:     TTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: TTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|86484646|gb|CI127279.1|CI127279
EST:     AGTGCATCAGAGGGACAG                         CTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: AGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|29662329|gb|CB658604.1|CB658604
EST:     GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|88837962|gb|CI371540.1|CI371540
EST:     TGTTGGTGGAAGTGCATCAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: TGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|86415306|gb|CI069709.1|CI069709
EST:     GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|58689592|gb|CK078279.1|CK078279
EST:     CAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: CAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|86832419|gb|CI342073.1|CI342073
EST:     G-ACCCCT-CCAATTTTCTTAATGTTGGTGGAAGTGCATCAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|88964277|gb|CI045470.1|CI045470
EST:     GGTGGAAGTGCATCAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: GGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|29662111|gb|CB658386.1|CB658386
EST:     GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|86501937|gb|CI144570.1|CI144570
EST:     GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|88248561|gb|CI248410.1|CI248410
EST:     CCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: CCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|88247312|gb|CI247161.1|CI247161
EST:     GTACGCCTGCCAATTTTCTTGATGTTGGAGGAAGTGCATCAGAAGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: GTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|86421076|gb|CI057065.1|CI057065
EST:     TTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: TTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
EST: gi|88982951|gb|CI250555.1|CI250555
EST:     CTGCCAATTTTCTTGATGTTGGTGGAAGTGCATAAGAGGGACAG                         GTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT
genomic: CTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATT

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), 75 (downstream exon)
Score: 76

CGGTGCAGGATTGGCAATGGCTACAATGGACATCATTAAGTTGCATGGGGGTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataag ... ttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATTCTAGTGAACATTTTTGGTGGTATCATGAAATGTGATGTGATAGCAAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttatgcttcccagtttggtcatttataaactttttatataacttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATTCTAGTGAACATTTTTGGTGGTATCATGAAATGTGATGTGATAGCAAGTG
                                      atataac  putative branch site (score: 76)
                     tcatttataaactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatctgtttgttggaatccatgctaaattgttattttgtttttgcatgttatgcttcccagtttggtcatttataaactttttatataacttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATTCTAGTGAACATTTTTGGTGGTATCATGAAATGTGATGTGATAGCAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- -ctgtttg
- - - - - - - - tccatgc
- - - - - - - - - - - - - - - - - - - - - tgcatgt