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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtagtggcgtggtactgtgaatttgtgactgattctcattgaattatttgctcattgcttctgtttctttcatatgcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTCATGAATCCACAGAATGGTCTTGTGATCAAACCATACAAGAGGACCCATT

Basic information

species Oryza sativa
transcript LOC_Os01g65450.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65450.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G427526_T01 (Zea mays), 3'ss of exon 1
-----------------------gttagtagtggcgtggtactgtgaatttgtgactgattctcattgaattatttgctcattgcttctgtttctttcatatgcagTA----------CAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTCATGAATCCACAGAATGGTCTTGTGATCAAACCATACAAGAGGACCCATT---------------------------------------------------------------
                       | | ||  |  |    || ||||||  || |   | | |||||  |||| |||||   ||||| |||| |    |||||||||||          ||| ||||  ||||| |||||||||||||| || |||||||| || ||||||||||||||||| ||||| |||||||| |||| || || ||  |||                                                                
gttagtattctatttatttctgtgcttgtgttaccaatttaatgtgaaactgggttaggtcctcatctaattctttgccgcttgctcctgtcttccccatatgcagtagcctgtactacaacgaaaagaacaccatcatgtttgatgatctaagaaggaatttcgtcatgaatccacagAACGGTCTCGTGATCAAGCCATTCAGGAAGAGGCATAATGATCATGAGCTGGTGAAGCTTGCACACTACCTGCTTTCAATCGGAGACCTAGAAGATCTGA

upper sequence: LOC_Os01g65450.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G114172_T03 (Zea mays), 3'ss of exon 4
-------------------gttagtagtggcgtggtactgtgaatttgtgactgattctcattgaattatttgctcattgcttctgtttctttcatatgcagTAC---AATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTCATGAATCCACAGAATGGTCTTGTGATCAAACCATACAAGAGGACCCATT
                   | | ||| |  |    || |||| |  ||||   | |  ||||  ||||  ||||   ||||| |||| |  | ||||||||||||   || ||||  ||||| || ||||||||||| || |||||||| || ||||||||||||||||| ||||| |||||||| |||| || ||   | |   
gttagtactctatttctgtgctcgtattaccaatttaatgtggacctgtgttaggtcttcatctaattccttgccgcttgctcctgtcttctccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTCGTCATGAATCCACAGAACGGTCTCGTGATCAAGCCATTCAGGAAAGCGC---

upper sequence: LOC_Os01g65450.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G13320.1 (Glycine max), 3'ss of exon 5
-----------------gttagtagtggcgtggtactgtgaatttgtgactgattctcattg---aattat-ttgctcattgcttctgtttctttcatatgcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTCATGAATCCACAGAATGGTCTTGTGATCAAACCATACAAGAGGACCCATT
                  |  ||| ||      |  | || ||  || |   || | |||     | || | ||| |  | | ||||  |||| |   | |   |||||||   |||| || ||||||||||||||||| ||||| || ||||| ||||| |||||||||||| |    || ||||||| || || | | |   
atctggttttcatttatttctgtactgtttgaattttatgcatcagtcaaccatgcccatgatctagttgtcttgatggtggtttcttattctatttca-gTTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTTGTGATGAACCCACAGAATGGTTTGACAATTAAACCATTCAGGAAGGCTC---

upper sequence: LOC_Os01g65450.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA05G30160.1 (Glycine max), 3'ss of exon 5
----------------gttagtagtggcgtggtactgtgaatttgtgactgattctcattgaattatttgctcattgcttctgtttctt-tcatat----gcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTCATGAATCCACAGAATGGTCTTGTGATCAAACCATACAAGAGGACCCATT
                  |  |  |    |  | |||| | | | | | |  ||  |||      |  ||| | |    |  ||||||| |  |||    |   |||||||   |||| || ||||||||||||||||| ||||| || ||||| ||||| |||||||||||| |    || ||||||| || || | | |   
attgctgtaatctatatctgcttttcatttatttctgt-attgtttcaattttttgcatcagtcaacatgcccttgatgttggtttcttattctatttcagTTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTTGTAATGAACCCACAGAATGGTTTGACAATTAAACCATTCAGGAAGGCTC---

upper sequence: LOC_Os01g65450.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv12s0035g00640.t01 (Vitis vinifera), 3'ss of exon 5
---------------gttagtagtggcgtggtactgtgaatttgtgactgat-----tctcattgaattatttgctcattgcttctgtttctttcatatgcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTCATGAATCCACAGAATGGTCTTGTGATCAAACCATACAAGAGGACCCATT
               |  | | |     | | | | |   | || | |  ||     ||  | |  |  ||   ||  | |  |||  || |||     |   |||| |  || |||||| |||||||||||||||||  |||| || ||||| ||||| |||||||| ||| |    ||||| |||| || || | | |   
ttcaaatgctatatagaaaattgaattattgcatttttcttgtgggcccaatgatcttcctacttgacaatagactggtggtatcttgttatttttgcagTTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTTGTGATGAACCCACAGAACGGTTTGACAATCAAGCCATTCAGGAAGGCTC---

upper sequence: LOC_Os01g65450.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ35150 (Selaginella moellendorffii), 3'ss of exon 5
gttagtagtggcgtggtactgtgaatttgtgactgattctcattgaattatttgctcattgcttctgtttctttcatatgcagTACAATGAAACAAACA---CAATCATGTTTGATGACCTCAGAAGGAACTTTGTCATGAATCCACAGAATGGTCTTGTGATCAAACCATACAAGAGGACCCATT
          |    |   | |  ||   |   |   |||| |   ||| |||     ||| ||   | | | |    | ||||   ||| | ||||||   | |||||||| ||||| ||||  |||||||| || ||||||||||| |||||||| ||||||   || |  || |   | |   
----------gtaaagcgtt-tagatccttctttagatctcttatcattttttaaattttggtttcttctttctttgctacagTTTTATGGACCAAACAACACGATCATGTTGGATGATCTCAAGAGGAACTTCGTGATGAATCCACAAAATGGTCTCGTGATCCGGCCTTTTAAAAAAGCTC---

upper sequence: LOC_Os01g65450.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ24099 (Selaginella moellendorffii), 3'ss of exon 5
gtta-gtagtggcgtggtactgtgaatttgtgactgattctcattgaattatttgctcattgcttctgtttctttcatatgcagTACAATGAAACAAACA---CAATCATGTTTGATGACCTCAGAAGGAACTTTGTCATGAATCCACAGAATGGTCTTGTGATCAAACCATACAAGAGGACCCATT
|| | |   |    |  | || |  || | | |    ||     ||  || |||  || | | ||||  ||  ||    | ||||   ||| | ||||||   | |||||| | ||||| ||||  |||||||| || ||||||||||| |||||||| ||||||   || |  || |   | |   
gtaaagcgtttagatccttctttagatctcttatcagtt-----tgtttttttttttcttggtttcttctttctttgc-tacagTTTTATGGACCAAACAACACGATCATGCTGGATGATCTCAAGAGGAACTTCGTGATGAATCCACAAAATGGTCTCGTGATCCGGCCTTTTAAAAAAGCTC---

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|86495698|gb|CI138331.1|CI138331
EST:     AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAG                         TACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
genomic: AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAGgttagtagtg ... tcatatgcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
EST: gi|86527359|gb|CI167565.1|CI167565
EST:     AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAG                         TACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
genomic: AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAGgttagtagtg ... tcatatgcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
EST: gi|33819320|gb|CF335480.1|CF335480
EST:     AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAG                         TACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
genomic: AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAGgttagtagtg ... tcatatgcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
EST: gi|86495747|gb|CI138380.1|CI138380
EST:     AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAG                         TACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
genomic: AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAGgttagtagtg ... tcatatgcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
EST: gi|86539775|gb|CI179981.1|CI179981
EST:     AGTTCCCCGAG                         TACAATGAAACATACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
genomic: AGTTCCCCGAGgttagtagtg ... tcatatgcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
EST: gi|86434177|gb|CI094520.1|CI094520
EST:     AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAG                         TACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
genomic: AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAGgttagtagtg ... tcatatgcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
EST: gi|86543608|gb|CI183814.1|CI183814
EST:     AGTTCCCCGAG                         TACAATGAAACAAACACTATCATGTTTGATGACCTCAGAAGGAACTTTGTC
genomic: AGTTCCCCGAGgttagtagtg ... tcatatgcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
EST: gi|29676776|gb|CB673051.1|CB673051
EST:     AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAG                         TACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
genomic: AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAGgttagtagtg ... tcatatgcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
EST: gi|88226719|gb|CI226635.1|CI226635
EST:     AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAG                         TACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
genomic: AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAGgttagtagtg ... tcatatgcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
EST: gi|89181139|gb|CI045222.1|CI045222
EST:     AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAG                         TACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
genomic: AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAGgttagtagtg ... tcatatgcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
EST: gi|87007353|gb|CI279024.1|CI279024
EST:     AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAG                         TACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
genomic: AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAGgttagtagtg ... tcatatgcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
EST: gi|29685722|gb|CB681997.1|CB681997
EST:     AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAG                         TACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
genomic: AAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAGgttagtagtg ... tcatatgcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
EST: gi|87032305|gb|CI264086.1|CI264086
EST:     TTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAG                         TACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC
genomic: TTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAGgttagtagtg ... tcatatgcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTC

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: 73 (upstream exon), 55 (downstream exon)
Score: 17

GGATCACTTGGCGATGATAACTGTGCAATCTGAAAACCTGTCAGAAAAGAAAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAGgttagtagtg ... tcatatgcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTCATGAATCCACAGAATGGTCTTGTGATCAAACCATACAAGAGGACCCATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgactgattctcattgaattatttgctcattgcttctgtttctttcatatgcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTCATGAATCCACAGAATGGTCTTGTGATCAAACCATACAAGAGGACCCATT
  gactgat  putative branch site (score: 17)
                          ctcattgcttctgttt  putative PPT
           tcattgaattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtagtggcgtggtactgtgaatttgtgactgattctcattgaattatttgctcattgcttctgtttctttcatatgcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTCATGAATCCACAGAATGGTCTTGTGATCAAACCATACAAGAGGACCCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA