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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaccattttagtcctggacttgttaagttgaacattcccgtttctagtttctggttttcaaaaataattaggaagtatatccattttaactgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAAGTATTCTACATTGACTATGGCAACCAAGAAGTCGTTCCTTACAGTCGCA

Basic information

species Oryza sativa
transcript LOC_Os02g32350.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 14
lower sequence: AC207890.3_FGT002 (Zea mays), 3'ss of exon 14
-----aac-cattttagtcctggacttgttaagttgaacattcccgtttctagtttctggt--tttcaaaaataattaggaagtatatccattttaactgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAAGTATTCTACATTGACTATGGCAACCAAGAAGTCGTTCCTTACAGTCGCA---
     | | || | ||||  |  |||  |    | |||  ||  | ||   || | |||||  ||  | ||||  |   |     | | ||| |    ||   |||||||||| |||||||||||     ||||   |||||  ||||||||||||||||||||||| |||||||||||||||||||| || ||| | ||||||||     
ttcttatcacaatatagttgtatactcttc---tcgaa--ttgtcattgtcagctcctggtcattctagaaattttattgcgaagtcttcatgtcgtttg---tgcagATTGTTAATGGACCTCGT---TCTGTTGAATCTCCGGACGACAAGTTTGAAGTATTCTATATTGACTATGGCAACCAAGAGGTGGTTACCTACAGTCGTTTAC

upper sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G136296_T01 (Zea mays), 3'ss of exon 15
---aac-cattttagtcctggacttgttaagttgaacattcccgtttctagtttctggttttcaaaaataattaggaagtatatccattttaactgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAAGTATTCTACATTGACTATGGCAACCAAGAAGTCGTTCCTTACAGTCGCA---
   | | ||  |||||  |  |    ||| | |  | ||| |||||  ||| | |||||  |   | | | ||    | | | | ||| |    || ||   ||||||| |||||||||||     |||||  ||||| | |||||||||||||||||||||| || ||||||||||||||||| || ||||| ||||||||     
cttatcacaacttagttttatatactttatgcttga-attgccgttattagctcctggtcgttctagaaattttattattgtcttcatgtggtttgttc---agATTGTTAATGGACCTCGC---TCTGTAGAATCTCTAAACGACAAGTTTGAAGTATTCTATATCGACTATGGCAACCAAGAGGTGGTTCCCTACAGTCGTCTAC

upper sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA05G33320.1 (Glycine max), 3'ss of exon 15
aaccattttagtcctggacttgttaagttga-acattcccgtttctagtttctggttt-tcaaaaataattaggaagtatatccattttaactga--tctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAAGTATTCTACATTGACTATGGCAACCAAGAAGTCGTTCCTTACAGTCGCA
    | |   ||    ||  ||  || | |  | | |  || || ||    || || | |  |    || |      | |||  | |   |  ||  | || || | || ||||||||||||||| ||||   ||||| | |||||| ||||||||||||||| ||||| ||||| || |||||||  || ||||||  ||   
----aatagggttgatgagatgcaaaatagtcagagtgtcgcttgtaccacctagtctgttcagtcaaacttacttctttatgaaatggtatggaattgtgtagGTAGTCAATGGACCTCGAGGACCTGTTGAATCTCCAAACGACATGTTTGAAGTATTCTATATTGATTATGGAAATCAAGAAGAAGTACCTTACTCTCAGC

upper sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA08G00910.1 (Glycine max), 3'ss of exon 15
-----aaccattttagtcctggacttgttaag---ttgaacattcccgtttctagtttctggttttcaaaaataattaggaagtatatccattttaactgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAAGTATTCTACATTGACTATGGCAACCAAGAAGTCGTTCCTTACAGTCGCA
        |||  || |  |  ||   ||  |   ||| || ||       ||||| | |     |||||  |  ||| ||| |       | |    ||   || || | || ||||||||||||||| ||||   ||||  | | |||| ||||||||||||||||||||| ||||| || |||||||| || ||||||  ||   
tttgtgcacatgctatttgtcaacacattttgcacttgtactttgtaccacctagtctgtt-cagtcaaacttctttatgaaatg-----gtatgggatg--ttgtagGTAGTCAATGGACCTCGAGGACCTGTTGAATCTTCAAATGACATGTTTGAAGTATTCTACATTGATTATGGAAATCAAGAAGTAGTACCTTACTCTCAGC

upper sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 14
lower sequence: AT5G61780.1 (Arabidopsis thaliana), 3'ss of exon 14
aaccattttagtcctggacttgttaagttgaacattcccg--tttctagtttctggttttcaaaaataattaggaagtatatccattttaactgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAAGTATTCTACATTGACTATGGCAACCAAGAAGTCGTTCCTTACAGTCGCA-
       | | |  |  | ||  ||| |    ||  |  |  ||  |  ||| |   | |||   ||  ||    | | |||   ||   | |  | |  ||||||| ||||||||||||||||| ||   ||||| ||| ||  | |||||||| |||||||| || ||||| ||||||||| | ||||| ||||| |||| 
------gtaaattataaagtttctaaatatgccaaccatgatttcttctttttttactatcacttatggttgtttattgtat---ttcgtatttgtgttaagATTGTTAATGGACCTCGAGGAGCAGTTCAATCTCCAGAGGAGGAATTTGAAGTGTTCTACATCGATTATGGAAACCAAGAAATAGTTCCGTACAG-CGCAA

upper sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv00s0283g00020.t01 (Vitis vinifera), 3'ss of exon 15
--aaccattttagtcctggacttgttaagttgaacattcccgtttctagtttctggttttcaaaaataattaggaagtatatccattttaactgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAAGTATTCTACATTGACTATGGCAACCAAGAAGTCGTTCCTTACAGTCGCA
  || || |  | |  |     |  ||| |  || |   |  ||||   | | | || |||     |  ||||   | || |   |  |     || | |||||||| |||| |||||| || |||||   ||| | | | ||||| |||||||| ||||||||||||||||| || |||||| |  ||||||||||||   
agaagcaata-acttatttctctaataattacaagaagtctatttcagttatattgtgttcctgtttc-ttagtttgaatctttctcatttgacatgtacagATTGTTAATGCACCTCGGGGGGCTGTTGAATCCCCAAAAGACAAATTTGAAGTGTTCTACATTGACTATGGAAATCAAGAAATTATTCCTTACAGTCAGT

upper sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 14
-----aaccatttta--gtcctggacttgttaagttgaacattcccgtttctagtttctggttttcaaaaataattaggaagtatatccattttaactgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAAGTATTCTACATTGACTATGGCAACCAAGAAGTCGTTCCTTACAGTCGCA
      ||  ||  |  |   || | | |||    |  | |      ||| |  ||| ||||  |       | || |   || | |    | || |        ||||||| |||| ||  |||||||||||   ||| | | | ||  | |||||||| ||||||||||||||||| || |||||||| ||||||||   |||  
tctcccactgttcaaaagagatgtagtagtttcagtccaaaacatttttttttttttttggtccttgtgctaattttgactgtttgtttgatgtatca-------agATTGTCAATGCACAACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAAGTTTTCTACATTGACTATGGGAATCAAGAAGTAGTTCCTTATGATCGGT

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|2799427|gb|AA752416.1|AA752416
EST:     AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATG                         WTTGTGAATGGAC
genomic: AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATGgtacgtttca ... tgatctgcagATTGTGAATGGAC
EST: gi|2311450|gb|C27605.1|C27605
EST:     AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGGATAGAGCAATG                         ATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAA
genomic: AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATGgtacgtttca ... tgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAA
EST: gi|29622581|gb|CB627592.1|CB627592
EST:     AATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATAG                         ATTGTGAATGGACCTCGA
genomic: AATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAAT-Ggtacgtttca ... tgatctgcagATTGTGAATGGACCTCGA
EST: gi|29674464|gb|CB670739.1|CB670739
EST:     AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATG                         GTTGTGAATGGACCTC
genomic: AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATGgtacgtttca ... tgatctgcagATTGTGAATGGACCTC
EST: gi|163928125|gb|EG712993.1|EG712993
EST:     AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATG                         ATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAA
genomic: AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATGgtacgtttca ... tgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAA
EST: gi|218498571|gb|FG951792.1|FG951792
EST:     AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATG                         ATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAA
genomic: AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATGgtacgtttca ... tgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAA
EST: gi|88310682|gb|CI672545.1|CI672545
EST:     AAATAGTCCTGGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATG                         ATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAA
genomic: AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATGgtacgtttca ... tgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAA
EST: gi|325493413|gb|JG457937.1|JG457937
EST:     AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCCATG                         ATTGTGAATGGACCTCGAGGAGCTGTGTCATCTCAAGACGACCAGTTTGAA
genomic: AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATGgtacgtttca ... tgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAA
EST: gi|29623578|gb|CB628589.1|CB628589
EST:     AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATG                         AGTGTGAATGGACCTCGA
genomic: AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATGgtacgtttca ... tgatctgcagATTGTGAATGGACCTCGA
EST: gi|29623985|gb|CB628996.1|CB628996
EST:     GAATAGAGCAATG                         ATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAA
genomic: GAATAGAGCAATGgtacgtttca ... tgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAA
EST: gi|29627293|gb|CB632304.1|CB632304
EST:     AAATAGTTCGGGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAAAA                         AGTGTGAATGGACCTCGA
genomic: AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATGgtacgtttca ... tgatctgcagATTGTGAATGGACCTCGA
EST: gi|29631512|gb|CB636521.1|CB636521
EST:     AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATG                         ATTGTGAATGGA
genomic: AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATGgtacgtttca ... tgatctgcagATTGTGAATGGA
EST: gi|38476461|gb|CF960594.1|CF960594
EST:     AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATG                         ATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAA
genomic: AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATGgtacgtttca ... tgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAA
EST: gi|88593193|gb|CI711352.1|CI711352
EST:     AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATG                         ATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAA
genomic: AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATGgtacgtttca ... tgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAA
EST: gi|29644259|gb|CB649266.1|CB649266
EST:     AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATG                         ATTGTGAATGGACCTCGA
genomic: AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATGgtacgtttca ... tgatctgcagATTGTGAATGGACCTCGA
EST: gi|33683617|gb|CF311856.1|CF311856
EST:     AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATG                         ATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAA
genomic: AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATGgtacgtttca ... tgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAA
EST: gi|27576732|gb|CA999426.1|CA999426
EST:     AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATG                         ATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAA
genomic: AAATAGTTCTTGCTCAGTTTAGTGCTGACAACTCCTGGAATAGAGCAATGgtacgtttca ... tgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttctggttttcaaaaataattaggaagtatatccattttaactgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAAGTATTCTACATTGACTATGGCAACCAAGAAGTCGTTCCTTACAGTCGCA
              aaaaataattaggaag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaccattttagtcctggacttgttaagttgaacattcccgtttctagtttctggttttcaaaaataattaggaagtatatccattttaactgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAAGTATTCTACATTGACTATGGCAACCAAGAAGTCGTTCCTTACAGTCGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - cctggac
- - - - - - - - - - - - - - - - cattccc
- - - - - - - - - - - - - - - - - - - - - - - gtttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaata