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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttcaaattttgctaggtttttttttttatctacaatatggcttgatctttctttatttcacaacacttaataatgattttgttcttcacttag...

Basic information

species Oryza sativa
transcript LOC_Os03g52840.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G135283_T02 (Zea mays), 5'ss of exon 10
GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtat--gtgttcaaattt--tgctaggtttttttttttatctacaatatggcttgatctttctttatttcacaacacttaataatgattttgttcttcacttag
||||||||||| || ||||||||||| |||||||||||||| ||||| ||||| |||||||| |||||||  ||||||| ||||  | | |     || | || | ||     | |  | | | |    |  || | || ||||  |  |||  |    ||||||||   
GCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgttcacatttagtacaaaaaacttatcttcaactcttggaggattaggtttaagatacttgctcaccact--aggatgcgtagcatcttcactg--
















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|58691302|gb|CK079989.1|CK079989
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|38474524|gb|CF958657.1|CF958657
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|38479794|gb|CF963883.1|CF963883
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29687054|gb|CB683329.1|CB683329
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29678031|gb|CB674306.1|CB674306
EST:     AGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTGGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: AGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29613559|gb|CB618572.1|CB618572
EST:     CAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: CAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29672939|gb|CB669214.1|CB669214
EST:     AGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: AGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|4716856|gb|AU057972.1|AU057972
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|38474897|gb|CF959030.1|CF959030
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|13420583|gb|AU174673.1|AU174673
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCT
EST: gi|29624607|gb|CB629618.1|CB629618
EST:     CAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: CAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29614629|gb|CB619642.1|CB619642
EST:     GCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: GCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29618932|gb|CB623944.1|CB623944
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29622695|gb|CB627706.1|CB627706
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29638079|gb|CB643088.1|CB643088
EST:     CAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: CAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|11442748|gb|BF430651.1|BF430651
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29675548|gb|CB671823.1|CB671823
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|38476360|gb|CF960493.1|CF960493
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29629705|gb|CB634714.1|CB634714
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29687894|gb|CB684169.1|CB684169
EST:     CAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: CAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29662689|gb|CB658964.1|CB658964
EST:     AGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: AGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29621679|gb|CB626690.1|CB626690
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29664044|gb|CB660319.1|CB660319
EST:     CAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: CAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29674038|gb|CB670313.1|CB670313
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAAGCTACGAACTTGTCTCTGGTGGGACTGACAACCA
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCA
EST: gi|29646106|gb|CB651113.1|CB651113
EST:     TCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: TCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|33663440|gb|CF294407.1|CF294407
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29646446|gb|CB651453.1|CB651453
EST:     TCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: TCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|38482519|gb|CF966548.1|CF966548
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTGGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29665919|gb|CB662194.1|CB662194
EST:     GAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: GAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29629706|gb|CB634715.1|CB634715
EST:     GTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: GTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29687453|gb|CB683728.1|CB683728
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29613482|gb|CB618495.1|CB618495
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|58692040|gb|CK080727.1|CK080727
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|55410185|gb|CV722561.1|CV722561
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|38472677|gb|CF956809.1|CF956809
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29674139|gb|CB670414.1|CB670414
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCANAATTTGCACAG                         AGCTTGACAGCAAAAGGCTA
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTA
EST: gi|38478032|gb|CF962165.1|CF962165
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|428581|gb|D24733.1|D24733
EST:     ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTNACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
EST: gi|29674140|gb|CB670415.1|CB670415
EST:     TCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG                         AGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT
genomic: TCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttc ... tcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAGgtatgtgttcaaattttgctaggtttttttttttatctacaatatggcttgatctttctttatttcacaacacttaataatgattttgttcttcacttag

- - - - - - - - - AGAGCT
- - - - - - - - -  GAGCTT
- - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - -  AGCAAG