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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaacctgcaaatgataatactagtatgatttttatactcatgttaattacataccatcattctccatgatatctaacgcaatgtgttttaacggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTGTTGCTGCCTGAACCATGGACTCCAGAGTCTGGGCTGGTGACAGCTGCAC

Basic information

species Oryza sativa
transcript LOC_Os05g25310.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g25310.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM5G840955_T01 (Zea mays), 3'ss of exon 5
--ttaacctgcaaatgataatactagtatgatttttatactcatgttaattacataccatcattctccatgatatctaa-cgcaatgtgttttaac-ggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTGTTGCTGCCTGAACCATGGACTCCAGAGTCTGGGCTGGTGACAGCTGCAC
  |     |     | ||  | | |   ||  ||  |  |  ||||  |  |  |    |  || || ||  ||   |   |  |  |  |  ||| ||||||||| ||||||||||||||||| ||||| || ||  | ||||| ||||| ||| || |||||||||| ||||| || ||||| ||||||||||| || || |
gctaggttttttgtttatgttgcaacggtggattaga-gcctatgtggaccattt---ttttttttcaattttacaaaggtgtgacatactcgaactggtgcagGCCGCAAAAGCAGCGAGGCTCGAGAAATTCGAGGTGCCAGCGAAGATCGTGCTGTTGCCTGAACCGTGGACGCCGGAGTCCGGGCTGGTGACCGCAGCGC
















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|89173679|gb|CI041572.1|CI041572
EST:     TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAG                         GCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
genomic: TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAGgttagacttg ... aacggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
EST: gi|88249513|gb|CI249362.1|CI249362
EST:     TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAG                         GCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
genomic: TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAGgttagacttg ... aacggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
EST: gi|88983267|gb|CI028504.1|CI028504
EST:     TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAG                         GCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
genomic: TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAGgttagacttg ... aacggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
EST: gi|88509422|gb|CI436928.1|CI436928
EST:     CAATCTCTATCAAAG                         GCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
genomic: CAATCTCTATCAAAGgttagacttg ... aacggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
EST: gi|88906077|gb|CI089663.1|CI089663
EST:     TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAG                         GCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
genomic: TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAGgttagacttg ... aacggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
EST: gi|89191124|gb|CI392977.1|CI392977
EST:     TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAG                         GCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
genomic: TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAGgttagacttg ... aacggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
EST: gi|58690554|gb|CK079241.1|CK079241
EST:     TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAG                         GCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
genomic: TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAGgttagacttg ... aacggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
EST: gi|9864962|gb|AU100712.1|AU100712
EST:     TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAG                         GCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
genomic: TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAGgttagacttg ... aacggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
EST: gi|86837233|gb|CI347713.1|CI347713
EST:     GGAGGTCCAGCAATCTCTATCAAAG                         GCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
genomic: GGAGGTCCAGCAATCTCTATCAAAGgttagacttg ... aacggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
EST: gi|86478102|gb|CI120735.1|CI120735
EST:     TGTGCCACAATGATCAAGCCATTAAGGAGGCCCAGCAATCTCTATCAAAG                         GCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
genomic: TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAGgttagacttg ... aacggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
EST: gi|218480450|gb|FG952431.1|FG952431
EST:     AAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAG                         GCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
genomic: AAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAGgttagacttg ... aacggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
EST: gi|89194911|gb|CI003375.1|CI003375
EST:     TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAG                         GCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
genomic: TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAGgttagacttg ... aacggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
EST: gi|88265053|gb|CI368827.1|CI368827
EST:     CCATTAAGGAGGTCCAGCAATCTCTATCAAAG                         GCTGCAAAATCATCGATTCCTTCTTAAGTTTGAAATACCAGCAAAGATTGT
genomic: CCATTAAGGAGGTCCAGCAATCTCTATCAAAGgttagacttg ... aacggtgcagGCTGCAAAAGCAGCGA-GGCTTGAGAAGTTTGAAATACCAGCAAAGATTGT
EST: gi|163923598|gb|EG713315.1|EG713315
EST:     TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAG                         GCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
genomic: TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAGgttagacttg ... aacggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
EST: gi|218499205|gb|FG956937.1|FG956937
EST:     TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAG                         GCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
genomic: TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAGgttagacttg ... aacggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
EST: gi|88251046|gb|CI349276.1|CI349276
EST:     TCCAGCAATCTCTATCAAAG                         GCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCACCAAAGATTGTG
genomic: TCCAGCAATCTCTATCAAAGgttagacttg ... aacggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
EST: gi|86896789|gb|CI317329.1|CI317329
EST:     T-TGCCACAATGATCAA-CCATTAAGGAG-TCCAGCAATCTCGATCAAAG                         -CTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG
genomic: TGTGCCACAATGATCAAGCCATTAAGGAGGTCCAGCAATCTCTATCAAAGgttagacttg ... aacggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattacataccatcattctccatgatatctaacgcaatgtgttttaacggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTGTTGCTGCCTGAACCATGGACTCCAGAGTCTGGGCTGGTGACAGCTGCAC
                                         ttttaac  putative branch site (score: 2)
                        atatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaacctgcaaatgataatactagtatgatttttatactcatgttaattacataccatcattctccatgatatctaacgcaatgtgttttaacggtgcagGCTGCAAAAGCAGCGAGGCTTGAGAAGTTTGAAATACCAGCAAAGATTGTGTTGCTGCCTGAACCATGGACTCCAGAGTCTGGGCTGGTGACAGCTGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC