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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaagtcatcgattctgcattgtgaatatgccttcgttactatgcttgtttactttggagctctgatctcaatgacttatatggctgttgttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCAGGTATGGAAGAATAGAAAGGAGCTCAAGGTAGAGGACCTTGGAATTGTG

Basic information

species Oryza sativa
transcript LOC_Os01g41610.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g41610.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G042078_T01 (Zea mays), 3'ss of exon 1
tcaagtcatcg-attctgcattgtgaatatgccttcgttactatgcttgtttactttggagctctgatctcaatgacttata-tggctgttgt-tttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCAGGTATGGAAGAATAGAAAGGAGCTCAAGGTAGAGGACCTTGGAATTGTG
   | | || | |||  | |  |    ||  |   |  ||     |||||    ||  |   | |  | |  |||  || ||     |||||| ||| |||||  | ||||| ||||||||| |||| ||||||||  ||||| |||||||||||||||||||||| || ||||| |||| ||| ||||||||||| |||| |
-ttaataatagcattaggaacagcagttagacg--caatatgtaacttgtgccattcaggattttacttttcatggtttctaacctttgttgtgtttgttcagCCTACCAGGTCGCTATGAGTCATTCTGGAAGGAGCTTGATTGTGTCAAGCAGGTATGGAAGAACAGGAAGGACCTCACGGTCGAGGACCTTGGCATTGCG

upper sequence: LOC_Os01g41610.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AC194341.4_FGT002 (Zea mays), 3'ss of exon 1
tcaagtcatcgattctgcattgtgaatatgccttcgttactatgcttgtttactttggagctctgatctcaatgacttatatggctgttgt-tttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCAGGTATGGAAGAATAGAAAGGAGCTCAAGGTAGAGGACCTTGGAATTGTG
    |||||   ||   | |  |     |     |  ||     |||||  | || ||   | |  | |  |||  ||  |    || ||| ||| |||||  | ||||| || |||||| |||| ||||||||  |||||||||||||||||||||||||||| || ||||| |||||||| ||||||||||| |||| |
gtccgtcattatttgcccctgctcttggtagacgcaatatgtaacttgtgcaattagggagt-tacttttcatggttttaaccattgctgtgtttgttcagCCTACCAGGTCGGTATGAGTCATTCTGGAAGGAGCTTGATGGTGTCAAGCAGGTATGGAAGAACAGGAAGGACCTCAAGGTTGAGGACCTTGGGATTGCG

upper sequence: LOC_Os01g41610.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv04s0008g00810.t01 (Vitis vinifera), 3'ss of exon 2
-tcaagtcatcgattctgcattgtgaatatgccttcgttactatgcttgtttactttggagctctgatctcaatgacttatatggctgttgttttctt-cagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCAGGTATGGAAGAATAGAAAGGAGCTCAAGGTAGAGGACCTTGGAATTGTG
 |  | |  |   |   ||| |   |    | || | || |  | |||||| |  ||  | |    ||   |    ||||| |   ||   | ||  | |||| | || || ||||||||||| |||||||||||| ||||| ||||||||||  |||||||||| ||  ||||| | ||||| |||||    || ||||  
atgcactgtttcctcaagcaattcaatgtggactccttttcctttcttgttcatgttaaatcatcaatg--atcagcttatctaattgacttattggtacagTATTCCTGGACGCTATGAGGCCTTTTGGAAGGAACTTGATTGTGTCAAGCAACTATGGAAGAACAGGCAGGAGATGAAGGTCGAGGATGCAGGCATTGCT

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|88997419|gb|CI390085.1|CI390085
EST:     GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|88482105|gb|CI419376.1|CI419376
EST:     CAAGCAGCTCTTCTACACCCGCCTCGCCAG                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: CAAGCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|3761029|gb|C98283.1|C98283
EST:     CCAGGAGCTCTCCCAAGCAGCTCTTCTACACCCGCCTCNCCAG                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: CCAGGAGCTCT-CCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|88474478|gb|CI411749.1|CI411749
EST:     CTTCTACACCCGCCTCGCCAG                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: CTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|86499473|gb|CI142106.1|CI142106
EST:     GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|88530371|gb|CI458761.1|CI458761
EST:     GAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAT                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: GAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|86544505|gb|CI184711.1|CI184711
EST:     GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|88270451|gb|CI385709.1|CI385709
EST:     GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|33822232|gb|CF336933.1|CF336933
EST:     AAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: AAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|86821372|gb|CI266819.1|CI266819
EST:     GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|88548918|gb|CI478755.1|CI478755
EST:     TGCCAGGAGCTCTCCAAGCAGCTCTTNTACACCCGCCTCGCCAT                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: TGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|27578248|gb|CB000943.1|CB000943
EST:     GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|88551711|gb|CI481793.1|CI481793
EST:     GCAGCTCTTCTACACCCGCCTCGCCAT                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: GCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|88828540|gb|CI073410.1|CI073410
EST:     GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|86258333|gb|CI064686.1|CI064686
EST:     GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|88997821|gb|CI390355.1|CI390355
EST:     AGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAAG                         TTTGCCAGGCCGCTATGAGGCATTTTTGAAGGAATTTGATGGTGTCAAGC
genomic: AGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCC-AGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGC
EST: gi|88549839|gb|CI479765.1|CI479765
EST:     CAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAT                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: CAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|88527971|gb|CI456171.1|CI456171
EST:     GCAGCTTTTTTACACCCGCCTCGCCAT                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: GCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|86509413|gb|CI152046.1|CI152046
EST:     GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|86593050|gb|CI255512.1|CI255512
EST:     GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|38479680|gb|CF963769.1|CF963769
EST:     GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAG                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|55442101|gb|CV734372.1|CV734372
EST:     AAGTGCCAGGAGCTCTCCAAGCAGCTTTTCTACACCCGCCTCGCCAG                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: AAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
EST: gi|58677584|gb|CK066271.1|CK066271
EST:     GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCGCGCCAG                         TTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA
genomic: GAGAAGTGCCAGGAGCTCTCCAAGCAGCTCTTCTACACCCGCCTCGCCAGgtgatccccg ... ttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttactttggagctctgatctcaatgacttatatggctgttgttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCAGGTATGGAAGAATAGAAAGGAGCTCAAGGTAGAGGACCTTGGAATTGTG
               ctctgat  putative branch site (score: 4)
                                       ctgttgttttcttc  putative PPT
                             acttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaagtcatcgattctgcattgtgaatatgccttcgttactatgcttgtttactttggagctctgatctcaatgacttatatggctgttgttttcttcagTTTGCCAGGCCGCTATGAGGCATTTTGGAAGGAATTTGATGGTGTCAAGCAGGTATGGAAGAATAGAAAGGAGCTCAAGGTAGAGGACCTTGGAATTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA