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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataattttgttataatataaccttttattgccagagtttcatctgctacatcttatctgcggtttgttgatttatttattgctgcggctgttatttgcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT

Basic information

species Oryza sativa
transcript LOC_Os02g58020.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 13
--ataattttgttataatataaccttttattgccagagtttcatctgctacatcttatctgcggtttgttgattt-atttattgctgcggctgttatttgcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT
   |  |  | || |    || | |  || |||||   |  ||  |||   ||  | |||   ||||||| |||| |  | ||  || || |||| ||| |||||||||||||||||||||||||| || ||||||||||| |||||||| || ||||| |||||||||||||||||||  ||||| || 
gttttttccttttgtttactagcataatactgccaa--tcacaagtgcaggatgctctcttttgtttgtttatttgaaattttcttggggatgtt-tttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACGGTGAATCCCCTTTTGTACATGATGAAGTGCTATCCG

upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv02s0025g02160.t01 (Vitis vinifera), 3'ss of exon 13
ataattttgttataatataaccttttattgccagagtttcatctgctacatcttatctgcggtttgttgatttatttattgctgcggctgttattt--gcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT
  |||      | |||| |  |   || |  || | ||   |  |   ||     |||       ||| || || ||          ||||| | |  |||||||||||| ||||| |||| |||||||||||||||||| || ||  || |    || ||||||||||| |||||| | |||||||| 
-aaatggctacagaatacattcaactaattgcaaaattg-gtgaggatcactggttcttgcacacgttaatctaattgacatgagtactgttctctctgcagGTTCGCATTGCTGTGTTCAGTCAACACCATGTTGATGGCCTAGACCTATCTTCAAATCCCCTTTTGTATATGATGCGCTGCTACCCA
















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|427530|gb|D23597.1|D23597
EST:     TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
genomic: TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGgttcttttat ... ttatttgcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
EST: gi|27576082|gb|CA998776.1|CA998776
EST:     TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
genomic: TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGgttcttttat ... ttatttgcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
EST: gi|22304794|gb|BQ906016.1|BQ906016
EST:     CGCTCTCCCAAG                         TTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
genomic: CGCTCTCCCAAGgttcttttat ... ttatttgcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
EST: gi|29623431|gb|CB628442.1|CB628442
EST:     TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
genomic: TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGgttcttttat ... ttatttgcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
EST: gi|3766930|gb|AU031040.1|AU031040
EST:     TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
genomic: TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGgttcttttat ... ttatttgcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
EST: gi|29676044|gb|CB672319.1|CB672319
EST:     TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
genomic: TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGgttcttttat ... ttatttgcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
EST: gi|27546087|gb|CA764161.2|CA764161
EST:     TATCTGGAGATCTTCAGCCAACCTCAGGGACAGTGTTCCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
genomic: TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGgttcttttat ... ttatttgcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
EST: gi|29676045|gb|CB672320.1|CB672320
EST:     TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
genomic: TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGgttcttttat ... ttatttgcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
EST: gi|218495876|gb|FG947058.1|FG947058
EST:     TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
genomic: TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGgttcttttat ... ttatttgcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
EST: gi|29664090|gb|CB660365.1|CB660365
EST:     TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
genomic: TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGgttcttttat ... ttatttgcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
EST: gi|29662748|gb|CB659023.1|CB659023
EST:     TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
genomic: TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGgttcttttat ... ttatttgcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
EST: gi|58695639|gb|CK084326.1|CK084326
EST:     TATCTGGAGATCTTCAGCCTACTTCAGGGACAGTGTTCCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
genomic: TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGgttcttttat ... ttatttgcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
EST: gi|87016527|gb|CI273737.1|CI273737
EST:     ATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
genomic: ATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGgttcttttat ... ttatttgcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
EST: gi|29644367|gb|CB649374.1|CB649374
EST:     TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA
genomic: TATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGgttcttttat ... ttatttgcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacatcttatctgcggtttgttgatttatttattgctgcggctgttatttgcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT
                   tgttgat  putative branch site (score: 4)
                 tttgttgatttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataattttgttataatataaccttttattgccagagtttcatctgctacatcttatctgcggtttgttgatttatttattgctgcggctgttatttgcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG