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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctttattcctgctcatcactggacttgtctgattattgtcaaactcattcagtttatctgcagtttgtccagttactgacagtcaaatctttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGCAGGTAGCTGCTGCAGGTGCCACTGCCCAGGCAAAGGAAGAGAACGATGA

Basic information

species Oryza sativa
transcript LOC_Os03g63400.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63400.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G023242_T01 (Zea mays), 3'ss of exon 5
cctttattcctgctcatcactggacttgtctgat-tattgtcaaactcatt--cagtttatctgcagtttgtcc-agttactgacagtcaaatctttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGCAGGTAGCTGCTGCAGGTGCCACTGCCCAGGCAAAGGAAGAGAACGATGA
     | ||     ||  |    ||  |  |||   |     || ||  ||  ||   ||       | ||    ||  | | |||         |||||  ||| |||||||||||||||||||| ||||||||||| || ||||||||||||||||| |||||||| |||||  | || ||||  |||||||| ||||||||
----caatcaaatacaaaaagcaacaagcgtgaagcaaacagaagcttgttgccacaatacaaatgatatgaaagagggattaacaccttttctattcttccagGCCCTGACAACATGGAGCACCTGAAGAGGATTGCCGAGGAGATGCAGAAGCAGGTGGCTGCTGCCGGTGCGGCAGCACAGGTCAAGGAAGACAACGATGA
















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|88267599|gb|CI379534.1|CI379534
EST:     AGACCAAGAAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGACCAAGAAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|88205126|gb|CI204975.1|CI204975
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|88209060|gb|CI208909.1|CI208909
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|88294933|gb|CI522887.1|CI522887
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGGTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|38477612|gb|CF961745.1|CF961745
EST:     AGCTTCAACATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|55409416|gb|CV721792.1|CV721792
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAA
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAA
EST: gi|8528376|gb|AU093191.1|AU093191
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|86824271|gb|CI260854.1|CI260854
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|88213427|gb|CI213276.1|CI213276
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|5005069|gb|AU069686.1|AU069686
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|88483112|gb|CI420383.1|CI420383
EST:     TGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: TGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|86534548|gb|CI174754.1|CI174754
EST:     AAGAAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACGTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AAGAAGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|86823386|gb|CI256364.1|CI256364
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|13807920|gb|AU182155.1|AU182155
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|88452447|gb|CI558108.1|CI558108
EST:     ATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: ATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|88839904|gb|CI017669.1|CI017669
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|87015910|gb|CI279662.1|CI279662
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACTTAAAGAGGATTGCTGTGAGAGATGCAGAAG
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTG-AAGAGATGCAGAAG
EST: gi|88289615|gb|CI522748.1|CI522748
EST:     TCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: TCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|88487959|gb|CI425230.1|CI425230
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|88286187|gb|CI522487.1|CI522487
EST:     ATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: ATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|88545640|gb|CI475212.1|CI475212
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|86594523|gb|CI253422.1|CI253422
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|426706|gb|D22776.1|D22776
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|88977134|gb|CI024871.1|CI024871
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|3760604|gb|C97858.1|C97858
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|86526461|gb|CI166667.1|CI166667
EST:     GGGATCATNAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: GGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|58597162|gb|CK007690.1|CK007690
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCCATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|88970560|gb|CI384062.1|CI384062
EST:     AGCTTCAAGATTTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|86489014|gb|CI131647.1|CI131647
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|55440624|gb|CV733623.1|CV733623
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|86542346|gb|CI182552.1|CI182552
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCGGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|86821488|gb|CI266864.1|CI266864
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
EST: gi|88831984|gb|CI014543.1|CI014543
EST:     AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGG                         GTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC
genomic: AGCTTCAAGATGTTCTTCCTGGGATCATTAACCAATTGGgtatgtcctc ... tttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattcagtttatctgcagtttgtccagttactgacagtcaaatctttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGCAGGTAGCTGCTGCAGGTGCCACTGCCCAGGCAAAGGAAGAGAACGATGA
                             tactgac  putative branch site (score: 1)
                                           tctttcttgt  putative PPT
                                        aaatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctttattcctgctcatcactggacttgtctgattattgtcaaactcattcagtttatctgcagtttgtccagttactgacagtcaaatctttcttgtagGTCCTGACAACATGGAGCACCTAAAGAGGATTGCTGAAGAGATGCAGAAGCAGGTAGCTGCTGCAGGTGCCACTGCCCAGGCAAAGGAAGAGAACGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - cctgctc
- - - - - - - - - - - - - - tctgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - atctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttactga