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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGCCTTCTACTACGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtactactccttccatctcttctgcggatacctatctgttagtatcttctttgcccactaattaacactaatatcttttcag

Basic information

species Oryza sativa
transcript LOC_Os03g64020.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g64020.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G896082_T03 (Zea mays), 5'ss of exon 3
CAGGCCTTCTACTACGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtactactccttccatctcttctgcggatacctatctgttagtatcttctttgcccactaattaacactaatatcttttcag----------------------------------------
   ||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || |||||||| ||||||||||||||| | |  |  ||  || |  ||  |   || ||  ||| |   |  | |||     |  ||||||  ||||   |      |                                        
---GCCTTCTACTATGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcatttttagtta-atttgctccac---taactgcctgctctcaagtccttgaaaaaaaaattaatgctaacccccaaggtgtggcgtcgatacaaactacgttcctgtgtgttgtttccag

upper sequence: LOC_Os03g64020.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AC203966.5_FGT002 (Zea mays), 5'ss of exon 3
CAGGCCTTCTACTACGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCAT-GCTAAgtaagtactactccttccatctcttctgcggatacctatctgttagtatcttctttgcccactaattaacactaatatcttttcag----------------
   ||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| || |||||||| ||||| |||||||||| | |  |  ||  || |  ||  |   || ||  |||||   |  | ||| |   |  ||| || | |  |  |    ||                 
---GCCTTCTACTATGACCAGAAGGCCATCATGTCCAACGAGGAGTTTGACAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATTGCTAAgtaagcatttttagttt-atttgctccaccactaactgcctgttctcaagtcctt-gaaaaaaaataaataatgctgaccccccaaggtgtggcgttgatac

upper sequence: LOC_Os03g64020.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA17G14240.1 (Glycine max), 5'ss of exon 3
CAGGCCTTCTACTACGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtactactccttccatctcttctgcggatacctatctgttagtatcttctttgcccactaattaacactaatatcttttcag
   || ||||| || ||    ||||| |||||||| || || || || || || |||||||| || |||||||||||||| |||||||||||||||||||||| |    |      |  | |  | ||| | |       |      ||||| ||       | |||        |   | | |||
---GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAATTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatggggcaacttcgctctatagt-tgcagctgttgtcataacttcatctttttaaagtctttattggt-----tgattgtacag

upper sequence: LOC_Os03g64020.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA01G42360.2 (Glycine max), 5'ss of exon 3
CAGGCCTTCTACTACGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgta-agtactactcctt----------ccatctcttctgcggatacctatctgttagtatct-tctttgcccactaattaacactaatatcttttcag---------------------------
   || ||||| || ||   |||||| || ||||| || ||||| || || || || ||||| || |||||||||||||| |||| |||||| |||||||||| | || || |   |          | || || |   | || |  |    |   | ||   |   |||  |||   ||| | | || |  |||  |                           
---GCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAATCTTAAGGAAGAACTCATGTGGGAAGGGAGCACCGTTGTGATGCTAAgtatattattattatatatgtggctagcaatttcattcactgacagttgctagcatgcatgaattcctgctaactttgtaa-attgattttatttttgagtcattataattggttcgctgtgtag

upper sequence: LOC_Os03g64020.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA05G03730.1 (Glycine max), 5'ss of exon 3
CAGGCCTTCTACTACGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagta-ctactccttccatctcttctgcggatacctatctgttagtatcttctttgcccactaattaacactaatatcttttcag----------------------
   || ||||| || ||    ||||| |||||||| || || ||||| || || |||||||| || |||||||||||||| |||||||||||||||||||||| |   | ||| |   |       |||| | |       ||| | |   || | ||   ||        | | || | |||| ||                      
---GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggcaacttcactctcagtagctgcagctgttg--ttgtcattgaatt-tgtgttaacgcgggtgtatttatcttttttaagtctttgttggttgattgtacag

upper sequence: LOC_Os03g64020.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT4G11960.1 (Arabidopsis thaliana), 5'ss of exon 3
CAGGCCTTCTACTACGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtactactcct--tccatctcttctgcggatacctatctgt-tagtatcttctttgcccactaattaacactaatatcttttcag
    | || || |||||    || || || ||||| || || ||||| || ||||| || || ||| | ||||||||||| ||||| |||||||||||||||||  |  |||  |  |  ||   ||   |    | | ||  |  |||  ||||  ||    |   | |   |   || | || |   
---TCGTTTTATTACGAAGGCAAAGCGATTATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaatgaacacttatgatttatagttttgtcaataatccattcgcctaggttcttgattcttgatctaattttatctatgtattgtag-

upper sequence: LOC_Os03g64020.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT4G22890.1 (Arabidopsis thaliana), 5'ss of exon 3
CAGGCCTTCTACTACGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtactactccttccatctcttctgcggatacctatctgttagtatcttctttgccca---ctaa-----ttaacactaatatctttt-cag
    | ||||| || ||    || || |||||||| || || ||||| || ||||| || || ||| | ||||||||||| ||||| ||||| |||||||||||  |  |    |   |     | |    ||  || | | || || ||||   |||  |   ||||     |||    ||||||      |||
---TCTTTCTATTATGATGGCAAAGCGATCATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTAATGTGGGAAGGAAGCAGTGTTGTGATGCTAAgtaatcatcaactatgggactaaattt---catttctttgttttggtttctttggtgcaaagtcctaaatcttttattggtaatatgaaacacag

upper sequence: LOC_Os03g64020.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv02s0025g04710.t01 (Vitis vinifera), 5'ss of exon 3
CAGGCCTTCTACTACGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtact---actccttccatctcttctgcggatacctatctgttagtat--cttctttgcccactaattaacactaatatcttttcag--------
    | || || || ||    ||||| || ||||| || ||||| || |||||||||||||| || |||||||||||||| ||||||||||| ||||||||||  || |   | |   |  |||  |         |  ||   ||| |||   ||| ||    | ||||     |  | |  ||| |  |        
---TCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgtacatatttagattatcttaatcaatatctttatgatataatagtttgtaatactttttaaatctctaaaatgtaaaattggcttatgtgtaatgcag

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|117243743|gb|CT843209.1|CT843209
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
EST: gi|218487328|gb|FG968259.1|FG968259
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
EST: gi|58694129|gb|CK082816.1|CK082816
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
EST: gi|157651887|gb|EX451521.1|EX451521
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
EST: gi|58690623|gb|CK079310.1|CK079310
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
EST: gi|58692378|gb|CK081065.1|CK081065
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
EST: gi|58591285|gb|CF989593.1|CF989593
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
EST: gi|33801214|gb|CF326480.1|CF326480
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
EST: gi|58689767|gb|CK078454.1|CK078454
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
EST: gi|29687940|gb|CB684215.1|CB684215
EST:     GGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: GGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
EST: gi|29687939|gb|CB684214.1|CB684214
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
EST: gi|58606048|gb|CK034081.1|CK034081
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACA
EST: gi|313081134|gb|HO213720.1|HO213720
EST:     CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAA                         GCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA
genomic: CAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtacta ... atcttttcagGCCCTGACGAACAACGCCTGCTCGAAGCCTCCATGGCCTATGCTGCCGGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGCCTTCTACTACGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtactactccttccatctcttctgcggatacctatctgttagtatcttctttgcccactaattaacactaatatcttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA