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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAGAAACCGAAAGAAGGTGATAATATTGTTCAGGAAGCCCCAGCAGAGATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttcctgctcagtgagactaattcatcatgagttcatgtcgcttctagtaatgttggttgaagttaatgctaccccctcaggtcgcaaaatata...

Basic information

species Oryza sativa
transcript LOC_Os03g63430.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63430.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G468717_T01 (Zea mays), 5'ss of exon 7
AAAAGAAACCGAAAGAAGGTGATAATATTGTTCAGGAAGCCCCAGCAGAGATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttcctgctcagtga-gactaattcatcatgagttcatgtcgcttctagtaatgttggttgaagttaatgctaccccctcaggtcgcaaaatata-
||||||| || || || ||||| || ||||||||||| || || ||||| || ||||||||||| ||| ||||||| |||||||||||||||||||||||||||||| | || |||| |    | ||  | |   |           |||  |   | |||   |||   ||| |    | |    |  |  | |  | |  
AAAAGAACCCAAAGGAGGGTGACAACATTGTTCAGGATGCTCCTGCAGATATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatgcttctcaatctcaattagattaatgtactactggtctgctattttcattgtcaattgtcattatt--cgctcgtctacctgactacctctgg

upper sequence: LOC_Os03g63430.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G013750_T03 (Zea mays), 5'ss of exon 6
AAAAGAAACCGAAAGAAGGTGATAATATTGTTCAGGAAGCCCCAGCAGAGATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttcctgctcagtg------agactaattcatcatgagttcatgtcgcttctagtaatgttggttgaagttaatgctaccccctcaggtcgcaaaatata------------------------------------------------------------------------------------
|||||||||| || || ||||| || ||||||||||| || || ||||| || ||||||||||| ||| ||||||| |||||||||||||||||||||||||||||| | || |||| |       ||| ||||  |  |  |||            |   |||  |  ||    |     |||||     |  ||   || |                                                                                       
AAAAGAAACCAAAGGAGGGTGACAACATTGTTCAGGATGCTCCTGCAGATATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatgcttctcaatctcaattagattaatgtactaccagtctgctatttcattgtcaattgtcattattctctcgtctacctgactacctctggaactgccaatttctttgttctattgaacactatggttcacaatgacattttatattggagccaatcataattcttcgttatctcatcacag

upper sequence: LOC_Os03g63430.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G014116_T02 (Zea mays), 5'ss of exon 6
AAAAGAAACCGAAAGAAGGTGATAATATTGTTCAGGAAGCCCCAGCAGAGATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttcctgctcagtgagactaattcatcatgagttcatgtcgcttctagtaatgttggttgaagttaatgctaccccctcaggtcgcaaaatata--------
|||||||||| || |||||||| | |||||||||||| || || ||||| || |||||||| || ||| |||||||| ||||||| ||||||||||||||||||||| ||       || |||     |        | |  ||   |  ||| |  | || |||  | |||| ||||  |       |  ||   ||||        
AAAAGAAACCAAAGGAAGGTGACAGTATTGTTCAGGATGCTCCTGCAGATATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCGgtatgtcatc-------gttagatcgtctacctgactgcttctggaaccgctaatc-tctttgttctatttaacgctatgcttcacaatgacattttatattggagcc

upper sequence: LOC_Os03g63430.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA06G15330.1 (Glycine max), 5'ss of exon 6
AAAAGAAACCGAAAGAAGGTGATAATATTGTTCAGGAAGCCCCAGCAGAGATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgta--tgtcttcctgctcagtgagactaattcatcatgagttcatgtcgcttctagtaatgttggttgaa--gttaatgctaccccctcaggtcgcaaaatata
| || || || ||||||||||||||| ||||| | ||||| || ||||| || || || || |  ||  ||||||| |||||||||||||| |||||||||||  ||  |  || ||   ||   || |||   | ||  |  || |     || |||  |   ||| ||  ||  ||| |   |  | |  | |  |    | 
AGAAAAAGCCTAAAGAAGGTGATAATGTTGTTGAAGAAGCTCCTGCAGATATTCCATCTCTACCAGAGTTGAAGCGGATCTACTATGAACTAATGATTCGgtaactgattctctacttgttgt--cttattttgcttgt-tcaatatgctgcctggtagggggtgttaaaatgtggatgttgttctgttacatagttatcggt-

upper sequence: LOC_Os03g63430.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA04G39520.1 (Glycine max), 5'ss of exon 6
AAAAGAAACCGAAAGAAGGTGATAATATTGTTCAGGAAGCCCCAGCAGAGATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgta--tgtcttcctgctcagtgagactaattcatcatgagttcatgtcgcttc-tagtaatgttggttgaa-gttaatgctaccccctcaggtcgcaaaatata
| || || || ||||||||||||||| ||||| | ||||| || |  || ||||| || || | |||  ||||||| |||||||||||||| |||||||||||      | ||| ||   |    ||  ||  |     |||||    ||||| | | |  | || |  || ||  ||| |   |  | |         ||   
AGAAAAAGCCTAAAGAAGGTGATAATGTTGTTGAAGAAGCTCCTGTTGATATACCATCTCTACCGGAGTTGAAGCGAATCTACTATGAACTAATGATTCGgtaaccaattccctacttgttat--cttgtt--ttgcttgttcaatctgcttcctggcaggggtgttaaaatgtggatgttgttctgttacaaacagttatccg

upper sequence: LOC_Os03g63430.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 6
AAAAGAAACCGAAAGAAGGTGATAATATTGTTCAGGAAGCCCCAGCAGAGATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttcctgctcagtgagactaattc-atcatgagt-tcatgtcgcttctagtaatgttggttgaagttaatgctaccccctcaggtcgcaaaatata
| || || || ||||||||||||| | ||||  | ||||| ||||| || || |||||  | |  ||  ||||||||||||||||||||||||||||| ||||| |       ||  ||     || | | ||| |  || |    |   | ||   | ||   ||  | || |  |||      |    |     ||||||
AGAAAAAGCCCAAAGAAGGTGATAGTGTTGTAGAAGAAGCACCAGCTGACATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAGgtattttgggtgccttggtttccttattcctatcttttgtattgcattcttgctttgactgcatgtaaaggtgagagctttttgtt--atttattcaatata

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|29664786|gb|CB661061.1|CB661061
EST:     ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCG                         CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTC
genomic: ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttc ... ctctattcagCTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTC
EST: gi|29639942|gb|CB644951.1|CB644951
EST:     ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCG                         CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTC
genomic: ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttc ... ctctattcagCTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTC
EST: gi|33812345|gb|CF332062.1|CF332062
EST:     ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCG                         CTATTACTCGCACAACAATGATTACCTGGAAAT
genomic: ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttc ... ctctattcagCTATTACTCGCACAACAATGATTACCTGGAAAT
EST: gi|4715022|gb|AU056139.1|AU056139
EST:     ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCG                         CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTC
genomic: ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttc ... ctctattcagCTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTC
EST: gi|29664482|gb|CB660757.1|CB660757
EST:     ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCG                         CTATTACTCGCACAACAATGATTACCT
genomic: ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttc ... ctctattcagCTATTACTCGCACAACAATGATTACCT
EST: gi|29645308|gb|CB650315.1|CB650315
EST:     ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCG                         CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTC
genomic: ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttc ... ctctattcagCTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTC
EST: gi|29645307|gb|CB650314.1|CB650314
EST:     ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCG                         CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTA
genomic: ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttc ... ctctattcagCTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTA
EST: gi|33795887|gb|CF323811.1|CF323811
EST:     ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCG                         CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTC
genomic: ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttc ... ctctattcagCTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTC
EST: gi|29658196|gb|CB654471.1|CB654471
EST:     ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCG                         CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCG
genomic: ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttc ... ctctattcagCTATTACTCGCACAACAATGATTACCTGGAAATCTGCCG
EST: gi|29664785|gb|CB661060.1|CB661060
EST:     ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCG                         CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTC
genomic: ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttc ... ctctattcagCTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTC
EST: gi|33797492|gb|CF324606.1|CF324606
EST:     ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCG                         CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTC
genomic: ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttc ... ctctattcagCTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTC
EST: gi|300215653|gb|HO088279.1|HO088279
EST:     ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCG                         CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTC
genomic: ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttc ... ctctattcagCTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTC
EST: gi|29678374|gb|CB674649.1|CB674649
EST:     ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCG                         CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGNTGCTACAAGTC
genomic: ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttc ... ctctattcagCTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTC
EST: gi|58678571|gb|CK067258.1|CK067258
EST:     ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCG                         CTATTACTCGCACAACAATGATTACCTGGAAATCTGCC
genomic: ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttc ... ctctattcagCTATTACTCGCACAACAATGATTACCTGGAAATCTGCC
EST: gi|29637544|gb|CB642553.1|CB642553
EST:     ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCG                         CTATTACTCGCACAACAATGATTACCT
genomic: ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttc ... ctctattcagCTATTACTCGCACAACAATGATTACCT
EST: gi|117217926|gb|CT845200.1|CT845200
EST:     ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCG                         CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTC
genomic: ATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttc ... ctctattcagCTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAGAAACCGAAAGAAGGTGATAATATTGTTCAGGAAGCCCCAGCAGAGATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttcctgctcagtgagactaattcatcatgagttcatgtcgcttctagtaatgttggttgaagttaatgctaccccctcaggtcgcaaaatata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC