Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTAACAACCCGGCAGGCGGCTCGGTGTTTCCTCTCCATTGGGGAGTATTACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactcagaactgcttatctgaaaagaaaaaaaagatcaaataaactgttctaaatttccaaatcatttttcagccacattattgtactggaaggaa...

Basic information

species Oryza sativa
transcript LOC_Os01g64020.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64020.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G060216_T01 (Zea mays), 5'ss of exon 11
TTCTAACAACCCGGCAGGCGGCTCGGTGTTTCCTCTCCATTGGGGAGTATTACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactcagaactgcttatctgaaaagaaaaaaa---agatcaaataaactgttctaaatttccaaatcatttttcagc-cacattattgtactggaaggaa
| || || || |||||||| || ||||| |||||||||||||||||||| ||| |||||||| | |||||||||||||||||| |||| ||||| ||||||||||| |||||  || | | ||| ||| |    |    |      || |||||  ||  | ||       | |    |||   | ||| |    || |     
TCCTGACCACTCGGCAGGCTGCGCGGTGCTTCCTCTCCATTGGGGAGTACTACAGCCGCCTCAGAGCTCTCAGCAACCTCTGGGCTTCCCGTCCCCGCGAgtaagattcagacttgatcaactgcaaaaactggagtttattgttgatcaactgcactgtagttgttcccaactcccaagcatgccttaatcacatgtat----

upper sequence: LOC_Os01g64020.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AC232238.2_FGT004 (Zea mays), 5'ss of exon 11
TTCTAACAACCCGGCAGGCGGCTCGGTGTTTCCTCTCCATTGGGGAGTATTACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactcagaa--ctgcttatctgaaaagaaaaaaaagatcaaataaactgttctaaatttccaaatcatttttcagccacattattgtactggaaggaa
| || || || |||||||| || ||||| |||||||| ||||||||||| ||| |||||||  | |||||||||||||||||| |||| |||||  ||||||| |  ||| ||   || | | ||| ||| |    |     ||         |  | |    |   |   |   |   ||  |  || || ||| |    |
TCCTGACCACTCGGCAGGCTGCGCGGTGCTTCCTCTCTATTGGGGAGTACTACAGCCGCCTTAGAGCTCTCAGCAACCTCTGGGCTTCCCGTCCCGGCGAgtatgtttcacaagcttgatcacctgcaaaaacttgactctccattagtgtcatgttgatcaactgcactgtggctgttcccaaccat-gt-ctgaatcaca
















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|86827104|gb|CI270821.1|CI270821
EST:     TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGA                         GAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
genomic: TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactca ... cttgcaacagGAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
EST: gi|88832764|gb|CI369654.1|CI369654
EST:     TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGA                         GAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
genomic: TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactca ... cttgcaacagGAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
EST: gi|88235469|gb|CI236026.1|CI236026
EST:     TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGA                         GAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
genomic: TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactca ... cttgcaacagGAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
EST: gi|88297474|gb|CI547952.1|CI547952
EST:     TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGA                         GAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
genomic: TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactca ... cttgcaacagGAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
EST: gi|88517854|gb|CI444423.1|CI444423
EST:     TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGA                         GAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
genomic: TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactca ... cttgcaacagGAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
EST: gi|88428254|gb|CI562520.1|CI562520
EST:     TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGA                         GAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
genomic: TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactca ... cttgcaacagGAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
EST: gi|89164044|gb|CI101132.1|CI101132
EST:     TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGA                         GAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
genomic: TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactca ... cttgcaacagGAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
EST: gi|88383771|gb|CI545922.1|CI545922
EST:     TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGA                         GAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
genomic: TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactca ... cttgcaacagGAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
EST: gi|88529069|gb|CI456396.1|CI456396
EST:     TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGA                         GAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
genomic: TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactca ... cttgcaacagGAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
EST: gi|88409345|gb|CI559443.1|CI559443
EST:     TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGA                         GAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
genomic: TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactca ... cttgcaacagGAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
EST: gi|86482503|gb|CI125136.1|CI125136
EST:     TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGA                         GAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
genomic: TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactca ... cttgcaacagGAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
EST: gi|88523434|gb|CI451259.1|CI451259
EST:     TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGA                         GAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
genomic: TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactca ... cttgcaacagGAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
EST: gi|88550705|gb|CI480701.1|CI480701
EST:     TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGA                         GAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
genomic: TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactca ... cttgcaacagGAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
EST: gi|88549103|gb|CI478961.1|CI478961
EST:     TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGA                         GAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
genomic: TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactca ... cttgcaacagGAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
EST: gi|86594912|gb|CI258166.1|CI258166
EST:     TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTAACGTCCTCGCGA                         GAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
genomic: TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactca ... cttgcaacagGAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
EST: gi|88557241|gb|CI487634.1|CI487634
EST:     TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGA                         GAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
genomic: TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactca ... cttgcaacagGAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
EST: gi|88550734|gb|CI480731.1|CI480731
EST:     TACCNCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGA                         GAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
genomic: TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactca ... cttgcaacagGAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
EST: gi|88554492|gb|CI484675.1|CI484675
EST:     TACCNCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGA                         GAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
genomic: TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactca ... cttgcaacagGAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
EST: gi|87010099|gb|CI279196.1|CI279196
EST:     TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGA                         GAACTTCATTGGCACTGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC
genomic: TACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactca ... cttgcaacagGAACTTCATTGGCACCGAGAGCGTCAGTCCCACAGGAACCGAGCTGCAACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTAACAACCCGGCAGGCGGCTCGGTGTTTCCTCTCCATTGGGGAGTATTACCGCCGCCTCCGTGCTCTCAGCAACCTCTGGTCTTCACGTCCTCGCGAgtaagactcagaactgcttatctgaaaagaaaaaaaagatcaaataaactgttctaaatttccaaatcatttttcagccacattattgtactggaaggaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataaa