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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagggtacttataatttattatagcccttcatgtgtaatttgaagcagaaacttattttgttttcattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCGCAGATCGATGTTTCCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATT

Basic information

species Oryza sativa
transcript LOC_Os08g32630.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g32630.5 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM5G851815_T01 (Zea mays), 3'ss of exon 11
gttagggtacttataatttattatagcccttcatgtgtaatttgaagcagaaacttattttgttttcattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCGCAGATCGATGTTTCCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATT
          |||   | |   |||||| ||    |  |||||||||  ||| ||||||  |||||  | ||||||||||| |||||||||||||||||||||||| |||| ||||||| |||||| ||  || ||||||| ||||| ||||||||||||||||||||||||||||
---------gttagtgtatgccatagccatttcgatacaatttgaagtggaagcttattcggttttggtattgcagCCAAACTTAAGTGCATCATGGTTGTTCCAACGAGCGATGTCAGTAAGGCCACATGTCAATGTTTCACCAACCTTTATCAATGAGCTTCTCTTTGCTAATT

upper sequence: LOC_Os08g32630.5 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA14G05100.1 (Glycine max), 3'ss of exon 14
------gttagggtacttataatttattatagcc-cttcatgtgtaatttgaagcagaaacttattttgttttcattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCGCAGATCGATGTTTCCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATT
         |   |   || |   | ||  |||  ||  |  || || |  |  |     |  || |||| |  ||  ||||||| || || ||||| ||||||||||||||||||||||||||||||| |   |||  | ||||| || ||  |||||| ||||| ||||| | | | ||||
gtactttccaacttctctaaagactgtttcagcaactgtagatgaaactaaatacctgg-ccaatattgtgt--ataatgcagCCCAACTTGAGTGCTTCATGGTTGTTCCAAAGAGCAATGTCAGCAAAGAAACAGTCCAATGTTCCCGCAGATTTTATTAATGAACTTCTATATACCAATT

upper sequence: LOC_Os08g32630.5 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA02G43820.1 (Glycine max), 3'ss of exon 7
-------gttagggtacttataatttattatagcccttcatgtgtaatttgaagcagaaacttattttgtttt----cattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCGCAGATCGATGTTTCCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATT-----------
        ||  |  | ||| |   | | ||     || || |   | || |||||  ||  | | |   |||    || | |         ||| ||||| || |||||||||||||||||||||||||||| |   ||   | ||||| |  ||  |||||| ||||| ||||| | | | ||||           
gtgtgtctttgagtcaattaaagcatgtgat----ttttatattacaattaaagcatgaatatgtgtgtctttgaatcaatatatgtgtgtctttgagTGCTTCGTGGTTGTTCCAAAGAGCAATGTCAGCAAAGAAACAATCCAATGTTCCTGCAGATTTTATTAATGAACTTCTTTATACGAATTTTAGTTGTATG

upper sequence: LOC_Os08g32630.5 (Oryza sativa), 3'ss of exon 12
lower sequence: AT2G32640.2 (Arabidopsis thaliana), 3'ss of exon 13
--------gttagggtacttataatttattatagcccttcatg-tgtaatttgaagcagaaacttattttgttttcattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCGCAGATCGATGTTTCCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATT
        | |  |    |   |  | | |||    || | || | | |  |  |     ||   |||| | |||       |||||||| || || ||||||||| |||| |||||||||||||| |||| ||  ||| ||||||||||||     || | |||||||||||||  ||  ||||
gtaatatagctttgtggttctcagctaaatatctttctccctgctattaacttcactg--aatccatttggcttttgaacgacagCCAAACTTGAGCGCATCATGGCTGTTTCAAAGAGCAATGTCTGCAAAGCAACAGCTCGATGTTTCCCGTGGCTTCACCAATGAGCTTCTCCATGTAAATT

upper sequence: LOC_Os08g32630.5 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv12s0059g01150.t01 (Vitis vinifera), 3'ss of exon 13
gttagggtact-tataatttatt--atagcccttcatgtgtaatttgaagcagaaacttattttgttttcattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCGCAGATCGATGTTTCCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATT
||| | ||  | | ||||| |||    | |   |       ||||   |||  ||  | | | | | ||||   ||||||| ||  | |||||| |||||||||| ||||| ||||||||||||| ||  |||   |||||||| ||   ||| |||| ||||||||| | ||  ||||
gttcgtgttttctgtaattgatttagcaacttctaccacacaatt---agctcaa--tgaatatttgttcaa--tgcagCCCAACCTTAGTGCAGCATGGTTGTTTCAAAGGGCAATGTCAGCAAAGCAACAGTATGATGTTTCTCCTGATTTCATCAGTGAGCTTCTTTATGTCAATT

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|29670150|gb|CB666425.1|CB666425
EST:     CAGGAGATCTTCTGGATGCACGTAGTTTGCAGCTGCTGAACCCTTATATG                         CCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCG
genomic: CAGGAGATCTTCTGGATGCACGTAGTTTGCAGCTGCTGAACCCTTATATGgttagggtac ... cattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCG
EST: gi|29670151|gb|CB666426.1|CB666426
EST:     CAGGAGATCTTCTGGATGCACGTAGTTTGCAGCTGCTGAACCCTTATATG                         CCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCG
genomic: CAGGAGATCTTCTGGATGCACGTAGTTTGCAGCTGCTGAACCCTTATATGgttagggtac ... cattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCG
EST: gi|29677474|gb|CB673749.1|CB673749
EST:     CAGGAGATCTTCTGGATGCACGTAGTTTGCAGCTGCTGAACCCTTATATG                         CCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCG
genomic: CAGGAGATCTTCTGGATGCACGTAGTTTGCAGCTGCTGAACCCTTATATGgttagggtac ... cattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCG
EST: gi|29679962|gb|CB676237.1|CB676237
EST:     CAGGAGATCTTTTGGATGCACGTAGTTTGCAGCTGCTGAACCCTTATATG                         CCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCG
genomic: CAGGAGATCTTCTGGATGCACGTAGTTTGCAGCTGCTGAACCCTTATATGgttagggtac ... cattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagcccttcatgtgtaatttgaagcagaaacttattttgttttcattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCGCAGATCGATGTTTCCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATT
                                    ttttgttttcatttt  CT-rich tract
                             aaacttattttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagggtacttataatttattatagcccttcatgtgtaatttgaagcagaaacttattttgttttcattttgcagCCAAATTTAAGTGCATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCGCAGATCGATGTTTCCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT