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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaagaaatacagtaataaagcttgaaattgttacaaaagcctgggttctggaatcttactgtaatcatgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCCAGGAAAATCAGTCCTAGGGTATTTGATGCAGACCCGTCAAAGGAAAAAA

Basic information

species Oryza sativa
transcript LOC_Os03g63430.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63430.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G013750_T03 (Zea mays), 3'ss of exon 5
---------------------------gtatgaagaaatacagtaataaagcttgaaattgttac-aaaagcctgggttctg-gaatcttactgtaatcatgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCCAGGAAAATCAGTCCTAGGGTATTTGATGCAGACCCGTCAAAGGAAAAAA
                              ||   |  ||   |  |||  |||   ||| |||| ||||| ||   |  ||  || |||||| | ||  |  |||||||||||||| ||| | ||||||||||||||||| || ||||| |||||||| |||||||||||| |||| |||||||| ||||| || ||||         
aaaattgctttcattcttgagcaggtaacgtgccaacctattatgttaatactttgtatttttacgaaaaggcttattcatgcaaaacttactattattgTTGTCACAGGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCAAGGAAAATCAGTACTAGAGTATTTGACGCAGATCCATCAA---------

upper sequence: LOC_Os03g63430.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G013750_T04 (Zea mays), 3'ss of exon 5
---gtatgaagaaatacagtaataaagcttgaaattgttac-aaaagcctgggttctg-gaatcttactgtaatcatgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCCAGGAAAATCAGTCCTAGGGTATTTGATGCAGACCCGTCAAAGGAAAAAA
      ||   |  ||   |  |||  |||   ||| |||| ||||| ||   |  ||  || |||||| | ||  |  |||||||||||||| ||| | ||||||||||||||||| || ||||| |||||||| |||||||||||| |||| |||||||| ||||| || |||||||||||||
gtaacgtgccaacctattatgttaatactttgtatttttacgaaaaggcttattcatgcaaaacttactattattgttgtcacagGTCCGGCTATGCCTAGATCGTCAAGATTATGTCCGAGCACAAATTTTATCAAGGAAAATCAGTACTAGAGTATTTGACGCAGATCCATCAAAGGAAAAAA

upper sequence: LOC_Os03g63430.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G014116_T02 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------------------------------gtatgaagaaatacagtaataaagcttgaaattgttacaaaagcctgggttctgg--aatcttactgtaatcatgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCCAGGAAAATCAGTCCTAGGGTATTTGATGCAGACCCGTCAAAGGAAAAAA
                                                                                      ||||   |  |||  |  |||  ||||  ||| |||| |||   ||  |||  |  || |||||| | ||| |  |||||||||||||| ||| ||||||| ||||||| |||  | ||||| ||||||||||||||||||||| |||| |||||||| ||||| || |||||||||||||
gtattccctccgttcttttttatttgtcgcggtttagttcaaaaatgaattagcgggcgacaaatatttgagaacggaggtagtactatggcaacctactatgttaatacttggtattcttactaaaatgtgtattcatgcaaaacttactattatcgttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCCAGGAAAATCAGTACTAGAGTATTTGACGCAGATCCATCAAAGGAAAAAA

upper sequence: LOC_Os03g63430.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G468717_T01 (Zea mays), 3'ss of exon 6
---gtatgaagaaatacagtaataaagcttgaaattgttac-aaaagcctgggttctg-gaatcttactgtaatcatgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCCAGGAAAATCAGTCCTAGGGTATTTGATGCAGACCCGTCAAAGGAAAAAA
      ||   |  ||   |  |||  |||   ||| |||| ||||| ||   |  ||  || |||||| | ||  |  ||||||||||| || | | | ||||||||||||||||| || ||||| |||||||| |||||||||||| |||| |||||||| ||||| || |||||||||||||
gtatcgtgccaacctattatgttaatactttgtatttttacgaaaaggcttattcatgcaaaacttactattattgttgtcacagGTCCGACTATTCCTAGATCGTCAAGATTATGTTCGAGCACAAATTTTATCAAGGAAAATCAGTACTAGAGTATTTGACGCAGATCCATCAAAGGAAAAAA

upper sequence: LOC_Os03g63430.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 5
--------gtatgaagaaatacagtaataaa--gcttgaaattgttacaaaagcctgggtt--ctggaatcttactgtaatcatgatc-acagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCCAGGAAAATCAGTCCTAGGGTATTTGATGCAGACCCGTCAAAGGAAAAAA
         | || ||  |    | ||| ||    |||    ||||         || | |  ||   |   || |||  |||   |  | |||| ||  ||||||||||||||||||||| ||| || ||||| || ||||| ||||| |||| |||||| || ||||| |||||  |   ||| || || |
gtaaggacttgtgtagttacgttgcaattaataatttgctggtgttttctttcattgtgataactatcaaactattgtggtcaaactttaaagGTTCGCTTGTGCTTGGATCGTCAAGATTTTGTTCGTGCACAAATCTTATCTAGGAAGATCAATCCTAGAGTTTTTGACGCAGATACAAAAAAAGATAAGA

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|86420511|gb|CI056500.1|CI056500
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGAT-ATGTACGCGCACAGATTTTATCC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|29664786|gb|CB661061.1|CB661061
EST:     ATTNTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
genomic: ATT-TGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|29639942|gb|CB644951.1|CB644951
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|58685186|gb|CK073873.1|CK073873
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCTTTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|33812345|gb|CF332062.1|CF332062
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|88265103|gb|CI368877.1|CI368877
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|29664482|gb|CB660757.1|CB660757
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|88210956|gb|CI212596.1|CI212596
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGAT-ATGTACGCGCACAGATTTTATCC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|29645308|gb|CB650315.1|CB650315
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|58681237|gb|CK069924.1|CK069924
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCTTTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACA
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACA
EST: gi|29645307|gb|CB650314.1|CB650314
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|33795887|gb|CF323811.1|CF323811
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|29658196|gb|CB654471.1|CB654471
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|29664785|gb|CB661060.1|CB661060
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|58659555|gb|CK048235.1|CK048235
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCTTTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCCAGATTATGTACGCGCACAGATTTTATCC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|300215653|gb|HO088279.1|HO088279
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCTTTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|29678374|gb|CB674649.1|CB674649
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|58678571|gb|CK067258.1|CK067258
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCTTTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|29637544|gb|CB642553.1|CB642553
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|117217926|gb|CT845200.1|CT845200
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCTTTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|86534283|gb|CI174489.1|CI174489
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCC
EST: gi|19388435|gb|BM929262.1|BM929262
EST:     CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCTTTCATTCTAGAGCAG                         GTCCGGCTGTGCTTGGATCGTCAAGATTATGTAC
genomic: CATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaagaa ... atgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaaattgttacaaaagcctgggttctggaatcttactgtaatcatgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCCAGGAAAATCAGTCCTAGGGTATTTGATGCAGACCCGTCAAAGGAAAAAA
                               atcttac  putative branch site (score: 3)
         ttacaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaagaaatacagtaataaagcttgaaattgttacaaaagcctgggttctggaatcttactgtaatcatgatcacagGTCCGGCTGTGCTTGGATCGTCAAGATTATGTACGCGCACAGATTTTATCCAGGAAAATCAGTCCTAGGGTATTTGATGCAGACCCGTCAAAGGAAAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA