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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaattgaatgcttgctgaagttctgtatgcatgcaaactacattaccagaatctggcaccacttgctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC

Basic information

species Oryza sativa
transcript LOC_Os01g01710.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 5
gaattgaatgct-tgctgaagttctgta-tgcatgcaaactacattaccagaatc--tggcaccacttgctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC
 | |||||   | ||  |  | | |||  ||||| |||| || || | ||   |     |      | ||||| |||  |||||  |||  |||| ||||  |||||||||||||||||||||||||||| ||||| ||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| || |
-atttgaacattatgtggttgctttgtgctgcat-caaa-taaatgagcaattttatcagtgaatatagctgacttggttacttgtattg-tttgttctgttagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAAC

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G036290_T01 (Zea mays), 3'ss of exon 5
gaattgaatgcttgctgaagtt--ctgtatgcatgcaaactacattaccagaat-ctggcaccacttgctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC
 || | |||| |  |||   ||   |   ||||  || | || || | ||   | |  |      | | ||  | |   ||||    || |||| ||||| |||||||||||||||||||||||||||| ||||| ||||||||||| |||||||| || |||||||||||||||||||| ||||||||||||||||| || |
-aagttaatg-taactgggtttggtttggtgcacccaga-taaatgagcaatttaccagtgaatatagttgtctcggtaactttgtattgtttgttctgctagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAAGAAACGCTTATTGCAGGTGGTCCTTTCGTGCTTCCCCTTGCACACAAAC

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA05G02190.1 (Glycine max), 3'ss of exon 5
gaattgaatgcttgctgaagttctgtatgcatgcaaactacattaccaga-atctggcaccacttgctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC
| ||   |     |   |    ||   |  ||      |   ||  |||  ||| | || ||  |  |     ||  |  |   | || ||  | ||  |||| |||||||| || || ||||| |||||||| ||||| ||||| |||||||||||| | ||||| || ||||||||||| ||||| ||||| || ||||
gtataagaaaacagaaaatccactaactaaatatggtattggttgtcagttatcagacaacagatattagaaagctgaaatcc-tctcattattttgttagCCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAAGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGC

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G09740.1 (Glycine max), 3'ss of exon 5
gaattgaatgcttgctgaagtt-ctgtatgcatgcaaactacattaccaga-atctggcaccacttgctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC
   || |   |      |||   ||   |  |       | ||||  ||   ||| | || ||  |  |     ||  |  |   | |  ||  | |   |||| ||||||||||| || ||||| |||||| | ||||| || || |||||||||||| | ||||| || ||||||||||| ||||| ||||| || ||||
-gtttaagaacacagaaaagacactaactaaagatggtattcattgtcacttatcagacaacagatattagaaagctgaaatcc-tcttattattttattagCCAACAGTTGCTGCGATAGAAGCAGGGAAATACATAGCTTTAGCCAACAAAGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGC

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 5
gaattgaatgcttgctgaagttctgtatgcatgcaaactacattaccagaatctggcaccac----ttgctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC
        |   | ||  | || | | |  ||  ||||   ||||  || || ||  |  |     |||| |||       |||     |  ||  |    |||||||| ||||||||||||||||| || || || || ||  | || |||||||||||| | || |||||||||||||| |||||||| |||||  | || |
-------gtatatactctaattttttgt-tat-taaaccttattaagaggatatgaaaaaagaaagttgcagatgataaagcttgttgcttatttttactgcagCCTACGGTTGCTGCAATTGAAGCAGGAAAGGACATTGCTCTTGCAAACAAAGAGACATTAATCGCAGGTGGTCCTTTCGTGCTTCCGCTTGCCAACAAAC

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv17s0000g08390.t01 (Vitis vinifera), 3'ss of exon 5
gaattgaatgcttgctgaagttctgtatgcatgcaaactacattaccagaatctggcaccacttgctgatttg----cctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC
   |||| |   |  | |||  ||   |  ||| |||  |    |  |||| ||    | |  ||    | ||      | |||   | ||| |  |     |||||||||| |||||||| ||||| |||||||| ||||| || || ||||||||||| || ||||| || ||||||||||| ||||| |||||||| ||||
tccttgattttcttattaaggact---taaatgtaaataattggataagaaactaat-caagatgacagtctgaaaattttcttctgtgtctgtttttcattagCCTACAGTGGCTGCAATAGAAGCAGGGAAAGACATAGCCTTAGCCAACAAAGAGACCCTAATTGCTGGGGGTCCTTTTGTCCTTCCTCTTGCACACAAGC

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S73_243V6.1 (Physcomitrella patens), 3'ss of exon 7
gaattgaatgcttgctgaagttctgtatgcatgcaaacta-cattaccagaatctggcaccacttg--ctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC
   |  | | ||   |  || |||  ||  |     || |  |||| ||| |  ||  | |  |||  |    ||   || || ||  | | |    ||| |||| ||||||||||| ||||||||||| |||||||| || ||||| |||||||||||  | ||||| || ||||| | |||| | || || ||  | ||||
--gtctatttctaagtacaggtctacatctaaatcgacaaatattatcagtaggtgataacgtttggacgaggttttttaattgaaggtttgtttgttgc-agCCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAAGAGACTTTGATTGCTGGAGGTCCATATGTGTTACCTCTGGCTAAGAAGC

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|38474648|gb|CF958781.1|CF958781
EST:     C-GATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGACAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|58607529|gb|CK035562.1|CK035562
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|58689337|gb|CK078024.1|CK078024
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGA
EST: gi|33676538|gb|CF304777.1|CF304777
EST:     AGATGCAGTTACAGTTGTTACTGGGATAGTAGGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: AGATGCAGTTACAGTTGTTACTGGGATAGTAGGG-TGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|29613664|gb|CB618677.1|CB618677
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|29620639|gb|CB625650.1|CB625650
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|29688464|gb|CB684739.1|CB684739
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|29681868|gb|CB678143.1|CB678143
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|29617049|gb|CB622061.1|CB622061
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|58669161|gb|CK057847.1|CK057847
EST:     GTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: GTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|29620626|gb|CB625637.1|CB625637
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|29620641|gb|CB625652.1|CB625652
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|33381852|gb|CF197195.1|CF197195
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCNNNACTGANG                         NCTACAGTTGCTGCAATTG
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTG
EST: gi|58688021|gb|CK076708.1|CK076708
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|58694512|gb|CK083199.1|CK083199
EST:     CTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|58589270|gb|CF987578.1|CF987578
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTG
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTG
EST: gi|58690161|gb|CK078848.1|CK078848
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagaatctggcaccacttgctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC
                  tgctgat  putative branch site (score: 3)
                                      tttctttgctctgcc  putative PPT
                              tacttaaatttcttt  TA-rich tract