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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atactgcagcaagaagtttatgaggcaccgaattttaacaaatgtcttatttaggaataagaaccatcactcacctcataatatttatttcccttggcagTCAGATTGCCTCTACAATGCTGGATGGACAGAAGATCTCCGAGAAGTCATTAATTATCTCCATCACAAATATCCAAAGGCTCCAATGCTCTGTGTTGGTA

Basic information

species Oryza sativa
transcript LOC_Os01g65070.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65070.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G005444_T01 (Zea mays), 3'ss of exon 5
--ata-ctgcagcaagaagtttatgaggcaccgaattttaacaaatgtcttatttaggaataagaaccatcactcacctcataatatttatttccctt-ggcagTCAGATTGCCTCTACAATGCTGGATGGACAGAAGATCTCCGAGAAGTCATTAATTATCTCCATCACAAATATCCAAAGGCTCCAATGCTCTGTGTTGGTA
  |||  ||| |     | |  || | |   |  |    | |||| |  || || ||   ||   | |  |||| |     |||| ||  ||||| || |||||||||||||| ||||||||| ||| |||||||||||| ||||||| |||||||   | || ||||||| |||||| ||  |  || || | ||  ||||||
tcatagttgctgtttacactgcatcatgtttctgacgc-accaaacgattttttcag---tatccatcgccactgagtgtgtaattttggtttccttttggcagTCAGATTGCTTCTACAATGGTGGTTGGACAGAAGATGTCCGAGAGGTCATTACACACCTGCATCACAGATATCCGAAAACCACACTGTTTTGCATTGGTA

upper sequence: LOC_Os01g65070.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G34340.1 (Arabidopsis thaliana), 3'ss of exon 5
atactgcagcaagaagtttatgaggcaccgaattttaacaaatgtcttatttaggaataagaaccatcactcacctcataatatttatttcccttg-gcagTCAGATTGCCTCTACAATGCTGGATGGACAGAAGATCTCCGAGAAGTCATTAATTATCTCCATCACAAATATCCAAAGGCTCCAATGCTCTGTGTTGGTA
         |   |  |||||||  |  ||||   |    | |  ||||| ||   |||    |  | |   |  |  |  | | |        |  | ||||||||||| |||| ||||||||||||||||| ||| |  | | |||  || ||||||| || |||||||| || | ||||||  |  |   | |||| |
--gtgagttcgctagttttatgaatctacgaaaagttgtgatta-cttatatac--atatattcttttatgtaagtgttgttttgtggcaaatgtatgtagTCAGATTGCTTCTATAATGCTGGATGGACAGATGATATAAGGGTAGTTCTTGATTATCTTCAACACAAATACCCGAGGGCTCCTCTCTTTGCTATTGGCA

upper sequence: LOC_Os01g65070.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv12s0035g00850.t01 (Vitis vinifera), 3'ss of exon 5
--atactgcagcaagaagtt-tatgaggcac-cgaattttaacaaatgtcttatttaggaataagaaccatcactcacctcataatatttatttcccttggcagTCAGATTGCCTCTACAATGCTGGATGGACAGAAGATCTCCGAGAAGTCATTAATTATCTCCATCACAAATATCCAAAGGCTCCAATGCTCTGTGTTGGTA
  ||  |  |   ||   || |||| ||     |    ||  || |  ||||  ||    |||| |   ||     |  ||    |  ||  ||   | ||||||| |||||| | |||||||||||||||||||| ||| |  |  || |  || || |||| |||    | |||||| |||||||  |  |   |||||| |
agatgttagatggagttcttgtatgtggattatgttccttttcagaattcttgatt----ataaaatttatggaagatgtctctgttgttcattgtttgggcagTCTGATTGCATGTACAATGCTGGATGGACAGAGGATATAAGGAAAATTGTTGATCATCTTCATTGTCAGTATCCAGAGGCTCCTCTATTTGCTGTTGGAA

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|28298246|gb|CB238476.1|CB238476
EST:     GTAACACTGTTGTAAGCA-TCACAGGGGTCTTGGTGGTGTGTCCATTACT                         TCAGATTGCCCCTACA-TGCTGGATGGACAGAAGATCTCCGAGAAGTCATT
genomic: GTAACACTGTTGTAAGCAATCACAGGGGTCTTGGTGGTGTGTCCATTACTgtaagttaac ... cccttggcagTCAGATTGCCTCTACAATGCTGGATGGACAGAAGATCTCCGAGAAGTCATT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatttaggaataagaaccatcactcacctcataatatttatttcccttggcagTCAGATTGCCTCTACAATGCTGGATGGACAGAAGATCTCCGAGAAGTCATTAATTATCTCCATCACAAATATCCAAAGGCTCCAATGCTCTGTGTTGGTA
                      cactcac  putative branch site (score: 2)
                                    tatttatttccctt  putative PPT
                              tcataatatttattt  TA-rich tract