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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcatagctttaattcgtctgcaatgccttgtgttggtgccctattttcctttacatggctaagtcttgctttcgtttttgattcttatgttgtatgaatagGCCATTAAAGATGATGTTGGAACTATTCGAATTCAGCGACCACACAAAGGACCATTTTATGTATCCCCGAAAAGCATCGATCAACTTATCATGAATCTTG

Basic information

species Oryza sativa
transcript LOC_Os07g45350.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g45350.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G873779_T01 (Zea mays), 3'ss of exon 2
--gtaattcatagctttaattcgtctgcaatgccttgtgttggtgccctattttcctttacatggctaagtcttgctttcgtttt---tgattcttatgttgtatgaatagGCCATTAAAGATGATGTTGGAACTATTCGAATTCAGCGACCACACAAAGGACCATTTTATGTATCCCCGAAAAGCATCGATCAACTTATCATGAATCTTG
   | |||  ||   |  ||| || ||   ||  |||  || ||    | ||  | | |  ||   |   |||| |||| ||| |   | ||| |||| |   ||||| ||||||||||||||||||||||||||||||||||||||||||| ||||||                                                    
gtattatttctattatccattggtatgtgctgtgttgcattagt-ttttcttggcatgtctatatttgtctcttccttttgttctatattattattatatcacatgaacagGCCATTAAAGATGATGTTGGAACTATTCGAATTCAGCGACCGCACAAA----------------------------------------------------

upper sequence: LOC_Os07g45350.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G871572_T01 (Zea mays), 3'ss of exon 6
--gtaattcatagctttaattcgtctgcaatgccttgtgttggtgccctat----tttcctttacatggctaagtcttgctttcgtttttgattcttatgttgtatgaatagGCCATTAAAGATGATGTTGGAACTATTCGAATTCAGCGACCACACAAAGGACCATTTTATGTATCCCCGAAAAGCATCGATCAACTTATCATGAATCTTG
   | |||  || | || ||  |||||   ||  | |  || ||      |    | ||   |  ||   |   |||| |||| ||| ||  ||||||| ||| ||||| |||| |||||||||||||||||||||||| ||||||||||||| || |||||||| || |||||||| || |||||||||||||||||||| ||||||||||
gtattatttctatcattcatcggtctgtgctgtgtggcattagtctttgttgacatgtctaatgtatatttgtctctttcttttgttatttgttcttatattgcatgaacagGCTATTAAAGATGATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGACCCTTCTATGTATCACCAAAAAGCATCGATCAACTTATTATGAATCTTG

upper sequence: LOC_Os07g45350.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G020574_T08 (Zea mays), 3'ss of exon 6
--gtaattcatagctttaattcgtctgcaatgccttgtgttggtgccctattttcctttacatggctaagtcttgctttcgtttt---tgattcttatgttgtatgaatagGCCATTAAAGATGATGTTGGAACTATTCGAATTCAGCGACCACACAAAGGACCATTTTATGTATCCCCGAAAAGCATCGATCAACTTATCATGAATCTTG
   | |||  ||   |  ||| || ||   ||  |||  || ||    | ||  | | |  ||   |   |||| |||| ||| |   | ||| |||| |   ||||| ||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||| |||  | || ||||| |||||||||||  |||||||||
gtattatttctattatccattggtatgtgctgtgttgcattagt-ttttcttggcatgtctatatttgtctcttccttttgttctatattattattatatcacatgaacagGCCATTAAAGATGATGTTGGAACTATTCGAATTCAGCGACCGCACAAAGGACCCTTTTATGCATCATCAAAGAGCATTGATCAACTTATTGTGAATCTTG

upper sequence: LOC_Os07g45350.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G020574_T07 (Zea mays), 3'ss of exon 6
--gtaattcatagctttaattcgtctgcaatgccttgtgttggtgccctattttcctttacatggctaagtcttgctttcgtttt---tgattcttatgttgtatgaatagGCCATTAAAGATGATGTTGGAACTATTCGAATTCAGCGACCACACAAAGGACCATTTTATGTATCCCCGAAAAGCATCGATCAACTTATCATGAATCTTG-------------
   | |||  ||   |  ||| || ||   ||  |||  || ||    | ||  | | |  ||   |   |||| |||| ||| |   | ||| |||| |   ||||| ||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||| |||  | || ||||| |||||||||||  |||||||||             
gtattatttctattatccattggtatgtgctgtgttgcattagt-ttttcttggcatgtctatatttgtctcttccttttgttctatattattattatatcacatgaacaggccattaaagatgatgttggaactattcgaattcagCGACCGCACAAAGGACCCTTTTATGCATCATCAAAGAGCATTGATCAACTTATTGTGAATCTTGGGAAATGGGCCAA

upper sequence: LOC_Os07g45350.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA02G16860.1 (Glycine max), 3'ss of exon 6
gtaattcatagctttaattcgtctgcaatgccttgtgttggtgccctattttcctttacatggctaagtcttgctttcgtttttgattcttatgttgtatgaatagGCCATTAAAGATGATGTTGGAACTATTCGAATTCAGCGACCACACAAAGGACCATTTTATGTATCCCCGAAAAGCATCGATCAACTTATCATGAATCTTG
  ||        |  ||||  |||    |   | |  |   |   |  || |  |||  ||    || | ||  |||   |||  ||| |||   ||||| |  ||||   |||||||||||||||  || |||||||||||||||| |||||||| ||||||||||| || || ||||  || |||||||| ||    ||||| |
agaaaaagggattgcaatt--tctatttttattcgaat---tcttcctttctattttcaattatcaacttttttttttaatttc-atttttaaaatgtatcatcagGCTGCTAAAGATGATGTTGGGGCTTTTCGAATTCAGCGACCCCACAAAGGGCCATTTTATGTCTCTCCCAAAACAATTGATCAACTAATTGCAAATCTGG

upper sequence: LOC_Os07g45350.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G02920.1 (Glycine max), 3'ss of exon 6
gtaattcatagctttaattcgtctgcaatgccttgtgttggtgccctattt-tcctttacatggctaagtcttgctttcgtttttgattcttatgttgtatgaatagGCCATTAAAGATGATGTTGGAACTATTCGAATTCAGCGACCACACAAAGGACCATTTTATGTATCCCCGAAAAGCATCGATCAACTTATCATGAATCTTG
     ||| |   | || ||   ||| ||   ||||||   |    ||||  ||||||||     | |   ||  |||    ||| ||| |||   ||||| |  ||||   |||||||||||||||  ||||||||||||||||||| |||||||| ||||||||||| || || ||||  || |||||||| ||    ||||| |
-----tca-attatcaactctggtgccat-ttttgtgtcaattaaatattaatcctttactgttttcaacttttttttttaatttcatttttaaaatgtatcatcagGCTGCTAAAGATGATGTTGGCGCTATTCGAATTCAGCGACCCCACAAAGGGCCATTTTATGTCTCTCCCAAAACAATTGATCAACTAATTGCAAATCTGG

upper sequence: LOC_Os07g45350.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv07s0104g00630.t01 (Vitis vinifera), 3'ss of exon 6
----------gtaattcatagctttaattcgtctgcaatgccttgtgttggtgccctattttcctttacatggctaagtcttgctttcgtttttgattcttatgttgtatgaatagGCCATTAAAGATGATGTTGGAACTATTCGAATTCAGCGACCACACAAAGGACCATTTTATGTATCCCCGAAAAGCATCGATCAACTTATCATGAATCTTG
          |  ||  |||    | |||  || |  | |  |||  |   | |||  ||||  ||| ||      | ||||   | ||| |||      | |  | |||||  |||| || ||||||||||||||||| ||||| |||||||| || || ||||||||||||||||| || || ||||| || ||||| ||| |    |||||||
cttgtatgaggagatctata----tgattgatcaggta-gttttgattgaataccccttttttttttgca------aatcttatatacgtgttt-----ctttaatatatgatcagGCTATCAAAGATGATGTTGGAACAATTCGTATTCAGCGGCCCCATAAAGGACCATTTTATGTCTCTCCCAAAAGTATTGATCATCTTGTTGCAAATCTTG

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|29684518|gb|CB680793.1|CB680793
EST:     GAACTGAAAGGGTTCTTCCAACTGGAACTTCATTGACTGTTGTTGGTGAG                         GCCATTAAAGATGATGTTGGAACTATTCGAATTCAGCGACCACACAAAGGA
genomic: GAACTGAAAGGGTTCTTCCAACTGGAACTTCATTGACTGTTGTTGGTGAGgtaattcata ... gtatgaatagGCCATTAAAGATGATGTTGGAACTATTCGAATTCAGCGACCACACAAAGGA
EST: gi|29680615|gb|CB676890.1|CB676890
EST:     GAACTGAAAGGGTTCTTCCAACTGGAACTTCATTGACTGTTGTTGGTGAG                         GCCATTAAAGATGATGTTGGAACTATTCGAATTCAGCGACCACACAAAGGA
genomic: GAACTGAAAGGGTTCTTCCAACTGGAACTTCATTGACTGTTGTTGGTGAGgtaattcata ... gtatgaatagGCCATTAAAGATGATGTTGGAACTATTCGAATTCAGCGACCACACAAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctttacatggctaagtcttgctttcgtttttgattcttatgttgtatgaatagGCCATTAAAGATGATGTTGGAACTATTCGAATTCAGCGACCACACAAAGGACCATTTTATGTATCCCCGAAAAGCATCGATCAACTTATCATGAATCTTG
                             ttttgat  putative branch site (score: 4)
                            tttttgattcttat  TA-rich tract