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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctcgcttgttggtattgtgcttgcttgttattcctgcaaaatgcattctcttgagtgggttaatgcttatagGTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAG

Basic information

species Oryza sativa
transcript LOC_Os04g51610.3
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G391042_T02 (Zea mays), 3'ss of exon 16
--gtatgctcgcttgttggtattgtg--cttgct-tgttattc-ctgcaaaatgcattctcttgagtgggttaatgct------tatagGTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAG
  || | | |   | |   ||   ||   ||| | || || |  || | | ||  | |    |||         | ||      ||||||| |||||||| |||||||| ||||| |||||||| ||||||||||| ||||| |||||||| || ||  |||| || ||||||
gtgtgttcccaactttctataccttggttttgttatgctactagctccgacatctaatgctatgaacactcacttcctatggaatatagGTGAGGAGGCTTTCTGCATGCGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTGACGTTAAATCAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 16
----------gtatgctcgcttgttggtattgtgcttgcttgttattcctgca--aaatgcatt-ctcttgagtgggttaatgcttatagGTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAG
             |         ||||| |||| | | ||  ||  |||  ||   ||||| || | |          ||  |  | |||||||||||||| |||||||||||||| |||||||| ||||||||||| ||||| |||||||| || ||  | ||||| ||||||
gtatgttcccaactttctataccttggttttgt-catactacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 15
gtatgctcgctt--gttggtattgt--gcttgcttgttattcctgcaaaatgcattctcttgagtgggttaatgc-ttatagGTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAG----
||||||    ||  ||| ||  | |  | ||  |   |||   |   | |     | | |    |     | ||  ||| |||| |||||||| ||||| ||||| || ||||| ||||||||||| |||||||| || ||||| |||||  ||||| ||||||||    
gtatgccaatttttgtttgtgctttaggatttttgcatatctatttgagaaatgctgtttaatataacacattgaattacagGTGAGGAGGCTTTCTGCCTGTGAGACAATGGGGTCAGCCACAACCATTTGCAGTGATAAGACTGGAACATTGACTATGAATCAGGTTA

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 18
gtatgctcgctt--gttggtattgtgcttgcttgttattcctgcaaaatgcattctcttgagtgggtta-at--gcttatagGTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAG
||||||   |||  ||| ||  | |      |||  ||  ||     |   || || ||   |     | ||    ||  |||| |||||||| ||||| ||||| || ||||| ||||||||||| |||||||| || ||||| |||||  ||||| ||||||||
gtatgccaacttttgtttgtgctataggattttggcatatctatttgagaaatgctgtttgatataacacattgaattgcagGTGAGGAGGCTTTCTGCCTGTGAGACAATGGGGTCAGCCACAACCATTTGCAGTGATAAGACTGGAACATTGACTATGAATCAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 18
gtatgctcgcttgttggtattgtgcttgcttgttattcctg--caaaatgcattctcttgagtgggttaatg-cttatagGTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAG
||| |     || |  | ||    |||  ||||||||  |      || |||| || |  |   |   |     ||  ||||  || |||| || || |||||||||||||| || ||||||||||||||||| || |||||||||||  |||| || ||||||
gtaagtatcattttatgcatcaatctt-tttgttatttttagttttaaggcatcctttctaacagccaaggaatttgcagGTACGGCGGCTATCAGCCTGTGAAACTATGGGCTCTGCCACAACAATTTGCAGTGATAAGACAGGAACATTGACCTTAAATCAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 17
gtatgctcgcttgttggta--ttgtgcttgcttgttattcctgcaaaatgcattctcttgagtgggttaatgctt----atagGTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAG
|| |   |    ||    |  |||   ||  |||||| |  | || | |   || |      |   ||  | |||      ||||  | ||||| || ||||| ||||||||||| || || |||||||||||||| || ||||| |||||  |||| || ||||||
gt-tctccaacagtcaacacattgcaattatttgttaatttt-catattcagttttgaaacatattttcttacttccgtgcagGTGCGAAGGCTGTCAGCATGCGAAACTATGGGATCTGCTACAACAATTTGCAGTGATAAGACTGGAACTTTGACCTTAAATCAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA07G00630.1 (Glycine max), 3'ss of exon 18
gtatgctcgcttgttggtattgtgcttgcttgttattcctg--caaaatgcattctcttgagtgggttaatgcttatagGTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAG
||| |     || |  | ||  |   |  ||||||||  |      || |||| || |  |   |   ||   ||  ||||  || |||| || || |||||||||||||| || ||||||||||||||||| || |||||||||||  |||| || ||||||
gtaagtatcattttatgcatc-tatctttttgttatttttagttttaaggcatcctttctaacagtaaaaaatttgcagGTACGGCGGCTATCGGCCTGTGAAACTATGGGCTCTGCCACAACAATTTGCAGTGATAAGACAGGAACATTGACCTTAAATCAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 16
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 15
----------gtatgctcgcttgttggtattgtgcttgcttgtta-ttcctgcaaaatgcattctcttgagtgggttaatgcttatagGTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAG
          | | |   | || | | | | || ||| ||| ||  ||  ||    |    || |||  | ||    ||     | |||| || ||||| || || |||||||| ||||| ||||| |||||||| ||||| ||||| || |||||  | ||||||||||||
gtaagaatcagaaggagtg-ttctcgctttagttctttcttcttggttattgtctgaccatttttctcaaatg--ccaa-----acagGTTAGAAGGCTTTCAGCTTGTGAAACCATGGGATCAGCAACAACAATCTGCAGTGACAAAACTGGAACTTTAACTTTGAATCAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 17
----gtatgctcgcttgttggtattgtgcttgcttgt-tattcctgcaaaatgc--attctcttgagtgggttaatgcttatagGTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAG
      ||              ||  | |||  |  | | ||    ||  || |   || | |        ||      |  ||||  | ||||| || || |||||||||||||| || || |||||||||||||| || ||||| |||||  | || |||||| ||
gtcatcatttctttcctccaaaataatccttaataatatcttgtctcattattctagttttataacaccattttggatatgcagGTGCGTAGGCTTTCAGCCTGTGAAACTATGGGCTCTGCAACAACAATTTGCAGTGATAAGACTGGAACATTAACCTTGAATAAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 18
------------------------gtatgctcgcttgttggtat-tgtgct-tgcttgttattcctgcaaaatgcattctc-ttgagtgggttaatgct--------tatagGTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAG
                         || |||  |       ||| | || | ||   || ||   |  |   |  ||   | | | |||| ||||            |  ||||  ||||||| ||||| ||||| || ||||| ||  |||| || |||||||| || ||||||||||| || ||||||||||||
gtatgtatgacaaatatttctgaactaagcttccacaagattatatatgttatgtgggtcatgagtatatgttatatatgcatcgggtggtttaacagcagttgaactgcagGTACGGAGGCTTTCTGCTTGTGAGACCATGGGCTCTTCCACGACTATTTGCAGTGATAAGACAGGAACTCTAACTTTGAATCAG

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|29667907|gb|CB664182.1|CB664182
EST:     GCTTGCCTTCTCTATGCGCAAGATGATGAGGGACAAAGCTCTG                         GTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGC
genomic: GCTTGCCTTCTCTATGCGCAAGATGATGAGGGACAAAGCTCTGgtatgctcgc ... atgcttatagGTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttgcttgttattcctgcaaaatgcattctcttgagtgggttaatgcttatagGTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAG
                                        ggttaat  putative branch site (score: 4)
       ttgttatt  TA-rich tract