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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAGAAAACTTGGGAAGGTTTTATTGGTGCATCTGTGACAACTATCATATCTGCTTTTGTGgtgagatgaaagcttctgttaattgtttttgtagttctctaactatgctagtctatgtcagttagcatggtttattttcacgcaagactactatgccact...

Basic information

species Oryza sativa
transcript LOC_Os01g55360.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55360.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G825110_T01 (Zea mays), 5'ss of exon 6
GTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAGAAAACTTGGGAAGGTTTTATTGGTGCATCTGTGACAACTATCATATCTGCTTTTGTGgtgaga-----tgaaagcttctgttaattgtttttgtagttctctaactatgctagtctatgtcagttagcatggtttattttcacgcaagactactatgccact
|||||||||||||||||||||  | |||||||| || ||||||||||| ||||||||||||||||||||||| |||||||||||||| ||||| ||| ||||||||     | |||   || |||  |  ||    || || | || | ||| |  | |   | |  |     | | | |||  | ||   |   || || | | 
GTTCTTTCTTGGGAGAACACCATTAATCAAGTTGTCCCCAAAGAAAACATGGGAAGGTTTTATTGGTGCATCCGTGACAACTATCATCTCTGCATTTCTGgtgagactttgttaaattctcggtttctcattaggataattttatagcaatgttttttt---tgaaattatgagatctgtttata-gccttatctctttggctc-

upper sequence: LOC_Os01g55360.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G452529_T02 (Zea mays), 5'ss of exon 6
GTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAGAAAACTTGGGAAGGTTTTATTGGTGCATCTGTGACAACTATCATATCTGCTTTTGTGgtgaga---tgaaagcttctgttaattgtttttgtagttctctaactatgctagtctatgtcagttagcatggtttattttcacgcaagactactatgccact
|||||||||||||||||||||  | |||||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||| ||| ||||||||   ||  |  |||   | |||  |  |   | |   | |    |    | | |   |  |  |    ||| | |  | |    ||  || ||    |
GTTCTTTCTTGGGAGAACACCATTAATCAAGTTGTCTCCAAAGAAAACTTGGGAAGGTTTTATTGGTGCATCAGTGACAACTATCATCTCTGCGTTTCTGgtgagactttgttaaattc--ctgattcctcatcaggatagtttatagcgacttttttttggaaatgacgacatttgtctata-gtgttacccctttgttttt

upper sequence: LOC_Os01g55360.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA10G32660.2 (Glycine max), 5'ss of exon 6
GTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAGAAAACTTGGGAAGGTTTTATTGGTGCATCTGTGACAACTATCATATCTGCTTTTGTGgtgagatgaaagcttctgttaattgtttttgtagttctctaactatgctagtctatgtcagttagcatggtttattttcacgcaagactactatgccact----
 |||||  |||| ||||| ||| ||||||||||||||||||||||||||||||| |||||||| || |||||||| || || ||||| ||||| ||| |||||||   | |  |||  ||  ||  |   |   | |   || |  | |  | | |        | || | || |  |      ||| |    ||    |    
TTTCTTCTTTGGAAGAACCCCTTTGATCAAGTTATCTCCAAAGAAAACTTGGGAGGGTTTTATAGGGGCATCTGTTACCACCATCATCTCTGCATTTATGgtgagc--agaatttcaatttgttaatcaag--atgcaacaattgggatgtttttttggttgggggattgcttgtcattgaatcagaatcacttgttgatgttt

upper sequence: LOC_Os01g55360.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA02G46440.1 (Glycine max), 5'ss of exon 6
GTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAGAAAACTTGGGAAGGTTTTATTGGTGCATCTGTGACAACTATCATATCTGCTTTTGTGgtgagatgaaagcttctgttaattgtttttgtagttctctaactatgctagtctatgtcagttagcatggtttattttcacgcaagactactatgccact-
 |||| | ||||||||||||||||||| ||| | |||||||||||||| ||||||||||| ||||| || |||||  | ||||| ||  |||| ||   ||| ||      |||| |||| | |   ||  ||  ||   ||  ||||||  | |   |  |    |     | |        |   || || |    || 
TTTCTATTTTGGGAGAACACCTCTGATAAAGCTTTCTCCAAAGAAAACCTGGGAAGGTTTCATTGGAGCGTCTGTTGCCACTATGATTGCTGCATTCACGgtaagcattctgcttttgtttagtcacttcttatgtcaggaaa-atgctaagcaactaccatcccaaaaaactttcaaactttacaccttctttattgctc

upper sequence: LOC_Os01g55360.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA14G02210.1 (Glycine max), 5'ss of exon 4
GTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAGAAAACTTGGGAAGGTTTTATTGGTGCATCTGTGACAACTATCATATCTGCTTTTGTGgtgagatgaaagc--ttctgttaattgtttttgta----gttctctaactatgc---tagtctatg--tcagttagcatggtttat-tttcacgcaagactactatgccact---------------------------------------------------------------
 |||| | ||||||||||||||||||||||| | |||||||||||||| ||||||||||| ||||| || |||||  | ||||| ||  |||| |||  ||| ||    |  |  |    | || |    |   |    | | || || |   |   | || |||   ||   ||| ||  ||| | ||| || ||  ||  | |    |                                                                 
TTTCTATTTTGGGAGAACACCTCTGATCAAGCTTTCTCCAAAGAAAACATGGGAAGGTTTCATTGGAGCGTCTGTTGCCACTATGATTGCTGCATTTACGgtaagcatcagtcagtgacatcaactaccatcccaaaaagctttcaaaattcacaccttgtttatagctctactag-atcttttgtgtttaactcacaacctccactttaagttgatttaatgatatttttcagtatttttgctttgcatgatgatgtcacttatgtttgtgcag

upper sequence: LOC_Os01g55360.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA20G34940.1 (Glycine max), 5'ss of exon 6
GTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAGAAAACTTGGGAAGGTTTTATTGGTGCATCTGTGACAACTATCATATCTGCTTTTGTGgtgagatgaaagcttctgttaattgtttttgtagttctctaactatgctagtctatgtcagttagcatg--gtttatt-ttcacgcaagactactatgccact--
 |||||  |||| ||||| ||| |||| |||||||||||||||||||||||||| ||||||||||| ||||| || || || ||||| ||||| ||| |||||||   | |  |||  ||  || ||   |   | |    | |  | | || | | |  | | |   |  | || |  || |  ||| |  ||| ||    |  
TTTCTTCTTTGGAAGAACCCCTTTGATTAAGTTATCTCCAAAGAAAACTTGGGAGGGTTTTATTGGGGCATCCGTTACCACCATCATCTCTGCATTTATGgtgagc--acaatttcaatttgttattcaag--atgcaactattgggatggtttttttttggtggggggttgcttgtcattgaatcaaaatcact-tgttgatgt

upper sequence: LOC_Os01g55360.4 (Oryza sativa), 5'ss of exon 6
lower sequence: AT4G26770.1 (Arabidopsis thaliana), 5'ss of exon 5
GTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAGAAAACTTGGGAAGGTTTTATTGGTGCATCTGTGACAACTATCATATCTGCTTTTGTGgtgagatgaaagcttctgttaattgtttttgtagttctctaactatgctagtctatgtcagttagcatggtttattttc-acgcaagactactatgccact
 |||| | | |||| ||| || || |||||||| |||||||||||||| ||||||||||| || || ||||| ||  ||||||| || ||||| ||| | || | |      ||||| | | || ||  | | ||||  ||||| |     |   | |||      || | ||||| ||  |     || ||         
TTTCTATTTCGGGAAAACTCCGCTCATCAAGTTGTCTCCAAAGAAAACATGGGAAGGTTTCATCGGAGCATCAGTTGCAACTATAATCTCTGCATTTATTgtaata-accttcttctatcatttattcat-tcgttcg-taactctttcttttggtctcaagactgatagattattatctgcttcgtacaacag-------

upper sequence: LOC_Os01g55360.4 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G62430.1 (Arabidopsis thaliana), 5'ss of exon 6
GTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAGAAAACTTGGGAAGGTTTTATTGGTGCATCTGTGACAACTATCATATCTGCTTTTGTGgtgagatgaaa--gcttctgtta----attgttt-ttgtagttctctaactatgctagtctatgtcagtt-agcatggttt---attttcacgcaagactactatgccact
 |||||  |||| ||||| ||| | || ||| | |||||||||||||| ||||| || || || || || ||||||||||||||||| ||||| ||||| |||||   |     ||| ||  |    || |    |   | | ||   |  ||   |   | | |   || | |||| ||    | | |   | | |  || | |  ||  
TTTCTTCTTTGGAAGAACGCCTTTAATAAAGCTGTCTCCAAAGAAAACATGGGAGGGATTCATCGGAGCCTCTGTGACAACTATCATCTCTGCATTTGTTgtgagtatatgttacttttgccaccacatggcacatcaaaatgcttacatcatttcatcatctttttcttcaccatgcttctgaaatgttttgtatgcgtaatgtttcag-

upper sequence: LOC_Os01g55360.4 (Oryza sativa), 5'ss of exon 6
lower sequence: AT4G22340.3 (Arabidopsis thaliana), 5'ss of exon 5
GTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAGAAAACTTGGGAAGGTTTTATTGGTGCATCTGTGACAACTATCATATCTGCTTTTGTGgtgagatgaaagcttctgttaattgtttttgtagttctctaactatgctagtctatgtcagttagcatggtttattttcacgcaagactactatgccact
 |||||  |||| ||||||||  ||||||||||||| ||||||||||| ||||| ||||| ||||| || ||| | || ||  | || ||||| ||  |||| || |       |  | ||||   | |    ||| | | || |   ||||   ||     ||   | | || ||||                      
TTTCTTCTTTGGAAGAACACCGTTGATCAAGTTATCACCAAAGAAAACATGGGAGGGTTTCATTGGAGCTTCTATTACCACAGTGATTTCTGCATTCCTGgtaagcttgttttatgggctaataagtatat--gttttttgacgag--tagtaattgattaataatcttgcttgtttttgtag-----------------

upper sequence: LOC_Os01g55360.4 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv19s0090g01220.t01 (Vitis vinifera), 5'ss of exon 5
GTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAGAAAACTTGGGAAGGTTTTATTGGTGCATCTGTGACAACTATCATATCTGCTTTTGTGgtgagatgaaagcttctgttaattgttttt--gtagttctctaactatgctagtctatgtcagttagcatggtttattttcacgcaagactactatgccact--
 |||||  |||| | ||| ||| |||||||  | |||||||||||||| ||||||||||||||||| | ||| ||  ||||| | || || || |||||||||||     |   |    | | |  |||   || | | | | |   |     |||    |   |  || |       |||     |      |||   | |  
TTTCTTCTTTGGAAAAACGCCTTTGATCAAACTCTCTCCAAAGAAAACATGGGAAGGTTTTATTGGAGGATCAGTTGCAACTGTGATCTCAGCATTTGTGgtgagt----attgttcactgactcctttgaagtcgatatttgagcttctccttctgctcctccttccaggcccccgcttccttttatttatttatttaattat

upper sequence: LOC_Os01g55360.4 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S106_169V6.1 (Physcomitrella patens), 5'ss of exon 4
GTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAGAAAACTTGGGAAGGTTTTATTGGTGCATCTGTGACAACTATCATATCTGCTTTTGTGgtgagatgaaagcttctgttaattgtttttgtagttctctaactatgctagt-ctatgtcagt-tagcatggtttattttcacgcaagactactatgccact------
  | ||| |||| | ||| ||| |||| ||  |||| || || || |||||||||||||||||||| |||||| | || ||| | || ||||||||| |||||||       ||||| |||    | ||||  | | || |||  | ||     | ||| | | || ||||   | |||  |    |||    |||            
CATTTTTTTTGGCAAAACTCCTTTGATTAAACTATCACCTAAAAAGACTTGGGAAGGTTTTATTGGAGCATCTATCACCACTGTTATGTCTGCTTTTATGgtgag-------cttcttttacacttctttgc-gctatccaacattcctctcgttctgtgaatataccatgagatgtttcgaatatagatatatatatataaaatata

upper sequence: LOC_Os01g55360.4 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ18455 (Selaginella moellendorffii), 5'ss of exon 4
GTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAGAAAACTTGGGAAGGTTTTATTGGTGCATCTGTGACAACTATCATATCTGCTTTTGTGgtgagatgaaagcttctgttaattgtttttgtagttctctaactatgctagtctatgtcagttagcatggtttattttcacgcaagactactatgccact
 |||||| ||||  |||| ||||| || ||| | || || ||||| |||||||| || ||||||||||| ||||| || ||||| |||||||||||| |||| |||  |       ||  |||  ||   |||| | |   ||| |  || |    |                                           
ATTCTTTTTTGGACGAACGCCTCTTATAAAGCTGTCGCCGAAGAAGACTTGGGAGGGCTTTATTGGTGCTTCTGTCACGACTATAATATCTGCTTTTTTGgtaagaccacga---gtgagaatatttgcagtagatttt--actgttgtaattgtag-------------------------------------------

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|29671303|gb|CB667578.1|CB667578
EST:     GGGAAGGTTTTATTGGTGCATCTGTGACAACTATCATATCTGCTTTTGTG                         TTAGCAAATGTAATGGGCCGTTTCCAATGGTTGACATGCCCAAGAAAA
genomic: GGGAAGGTTTTATTGGTGCATCTGTGACAACTATCATATCTGCTTTTGTGgtgagatgaa ... tttttggcagTTAGCAAATGTAATGGGCCGTTTCCAATGGTTGACATGCCCAAGAAAA