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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAACCTGCTTCGGCTCCGTGGATTTTGCATGACGCCTACAGAACGGTTACTTGTCTATCCCTACATGGCTAATGGGAGTGTCGCATCACGATTGCGAGgtgccttaatcttccttactttttcttagagtaaatccattaatagtttcttacacgtttgtttgcatgcttaaacataaatggcacagctattatggtt...

Basic information

species Oryza sativa
transcript LOC_Os04g38480.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g38480.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G870959_T01 (Zea mays), 5'ss of exon 9
AGGAACCTGCTTCGGCTCCGTGGATTTTGCATGACGCCTACAGAACGGTTACTTGTCTATCCCTACATGGCTAATGGGAGTGTCGCATCACGATTGCGAGgtgccttaatcttccttactttttcttagagtaaatccattaatagtttcttacacgtttgtttgcatgcttaaacataaatggcacagctattatggtt-------------------------------
|||||||| || |||||||||||||| |||||||| |||||||| ||| | || || ||||| ||||||||||| ||||| |||||||| ||  | ||||||  |   | |||  |  |||| ||   |   |||||         ||||||   | |||  ||| |  |  |      | ||   | | |  | || ||                               
AGGAACCTTCTCCGGCTCCGTGGATTCTGCATGACCCCTACAGAGCGGCTGCTAGTGTATCCATACATGGCTAACGGGAGCGTCGCATCGCGCCTTCGAGgtaaccagaccttatt--ctttctcgccgctcaaatct--------tttcttctgcatttaattggaaacagagtgtctactgttcctgatgctttgattgtctactgttcctgatgctttgatttcgtag

upper sequence: LOC_Os04g38480.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA20G31320.1 (Glycine max), 5'ss of exon 9
AGGAACCTGCTTCGGCTCCGTGGATTTTGCATGACGCCTACAGAACGGTTACTTGTCTATCCCTACATGGCTAATGGGAGTGTCGCATCACGATTGCGAGgtgccttaatcttccttactttttcttagagtaaatc----cattaatagtttcttacacgtttgtttgcatgcttaaacataaatggcacagctattatggtt
|| || || ||||| || ||||| || || ||||| || |||||| || ||||||| |||||||||||||||||||| ||||| || ||| | ||  |||||   |   |||  |||| | ||| |   | |   |     | ||  || | |||||    | |  || | | |||   |        |  | | |   |    
AGAAATCTCCTTCGACTACGTGGGTTCTGTATGACACCAACAGAAAGGCTACTTGTTTATCCCTACATGGCTAATGGAAGTGTTGCTTCATGCTTAAGAGgtagatct-tctgtcttattctttttagcaattgtttttgtcttttttattctcttatttctctcattcctttctttgcccctttccccctatccacccta---

upper sequence: LOC_Os04g38480.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA10G36280.1 (Glycine max), 5'ss of exon 9
AGGAACCTGCTTCGGCTCCGTGGATTTTGCATGACGCCTACAGAACGGTTACTTGTCTATCCCTACATGGCTAATGGGAGTGTCGCATCACGATTGCGAGgtg--ccttaatcttccttactttttcttagagtaaatccattaatagtttcttacacgtttgtttgcatgcttaaacataaatggcacagctattatggtt
|| || || || || || || || || || ||||| || |||||| || ||||||| |||||||||||||||||||| ||||| || ||  | ||  |||||    |||    ||  ||  ||||    |  || ||| |  |  |   | ||||    ||   || | | |||   |        |  | | |   |    
AGAAATCTCCTCCGACTACGCGGGTTCTGTATGACACCAACAGAAAGGCTACTTGTTTATCCCTACATGGCTAATGGAAGTGTTGCTTCTTGCTTAAGAGgtagatcttctgttttattctttttagcaattgttaatgcccttttgaatccttatttcttctattcctttctttgcccccttccccctacccaccctac--

upper sequence: LOC_Os04g38480.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA02G08360.1 (Glycine max), 5'ss of exon 7
AGGAACCTGCTTCGGCTCCGTGGATTTTGCATGACGCCTACAGAACGGTTACTTGTCTATCCCTACATGGCTAATGGGAGTGTCGCATCACGATTGCGAGgt---gccttaatcttccttactttttcttagagtaaatccat---taatagtttcttacacgtttgtttgcatgcttaaacataaat---ggcacagctattatggtt---------------------------------------------------------------------------
 | || || || ||  | ||||| || || ||||| ||||| ||| || ||||||| ||||| |||||||||||||| ||||| || ||| | ||  |||||   |||||    ||     | | |      | || |    |    || |   |   |||   |   ||   ||||      | | |   | | ||  ||||    ||                                                                           
CGAAATCTCCTCCGTTTACGTGGGTTCTGTATGACTCCTACTGAAAGGCTACTTGTATATCCTTACATGGCTAATGGTAGTGTTGCCTCATGCTTAAGAGgtacggcctttgctttttcctcctatatggccactagactagtaggcaacaaaataggacatactgtattttttgctatgttgtgactacggactcaattatttattttatttgtcaaatatgagtcttctacattatcttctacttagcattgtcttgtgatcttgtatttgcattattctag

upper sequence: LOC_Os04g38480.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv07s0031g01410.t01 (Vitis vinifera), 5'ss of exon 9
AGGAACCTGCTTCGGCTCCGTGGATTTTGCATGACGCCTACAGAACGGTTACTTGTCTATCCCTACATGGCTAATGGGAGTGTCGCATCACGATTGCGAGgtgc--cttaatcttccttactttttcttagagtaaatccattaatagtttcttacacgtttgtttgcatgcttaaacataaatggcacagctattatggtt-
 |||| ||||||||| | ||||| ||||||||||| || || || ||||||||||| ||||| |||||||||||||| ||||| || ||| |  |  ||||| |  |||  |  | ||| |   | ||     || ||  |  |  | ||   |      | |||   |     |  | |   | | |||   |  ||| || 
CGGAATCTGCTTCGGTTACGTGGTTTTTGCATGACACCAACTGAGCGGTTACTTGTTTATCCATACATGGCTAATGGAAGTGTTGCTTCATGCCTAAGAGgtactgcttgtttattcttccacgtgctatttttatattgaagag-aattggctgtgaaatggttctgaacagcagtcgtg--ttggacatgcacaatgcttg

upper sequence: LOC_Os04g38480.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv18s0164g00070.t01 (Vitis vinifera), 5'ss of exon 9
AGGAACCTGCTTCGGCTCCGTGGATTTTGCATGACGCCTACAGAACGGTTACTTGTCTATCCCTACATGGCTAATGGGAGTGTCGCATCACGATTGCGAGgtgccttaatcttccttactttttcttagagtaaatccattaatagtttcttacacgtttgtttgcatgcttaaacataaatggcacagctattatggtt---
 |||| || || || || ||||| ||||||||||| ||||| |||||| | ||||| ||||| || ||||||||||| || || |||||| | ||  |||||            | | |      |   ||| | | | ||   | || ||| |||      || | |  || ||  | | |||   |  | |  ||  |   
CGGAATCTCCTCCGTCTTCGTGGTTTTTGCATGACACCTACTGAACGGCTGCTTGTTTATCCGTATATGGCTAATGGAAGCGTTGCATCATGTTTAAGAGgtaatgcctgtcaacattccacacttaccagtgacttc-ttctcaattgctttcacaaggaatttctt--tttaatttcattggtggaattttcttgcctggt

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|29614687|gb|CB619700.1|CB619700
EST:     ACTTGTCTATCCCTACATGGCTAATGGGAGTGTCGCATCACGATTGCGAG                         AGCGGCAGCCAAATGATCCGCCGCTTGAATGGCAAACAAGAACTCGGATTG
genomic: ACTTGTCTATCCCTACATGGCTAATGGGAGTGTCGCATCACGATTGCGAGgtgccttaat ... gattttgtagAGCGGCAGCCAAATGATCCGCCGCTTGAATGGCAAACAAGAACTCGGATTG
EST: gi|58693053|gb|CK081740.1|CK081740
EST:     ACTTGTCTATCCCTACATGGCTAATGGGAGTGTCGCATCACGATTGCGAG                         AGCGGCAGCCAAATGATCCGCCGCTTGAATGGCAAACAAGAACTCGGATTG
genomic: ACTTGTCTATCCCTACATGGCTAATGGGAGTGTCGCATCACGATTGCGAGgtgccttaat ... gattttgtagAGCGGCAGCCAAATGATCCGCCGCTTGAATGGCAAACAAGAACTCGGATTG
EST: gi|87006023|gb|CI289440.1|CI289440
EST:     ACTTGTCTATCCCTACATGGCTAATGGGAGTGTCGCATCACGATTGCGAG                         AGCGGCAGCCAAATGATCCGCCGCTTGAATGGCAAACAAGAACTCGGATTG
genomic: ACTTGTCTATCCCTACATGGCTAATGGGAGTGTCGCATCACGATTGCGAGgtgccttaat ... gattttgtagAGCGGCAGCCAAATGATCCGCCGCTTGAATGGCAAACAAGAACTCGGATTG