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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGACAACCTTGCAAGCTGGATAGTGAACAATGAATTGTCCAGTGAAAATGTTGTCTGGCTGGTTCAGgtaccctttcactatttctgctcgtacttagctctagaaatttctataattgtcttgcagttattgaacctacatactctgaattgatttttgtgcttta...

Basic information

species Oryza sativa
transcript LOC_Os05g28180.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g28180.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G416667_T01 (Zea mays), 5'ss of exon 11
GATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGACAACCTTGCAAGCTGGATAGTGAACAATGAATTGTCCAGTGAAAATGTTGTCTGGCTGGTTCAGgtaccctttcactatttctgctcg--tacttagctctagaaatttctataattgtcttgcagttattgaacctacatactc-tgaattgatttttgtgcttta
|||||||||||| || ||||| || |||||||||||| | |||||||| |||||||||||||||||||||  ||||| ||||||||||||||||||||||||| |||||   ||||| |  |    || |||||| | | | | | | |||||  || |||  || |  | |||  | ||  |  | |   ||   |  |   
GATTTCAATCTACGGAAGGAAACAGAGTGAATGGGACCAACTTGCAAGTTGGATAGTGAACAATGAATTGCACAGTGGAAATGTTGTCTGGCTGGTTCAGgtatcctttatttatttgtattgtactagttagctgtggcagtgtttgtaatttcctggcacatagttgaactaattgctaatacactatgttggatagt---

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA01G29470.2 (Glycine max), 5'ss of exon 12
GATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGACAACCTTGCAAGCTGGATAGTGAACAATGAATTGTCCAGTGAAAATGTTGTCTGGCTGGTTCAGgtaccctttcactatttctgctcgtacttagctc--tagaaatttctataattgtcttgcagttattgaacctacatactctgaattgatttttgtgcttta-
 || ||||| ||||| |||||||||||||| |||||| | || || || ||||||||||| ||||| |||| ||| || ||||| || ||| || ||||||||  |||| | ||||| |  | |  |  || |   |   | ||   |||||  | | |||   ||| |   ||  |   |  |  |      | |  |  | 
AATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCGTTTGGTTGATTCAGgtattctttaattatttgt-ttagagcacagattggttttatttctcataatgatatggcaacaattta--ttatttctcccaatctacaaactattttggac

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA03G07460.1 (Glycine max), 5'ss of exon 11
GATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGACAACCTTGCAAGCTGGATAGTGAACAATGAATTGTCCAGTGAAAATGTTGTCTGGCTGGTTCAGgtaccctttcactatttctgctcgtacttagctc--tagaaatttctataattgtcttgcagttattgaacctacatac---tctgaattgatttttgtgcttta
 || ||||| ||||| |||||||||||||| |||||| | || || || ||||||||||| ||||| |||| |||||| |||||||| ||| || ||||||||  |||| | ||||| |  | | ||  || |   | | | ||   |||||  | | | |   ||| |   |   | |   ||| |||| ||||| |  ||   
AATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGTGAGAATGTTGTATGGTTGATTCAGgtattctttaattatttgt-ttagaacacagattggttgtatttctcataatgatatagtaacgatttattatttctcccaatctaaatt-attttgggact---

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 5'ss of exon 11
GATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGACAACCTTGCAAGCTGGATAGTGAACAATGAATTGTCCAGTGAAAATGTTGTCTGGCTGGTTCAGgtaccctttcactatttctgctcgtacttagctctagaaatttctataattgtcttgcag-ttattgaacctacata---ctctgaattgatttttgtgcttta
||| ||||| ||||| || ||||||||||| |||||| | ||||| || ||||||||||| ||||| |||| |||||| |||||||| ||| || ||||||||   ||||  | | ||     | | ||  |  || || ||| | | |||  |  | || ||||  |   || | |   | |||      |         || 
GATATCAATATATGGCAGAAAGCAAAGTGAGTGGGACCAACTTGCCAGTTGGATAGTGAATAATGATTTGTACAGTGAGAATGTTGTTTGGTTGATTCAGgta---tttccttgtatccctatgaaatttcccttataagtttattttatttaccggtaggttatatacagtaaaaaagtccctgtgcctgtgcacacatctt-

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S307_76V6.1 (Physcomitrella patens), 5'ss of exon 11
GATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGACAACCTTGCAAGCTGGATAGTGAACAATGAATTGTCCAGTGAAAATGTTGTCTGGCTGGTTCAGgtac-----cctttcactatttctgctcgtacttagctctagaaatttctataattgtc-ttgcagttattgaacctacatact-ctgaattgatttttgtgcttta
 ||||| ||||||||||||||| |||||||||||||| |  | || || ||||| || |  ||  || |    ||||| |||||    |||||| ||||||| |     |||| | | || |||  |  |  ||  || |  || |    |||||   | ||  | |  ||   || ||||||| ||  | ||| |  ||   |   
AATTTCTATCTATGGGAGGAAGGAAAGTGAATGGGACCAGTTAGCCAGTTGGATTGTCACTAACAAACTTCAAAGTGAGAATGTGACATGGCTGATTCAGgtccaactaccttcccccatgtctcttttt--ttgcctttttaattaatgataataaccattataatctttt--ccaacatactgctccaatgaatgatggaat---

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|58687285|gb|CK075972.1|CK075972
EST:     GGATAGTGAACAATGAATTGTCTAGTGAAAATGTTGTCTGGCTGGTTCAG                         ATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTC
genomic: GGATAGTGAACAATGAATTGTCCAGTGAAAATGTTGTCTGGCTGGTTCAGgtaccctttc ... tcctttgcagATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTC
EST: gi|33796571|gb|CF324153.1|CF324153
EST:     GTGAAAATGTTGTCTGGCTGGTTCAG                         ATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTC
genomic: GTGAAAATGTTGTCTGGCTGGTTCAGgtaccctttc ... tcctttgcagATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTC
EST: gi|88693457|gb|CI737032.1|CI737032
EST:     GGATAGTGAACAATGAATTGTCCAGTGAAAATGTTGTCTGGCTGGTTCAG                         ATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTC
genomic: GGATAGTGAACAATGAATTGTCCAGTGAAAATGTTGTCTGGCTGGTTCAGgtaccctttc ... tcctttgcagATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTC