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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattcaaagtggtatacacctcgttatgttactgatatatttatgatatttgatattcggagttgcattcagataattgtttttctacattcctttgcagATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTCCAAACTCTTCTGGACAACATTTTCCTTCCTCTGTTTGAGGTCACCATTG

Basic information

species Oryza sativa
transcript LOC_Os05g28180.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 11
---tattcaaagtggtatacacctcgttatgttactgatatatttatgatatttgatattcggagttgcattcagataattgtttttctacattcctttgcagATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTCCAAACTCTTCTGGACAACATTTTCCTTCCTCTGTTTGAGGTCACCATTG
   ||  ||      | |  ||||  ||     | ||| |||||||    |       | |    ||   ||| ||||  | ||| |  |||||| ||||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||||| |||||| |||||||||||| ||||||| |||||||| || ||||
tcttaaccatgacaatgt-taccttttt-ccccagtgaaatatttagtgcaaaaacattacattattcttttctgatatat-tttgtggacattcttttgcagATTCCACGCTTATATAATGTGTACAAGGAAATGGGTATCGTTACATCATTCCAAAATCTTCTTGACAACATTTTCGTTCCTCTTTTTGAGGTTACTATTG

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 12
tattcaaagtggtatacacctcgttatgttactgatatatttatgatatttgat-attcggagttgcattcagataattgtttttctacattcctttgcagATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTCCAAACTCTTCTGGACAACATTTTCCTTCCTCTGTTTGAGGTCACCATTG
 |||    | | | | |      ||   ||| ||   || ||     |    || ||   | |||       |||  | ||| || || ||  ||| |||| | ||||| || || ||||||||||| |||||||| ||||| ||||||||||| |   | || ||||| |||||| |||| || |||||||||||  |  
aatttggggagcttttcctgcttttcatttattgccttaatttgctcagccaattatatagtgttagcaattgatggtagttcttataaatgtctt-gcagCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTCCAGAACATGCTCGACAATATTTTCATTCCACTTTTTGAGGTCACTGTCA

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 11
--tattcaaagtggtatacacctcgttatgttactgatatatttatgatatttgatattcggagttgcattcagataattgtttttctacattcctttgcagATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTCCAAACTCTTCTGGACAACATTTTCCTTCCTCTGTTTGAGGTCACCATTG
   | |    |  |  |   |  | ||   ||  ||   || ||     |    ||  | |   | ||| | | ||  |  || || || ||  ||| |||| | ||||| || || ||||||||||| |||||||| ||||| ||||||||||| |   | || ||||| |||||  |||| || |||||||||||  |  
aagaatttggggagctttttctgctttccatttatggcttaatttgctcagccaattgtagtgttagcaatta-atggtaattcttataaatgtctt-gcagCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTCCAGAACATGCTTGACAATATTTTTATTCCACTTTTTGAGGTCACTGTCA

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 11
----------------------------------tattcaaagtggtatacacctcgttatgttactgatatatttatgatat--ttgatattcggagttgcattcagataattgtttttctacattcctttgcagATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTCCAAACTCTTCTGGACAACATTTTCCTTCCTCTGTTTGAGGTCACCATTG
                                  |  |   |   || ||    |  || |  |     | | ||| | | ||   || ||   | || |  |||    |  || | | | |    | ||    || |||||||||| || ||  | |||||||| ||||||||||| ||||| ||||| | | | |||||||| || ||| ||||||||||||| | |||  | |
gttagccatctctttgatacttgtgtgctccatgtccttccatgagtgtatgtgttttttttgtctccgtgtgtttgtaacatgactgctaactg-agctatattttccttgttttctgtttgt-ctgctcactagCTCCCACGCTTGTACAACATTTACAAGGACATGGGTATTGTGACATCGTTCCAGAATATCCTGGACAATATATTCATTCCTCTGTTTGAAGCCACGGTAG

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 11
tattcaaagtggtatacacctcgttatg----ttactgatatatttatgatatttgatattcggagttgcattcagataattgtttttctacattcctttgcagATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTCCAAACTCTTCTGGACAACATTTTCCTTCCTCTGTTTGAGGTCACCATTG
  |  || ||     ||    | || ||    ||  |   | |   |  || || ||| || |   |||   | |    ||  | |   |   ||  ||| ||| | || ||  | ||||||||||||||||| ||||| |||||||||||||| || |   | |||||||| || || ||||| ||||||||||| ||  |  
-ctggaatgtatctaacctgacattctggggtttgttagcaaaagcaaaatgttggat-tttgttattgttcttatggtataatatccttctgtt--tttccagCTTCCCCGGCTGTATAATGTGTACAAGGATATGGGAATTGTTACATCATTTCAGAACATGCTGGACAATATCTTTCTTCCCCTGTTTGAGGTTACTGTGA

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|33796571|gb|CF324153.1|CF324153
EST:     GTGAAAATGTTGTCTGGCTGGTTCAG                         ATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTC
genomic: GTGAAAATGTTGTCTGGCTGGTTCAGgtaccctttc ... tcctttgcagATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTC
EST: gi|88693457|gb|CI737032.1|CI737032
EST:     GGATAGTGAACAATGAATTGTCCAGTGAAAATGTTGTCTGGCTGGTTCAG                         ATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTC
genomic: GGATAGTGAACAATGAATTGTCCAGTGAAAATGTTGTCTGGCTGGTTCAGgtaccctttc ... tcctttgcagATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTC
EST: gi|58687285|gb|CK075972.1|CK075972
EST:     GGATAGTGAACAATGAATTGTCTAGTGAAAATGTTGTCTGGCTGGTTCAG                         ATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTC
genomic: GGATAGTGAACAATGAATTGTCCAGTGAAAATGTTGTCTGGCTGGTTCAGgtaccctttc ... tcctttgcagATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTC
EST: gi|58610210|gb|CK038109.1|CK038109
EST:     GGATAGTGAACAATGAATTGTCTAGTGAAAATGTTGTCTGGCTGGTTCAG                         ATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTC
genomic: GGATAGTGAACAATGAATTGTCCAGTGAAAATGTTGTCTGGCTGGTTCAGgtaccctttc ... tcctttgcagATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttgatattcggagttgcattcagataattgtttttctacattcctttgcagATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTCCAAACTCTTCTGGACAACATTTTCCTTCCTCTGTTTGAGGTCACCATTG
  atttgat  putative branch site (score: 5)
                                  tttttctacattcctt  putative PPT
                           ataattgtttttcta  TA-rich tract