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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtaattgtgcattatcttttcaatttcaatatcacacacacgcacaaaggtctcatcttttcctgatagctctgttgtctgtttgctgcattattttagCTCGATGTTTGGGCGAAGGAAAGAGAAGTTGCTGGGTTAAAGGCAAGCTTGAATACACTGACTTCTGAGGTACAGCGTCTGTACAAGTTATGTGCTGAGT

Basic information

species Oryza sativa
transcript LOC_Os09g21780.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g21780.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G116196_T01 (Zea mays), 3'ss of exon 4
----tgtaattgtgcattatctt-ttcaatttcaatatcacacacacgcacaaaggtctcatcttttcctgatagctctgttgtc-tgtttgctgcattattttagCTCGATGTTTGGGCGAAGGAAAGAGAAGTTGCTGGGTTAAAGGCAAGCTTGAATACACTGACTTCTGAGGTACAGCGTCTGTACAAGTTATGTGCTGAGT
    | ||||| |||||| |||| ||||||||    |||| | | ||  | |||    |    |  ||   |    | |||  |   ||   || | | ||||||| | || |||||||| ||||||||||||||||| ||  ||||||| ||||||| |||||| || ||||||||||| ||| |||| |||||||| |||||||
gctctttaattctgcattttcttattcaattt----atcatata-aca-aaaaaaactttggatgatcaatacttttttgtgataacgtagtctacctcattttagTTGGACGTTTGGGCCAAGGAAAGAGAAGTTGCAGGACTAAAGGCGAGCTTGAGTACACTTACATCTGAGGTACAACGTTTGTATAAGTTATGCGCTGAGT

upper sequence: LOC_Os09g21780.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G055917_T02 (Zea mays), 3'ss of exon 4
-------tgtaattgtgca-ttatctt-ttcaatttca-atatcacacacacgcacaaaggtctcatcttttcctgatagctctgttgtctgtttgctgcattattttagCTCGATGTTTGGGCGAAGGAAAGAGAAGTTGCTGGGTTAAAGGCAAGCTTGAATACACTGACTTCTGAGGTACAGCGTCTGTACAAGTTATGTGCTGAGT
       | ||||| |||| || |||| ||||||||   |||| ||| | |     | |      | |||||||||||| |   ||          || | | ||||||||| ||||||||||| ||||||||||||||||| ||  ||||||||||||||| |||||| || ||||||||||| ||| |||| ||||||||||||||||
ttagctttttaattttgcaattttcttattcaatttagcatataacaaaaaaagggataatcaataccttttcctgataacatagt----------ctacctcattttagCTGGATGTTTGGGCCAAGGAAAGAGAAGTTGCAGGACTAAAGGCAAGCTTGAGTACACTTACATCTGAGGTACAACGTTTGTATAAGTTATGTGCTGAGT

upper sequence: LOC_Os09g21780.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G50960.1 (Glycine max), 3'ss of exon 4
tgtaattgtgcattatcttttcaatttcaatatcacacacacgcacaaaggtctcatcttt---tcctgatagctctgttgtctgtttgctgcattattttagCTCGATGTTTGGGCGAAGGAAAGAGAAGTTGCTGGGTTAAAGGCAAGCTTGAATACACTGACTTCTGAGGTACAGCGTCTGTACAAGTTATGTGCTGAGT
| ||||| |  |||   ||   |||   |  |  |      | ||  ||  | | | ||     |      |  | |  ||| | |||  | ||    || |||| ||||||||||| |||||||||||||||||||| |||||||||||||| || ||  | |  |||||  |||| ||  || | ||||| ||||||||| 
tttaattct--attcctttcctaatgctagaaatatttcttcacagcaacatttgagctaggagtttacccacttattatgtatattttttccacgtgttcaGCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTTAAACACCTTAATGTCTGAAATACAACGCTTGAATAAGTTGTGTGCTGAG-

upper sequence: LOC_Os09g21780.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G27740.1 (Glycine max), 3'ss of exon 4
tgtaattgtgcattatcttttcaatttcaatatcacacacacgcacaaaggtctcatcttt---tcctgatagctctgttgtctgtttgctgcattattttagCTCGATGTTTGGGCGAAGGAAAGAGAAGTTGCTGGGTTAAAGGCAAGCTTGAATACACTGACTTCTGAGGTACAGCGTCTGTACAAGTTATGTGCTGAGT
  ||||| |  ||    || | |||   |  |         | ||  ||  | | | ||     |      |  | |  ||| | |||  | |||   ||||||| ||||||||||| |||||||||||||||||||| |||||||||||||| |||||  | |  |||||  |||| ||  || | || || ||||| ||| 
-ttaattct--atccatttcttaatgctagaaatgtttcttcacatcaacatttgaactaggagtttacccacttattctgtatattttttccatgtgtttagCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTTAAATACCTTAATGTCTGAAATACAACGCTTGAATAAATTGTGTGCCGAGA

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|66917271|gb|CX104119.1|CX104119
EST:     TGCCTACTGGGAACACCTCACAGAACATGACTAACAGCAGACACTTGGAG                         CTCGATGTTTGGGCGAAGGAAAGAGAAGTTGCTGGGTTAAAGGCAAGCTTG
genomic: TGCCTACTGGGAACACCTCACAGAACATGACTAACAGCAGACACTTGGAGgtacttattc ... attattttagCTCGATGTTTGGGCGAAGGAAAGAGAAGTTGCTGGGTTAAAGGCAAGCTTG
EST: gi|58665932|gb|CK054618.1|CK054618
EST:     TGCCTACTGGGAACACCTCACAGAACATGACTAACAGCAGACACTTGGAG                         CTCGATGTTTGGGCGAAGGAAAGAGAAGTTGCTGGGTTAAAGGCAAGCTTG
genomic: TGCCTACTGGGAACACCTCACAGAACATGACTAACAGCAGACACTTGGAGgtacttattc ... attattttagCTCGATGTTTGGGCGAAGGAAAGAGAAGTTGCTGGGTTAAAGGCAAGCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaggtctcatcttttcctgatagctctgttgtctgtttgctgcattattttagCTCGATGTTTGGGCGAAGGAAAGAGAAGTTGCTGGGTTAAAGGCAAGCTTGAATACACTGACTTCTGAGGTACAGCGTCTGTACAAGTTATGTGCTGAGT
                tcctgat  putative branch site (score: 3)
                                              ttatttt  putative PPT
                                             attatttta  TA-rich tract