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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagtgcctctgcctatattcctctgtgcttactgctagtgatgaaattattgtccatacgtgttacgctttcaactaatgatcacctacctctgtttgaagGTAACAAAACCACTATTGGAGACATCAAGAAGAGGGTATCTTGCTGCACTGTCAGCATCGAGTTACTCCTTCGTCTCTTTGCTTCAGCACTTCCTTCCTA

Basic information

species Oryza sativa
transcript LOC_Os08g23810.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G125052_T01 (Zea mays), 3'ss of exon 5
---gtatagtgcctctgcctatattcctctgtgcttactgctagtgatgaaattattgtccat-acgtgttacgctttc-aactaa--tgatcacc-tacctctgtttgaagGTAACAAAACCACTATTGGAGACATCAAGAAGAGGGTATCTTGCTGCACTGTCAGCATCGAGTTACTCCTTCGTCTCTTTGCTTCAGCACTTCCTTCCTA
     |||  ||    |||| | |   | ||||   |  |   ||| || |  | |||    | ||    |||  | || ||| |   | |  |||  |  ||  ||||||||||||||||||  | |||||||||||||||||||| |||||||| ||| | |||||||||||||||||||  || || ||||||||||| ||||||||||
gtacaatatcgcactcgcctgtgtatatgtgtgtgcagcgggtgtggtgcagcttttgcttgtgacactgtacattgtctaaccatcttaaaaaccacatgtcattttgaagGTAACAAAACCTTTGTTGGAGACATCAAGAAGAGGCTATCTTGCGGCAATTTCAGCATCGAGTTACTCCTATGTTTCATTGCTTCAGCATTTCCTTCCTA

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 7
gtatagtgcctctgcctatattcctctgtgcttactgcta-gtgatgaaattattgtccat-acgtgttacgctttcaact-aatgatcacctacctctgttt---gaagGTAACAAAACCACTATTGGAGACATCAAGAAGAGGGTATCTTGCTGCACTGTCAGCATCGAGTTACTCCTTCGTCTCTTTGCTTCAGCACTTCCTTCCTA
||| | |  | ||| |  | |   | ||||| ||| ||   ||| || |  | ||  |  | ||   ||       || || ||  | ||||||  |   |||   ||||||||| || ||  | ||||| || ||||||||||| |||||||| ||| | || ||||| ||||||||||  || || ||||||||||||||||||||||
gtacaatctccctgtcgctgtgtatatgtgcatacagcggtgtgctgcagctctttcctgtgacactttgtctaaccatcttaaaaaccacctatattcattttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATTTCTGCATCCAGTTACTCCTATGTTTCATTGCTTCAGCACTTCCTTCCTA

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 7
gtatagtgcctctgcctatattcctctgtgcttactgctagtgatgaaatta-ttgtccatacgtgttacgctttcaactaatgatcacctacctctgtttgaagGTAACAAAACCACTATTGGAGACATCAAGAAGAGGGTATCTTGCTGCACTGTCAGCATCGAGTTACTCCTTCGTCTCTTTGCTTCAGCACTTCCTTCCTA
                         ||||  || ||| | |||||   || | ||| |||| | | ||  |   |  || | | | || ||  ||    |   |||| || || || || ||||||||||| |||| ||| |||||||| ||| | || ||||| |||||||||| ||| ||||| ||  ||   ||| ||||||
----------------------gtactgt-tttgctggttgtgatcttatcagttgaccattcattttg-gtactttacaagtaaacatct--cttaaat---agGTGACCAAGCCTCTGTTGGAGACATCCAGAAAAGGTTATCTTGCGGCAATATCTGCATCAAGTTACTCCTACGTTTCTTTACTCAAGTGTTTCATTCCTA

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|58686263|gb|CK074950.1|CK074950
EST:     ACTTTGGCAGCATTGACATTTTGGTGCATTCTCTAGCTAATGGTCCAGAG                         GTAACAAAACCACTGTTGGAGACATCAAGAAGAGGGTATCTTGCTGCACTG
genomic: ACTTTGGCAGCATTGACATTTTGGTGCATTCTCTAGCTAATGGTCCAGAGgtatagtgcc ... ctgtttgaagGTAACAAAACCACTATTGGAGACATCAAGAAGAGGGTATCTTGCTGCACTG
EST: gi|29613728|gb|CB618741.1|CB618741
EST:     ACTTTGGCAGCATTGACATTTTGGTGCATTCTCTAGCTAATGGTCCAGAG                         GTAACAAAACCACTGTTGGAGACATCAAGAAGAGGGTATCTTGCTGCACTG
genomic: ACTTTGGCAGCATTGACATTTTGGTGCATTCTCTAGCTAATGGTCCAGAGgtatagtgcc ... ctgtttgaagGTAACAAAACCACTATTGGAGACATCAAGAAGAGGGTATCTTGCTGCACTG
EST: gi|29613729|gb|CB618742.1|CB618742
EST:     ACTTTGGCAGCATTGACATTTTGGTGCATTCTCTAGCTAATGGTCCAGAG                         GTAACAAAACCACTGTTGGAGACATCAAGAAGAGGGTATCTTGCTGCACTG
genomic: ACTTTGGCAGCATTGACATTTTGGTGCATTCTCTAGCTAATGGTCCAGAGgtatagtgcc ... ctgtttgaagGTAACAAAACCACTATTGGAGACATCAAGAAGAGGGTATCTTGCTGCACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattgtccatacgtgttacgctttcaactaatgatcacctacctctgtttgaagGTAACAAAACCACTATTGGAGACATCAAGAAGAGGGTATCTTGCTGCACTGTCAGCATCGAGTTACTCCTTCGTCTCTTTGCTTCAGCACTTCCTTCCTA
                          aactaat  putative branch site (score: 2)
                                      cctacctct  putative PPT
                          aactaat  TA-rich tract