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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catggctgcaccgtacttgcatttgttcgttagtcttgttccaattgttatgcactttaaaatcgtgctaaaataagacatctttatgctgacattttagGTTGAAGGTACAATTGAGTACATCTGTCGTCATGAAGGAGAAGGTGCAATCCTTGTGTTCCTTACTGGTTGGGATGAAATTTCGAAACTTTTGGATAAGA

Basic information

species Oryza sativa
transcript LOC_Os10g33275.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G395467_T01 (Zea mays), 3'ss of exon 3
-----catggctgcacc-gtacttgcatttgttcgttagtcttgttccaattgttatgcactttaaaatcgtgctaaaataagacatctttatgctgacattttagGTTGAAGGTACAATTGAGTACATCTGTCGTCATGAAGGAGAAGGTGCAATCCTTGTGTTCCTTACTGGTTGGGATGAAATTTCGAAACTTTTGGATAAGA
     |||   |||||| | |||   |||||  | ||| |    | | ||   | |  ||    |||    ||||   |    ||| || |||| ||||||||||||| ||| ||||||||||||| || ||||   |||||| |||||||||||||||||||||||||| ||| ||||||||||||||||| ||| |||| ||||
tgccacatttgtgcaccagaactattatttgaac-ttaatacactgctaaccat-acccaggaaaaatagttgctgcta----acacctctatgttgacattttagGTGGAAAGTACAATTGAGTATATTTGTCACTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTATTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA

upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G381470_T01 (Zea mays), 3'ss of exon 8
catggctgcaccgtacttgcatttgttcgttagtcttgttccaattgttat-gcactttaaaatcgtgctaaaataagacatctttatgctgacattttagGTTGAAGGTACAATTGAGTACATCTGTCGTCATGAAGGAGAAGGTGCAATCCTTGTGTTCCTTACTGGTTGGGATGAAATTTCGAAACTTTTGGATAAGA
  |  |      | ||  | | |  ||  ||   |||  | || |  | |    ||     ||   |  | |      ||| || |||| ||||||||||||| ||| ||||||||||||| || | |||  |||||| |||||||||||||||||||||||||||||  ||||||||||||||||| ||| |||| ||||
tgtcacatttgtgcaccagaact-attatttgaacttaatacactgctaaccatacccaggaaaaatagttactgctaacacctctatgttgacattttagGTGGAAAGTACAATTGAGTATATTTATCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGACTGGGATGAAATTTCGAAGCTTCTGGACAAGA

upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G399212_T01 (Zea mays), 3'ss of exon 11
-----catggctgcacc-gtacttgcatttgttcgttagtcttgttccaattgttatgcactttaaaatcgtgctaaaataagacatctttatgctgacattttagGTTGAAGGTACAATTGAGTACATCTGTCGTCATGAAGGAGAAGGTGCAATCCTTGTGTTCCTTACTGGTTGGGATGAAATTTCGAAACTTTTGGATAAGA
     |||   |||||| | |||   |||||  | ||| |    | | ||   | |  ||    |||    ||||   |    ||| || |||| ||||||||||||| |||  ||||||||| || || |||||  |||||| |||||||||||||||||||||||||||||| ||||||||||||||||| ||| |||| ||||
tgtcacatttgtgcaccagaactattatttgaac-ttaatacactgctaaccat-acccaggaaaaatagttgctgcta----acacctctatgttgacattttagGTGGAAAATACAATTGAATATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA

upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G863698_T01 (Zea mays), 3'ss of exon 4
-----catggctgcacc-gtacttgcatttgttcgttagtcttgttccaattgttatgcactttaaaatcgtgctaaaataagacatctttatgctgacattttagGTTGAAGGTACAATTGAGTACATCTGTCGTCATGAAGGAGAAGGTGCAATCCTTGTGTTCCTTACTGGTTGGGATGAAATTTCGAAACTTTTGGATAAGA
     |||   |||||| | |||   |||||  | ||| |    | | ||   | |  ||    |||    ||||   |    ||| || |||| ||||||||||||| ||| ||||||||||||| || ||||   |||||| |||||||||||||||||||||||||| ||| ||||||||||||||||| ||| |||| ||||
tgtcacatttgtgcaccagaactattatttgaac-ttaatacactgctaaccat-acccaggaaaaatagttgctgcta----acacctctatgttgacattttagGTGGAAAGTACAATTGAGTATATTTGTCACTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTATTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA

upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G052798_T01 (Zea mays), 3'ss of exon 3
-----catggctgcacc-gtacttgcatttgttcgttagtcttgttccaattgttatgcactttaaaatcgtgctaaaataagacatctttatgctgacattttagGTTGAAGGTACAATTGAGTACATCTGTCGTCATGAAGGAGAAGGTGCAATCCTTGTGTTCCTTACTGGTTGGGATGAAATTTCGAAACTTTTGGATAAGA
     |||   |||||| | |||   |||||  | ||| |    | | ||   | |  ||    |||    ||||   |    ||| || |||| ||||||||||||| ||| ||||||||||||| || |||||  |||||| |||||||||||||||||||||||||||||| |||| |||||||||||| ||| | |||||||
tgtcacatttgtgcaccagaactattatttgaac-ttaatacactactaaccat-acccaggaaaaataattgctgcta----acacctctatgttgacattttagGTGGAAAGTACAATTGAGTATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGTTGAAATTTCGAAGCTTCTAGATAAGA

upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G119671_T01 (Zea mays), 3'ss of exon 2
catggctgcaccgtacttgcatttgttcgttagtcttgttccaattgttat-gcactttaaaatcgtgctaaaataagacatctttatgctgacattttagGTTGAAGGTACAATTGAGTACATCTGTCGTCATGAAGGAGAAGGTGCAATCCTTGTGTTCCTTACTGGTTGGGATGAAATTTCGAAACTTTTGGATAAGA
  |  |      | ||| | | |  ||  ||   |||  | || |  | |    ||     ||   |  |        ||| || |||| ||||||||||||| ||| ||||||||||||| || |||||  |||||| |||||||||||||||||||||||||||||| ||||||||||||||||| ||| |||| ||||
tgtcacatttgtgcactagaact-attatttgaacttaatacactgctaaccatacccaggaaaaatagttgttgctaacacctctatgttgacattttagGTGGAAAGTACAATTGAGTATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA

upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G806292_T01 (Zea mays), 3'ss of exon 3
-----catggctgcaccgtacttgc-atttgttcgttagtcttgttccaattgttatgcactttaaaatcgtgctaaaataagacatctttatgctgacattttagGTTGAAGGTACAATTGAGTACATCTGTCGTCATGAAGGAGAAGGTGCAATCCTTGTGTTCCTTACTGGTTGGGATGAAATTTCGAAACTTTTGGATAAGA
     |||   ||||||  |  |   |||||  | ||| |    | | ||   | |  ||    |||    ||||   |    ||| || |||| ||||||||||||| ||| ||||||||||||| || ||||   |||||| ||||||||||||||||| |||||||| ||| ||||||||||||| ||| ||| |||| ||||
tgtcacatttgtgcaccaaaactattatttgaac-ttaatacactgctaaccat-acccaggaaaaatagttgctgcta----acacctctatgttgacattttagGTGGAAAGTACAATTGAGTATATTTGTCACTATGAAGCAGAAGGTGCAATCCTTGCGTTCCTTATTGGCTGGGATGAAATTTTGAAGCTTCTGGACAAGA

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|58692363|gb|CK081050.1|CK081050
EST:     CTAGGCAATCCCTTGAAGCTTGGTCGGCTACCGAACTAAATTTGAGCCTT                         GTTGAAGGTACAATTGAGTACATCTGTCGTCATGAAGGAGAAGGTGCAATC
genomic: CTAGGCAATCCCTTGAAGCTTGGTCGGCTACCGAACTAAATTTGAGCCTTgtatggactt ... gacattttagGTTGAAGGTACAATTGAGTACATCTGTCGTCATGAAGGAGAAGGTGCAATC
EST: gi|86877298|gb|CI311526.1|CI311526
EST:     CTAGGCAATCCCTTGAAGCTTGGTCGGCTACCGAACTAAATTTGAGCCTT                         GTTGAAGGTACAATTGAGTACATCTGTCGTCATGAAGGAGAAGGTGCAATC
genomic: CTAGGCAATCCCTTGAAGCTTGGTCGGCTACCGAACTAAATTTGAGCCTTgtatggactt ... gacattttagGTTGAAGGTACAATTGAGTACATCTGTCGTCATGAAGGAGAAGGTGCAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttatgcactttaaaatcgtgctaaaataagacatctttatgctgacattttagGTTGAAGGTACAATTGAGTACATCTGTCGTCATGAAGGAGAAGGTGCAATCCTTGTGTTCCTTACTGGTTGGGATGAAATTTCGAAACTTTTGGATAAGA
                                         tgctgac  putative branch site (score: 2)
        actttaaaat  TA-rich tract