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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgccaattctggtgtttagttggccttgcgagttgttcggaggtgcagaagtttgtaacattaaaactgatcacacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG

Basic information

species Oryza sativa
transcript LOC_Os01g14860.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G835235_T04 (Zea mays), 3'ss of exon 8
gttagtgccaattctggtgtttagttggccttgcgagttgttcggaggtgcagaagtttgtaacattaaaactgatcacacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG
    ||  ||||| |     || ||   |  |     || | |  ||    | |  ||  | ||| |  |  ||||    |||||||||||||||| || || |||||||| ||||||||||||||||| || || || || ||||| ||||| ||||| || ||||| |||||||||||||||
----gtatcaattttacaaatttgtaaactatc----ttctgcatagacataaattttgatcacacttgatttgattttgcatcgcagGTCCTTGGTACTCCAACAAGGGAAGAAATTAAATGCATGAACCCGAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCTCACCCATGGCACAAG

upper sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G129482_T01 (Zea mays), 3'ss of exon 3
----------------gttagtgccaattctggtgtttagttggccttgcgagttgttcggaggtgcagaagtttgtaacattaaaactgatcacacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG
                ||   |  ||||| |     || ||   |  |     || | |  ||    | |  ||  | ||  |  |  ||||    |||||||||||||||| || || |||||||| ||||||||||||||||| || || |  || ||||| ||||| ||||| || |||||||||||||||||||||
cgtagaaatcatcaaggtagttatcaattttacaaatttgtaaactatc----ttctgcatagacataaattttgatcacgcttgatttgattttgcatcgcagGTCCTTGGTACTCCAACAAGGGAAGAAATTAAATGCATGAACCCGAATTGCACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG

upper sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G835235_T02 (Zea mays), 3'ss of exon 8
gttagtgccaattctggtgtttagttggccttgcgagttgttcggaggtgcagaagtttgtaacattaaaactgatcacacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG----
    ||  ||||| |     || ||   |  |     || | |  ||    | |  ||  | ||| |  |  ||||    |||||||||||||||| || || |||||||| ||||||||||||||||| || || || || ||||| ||||| ||||| || ||||| |||||||||||||||    
----gtatcaattttacaaatttgtaaactatc----ttctgcatagacataaattttgatcacacttgatttgattttgcatcgcagGTCCTTGGTACTCCAACAAGGGAAGAAATTAAATGCATGAACCCGAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCTCACCCATGGCACAAGGTGT

upper sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 8
gttagtgccaattctggtgtttagttggccttgcgagttgttcggaggtgcagaagtttgtaacattaaaactgatcacacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG
|| | || |  ||||       || | |      |  || |   || |   | ||  |  | ||    ||| ||||     || ||||||||| || || || |||||||| ||||||||||||||||| ||||| || || ||||| ||||| ||||| || |||||||||||||||||||||
gtaattgtcggttcta----caagcttgtgaattgtcttctatagaagcataaaatctgatcacccctaaaatgattttgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG

upper sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------------------------------------------------------------------------gtt--agtgccaattctggtgtttagttggcct--tgcgagttgt----tcggaggtgcagaagtttgtaacattaa---aactgatcacacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG
                                                                                                |||  |  |      |||||  ||  | ||  |  ||  |||| |    |||   |    ||  | |   || |      |  ||       ||   ||||  | || ||||| ||| | ||||| || || ||||||||||| ||||| || |||||||||||||| || ||||| || || || |||||||||
gtagcttacatatggtagatgttgaggaagtgcaggggtctacagcagatgtcggtgctggtgtttgggttttgtccgtttgaaatgttgtgttgcgttgaaaggttgtagctggtacttgctcggtgtgatgttagttatgacttcgctagaatggatatgtaggacttatgggtagttgggtgttaatgttagGTGTTGGGGACACCCACACGCGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCATCCTTGGCACAAG

upper sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------gttagtgccaattctggtgtttagttggccttgcgagt-tgttcggaggtgcagaagtttgtaacattaaaactgatcacacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG
                                   | | | |    | || |    | ||     ||||| |  ||||  || |    | ||| | |   ||| |     |       | ||||||  | || ||||| ||  | ||||| || || ||||||||||| ||||| || |||||||||||||| || || || || |||||||||||||| 
gtagggcacaggcgatgcacggtgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggagtgttatgatgctgtggagtgtatgttattgaggaaaagt-tttgtggcagGTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA

upper sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------gttagtgccaattctggtgtttagttggccttgcgagt-tgttcggaggtgcagaagtttgta-acattaaaactgatcac--acatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG
                                   | | | |    | || |    | ||     ||||| |  ||||  || |    | ||| ||   |  |||     ||  ||     | ||||||  | |||||||| ||  | ||||| || || ||||||||||| ||||| || |||||||||||||| || || || || ||||| |||||||| 
gtagggcacaggcggtgcacggcgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggggtgttatgatgctgtggagtgtgagtatgttattgaggagtacttgtgtggcagGTGTTGGGAACACCGACTCGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCGTGGCACAAA

upper sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------gttagtgccaattctggtg-tttagtt---ggccttgcgagttgttcggaggtgcagaagtttgtaacattaa--aactgatcacacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG
                                     ||      |     ||| | ||| |||    ||  ||  |  |  |  | | || |   |  | |  | || |  |   | |  |   | ||||||  | || ||||| ||  | ||||| || || ||||||||||| ||||| || ||||||||||||||||| || || || ||||| |||||||| 
gtgggacacacgtggtacacgttgtttgtgtggaagggtcgccttctgggttggcggtttggtttgtagctgtggtatcttgttcgtgttggatgtgagtatggcgttgaccagacgtttccgtgtggcagGTTTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAA

upper sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------------------------------------------------------gttagtgccaattctggtgtttagttggccttgcgagttgttcggaggtgcagaagtttgtaac--atta--aaactgatcac-acatcg-cagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG
                                                                                                   |||||   |  || | |  ||  | |||  |||||       || | | |    | | |  | |  || |  |  | |||    |  | | |||||  | || ||||||||| | ||||| || || ||||||||||| ||||| || |||||||||||||| || ||||| || ||||| |||||||||
gtatgttatacatggtagagtggaagcatatggagctgaagtcgtttgtactgatgtttgatgtgtatcgattaaaagtattgtattatatttaaagatgttagctgctcttgttgc-ttcgggtggtgttgcggtgatagcgcaagagtgatactgtagagcttatgagtaggcggatggtgatgttgacagGTGTTAGGGACACCTACACGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCACCCGTGGCACAAG

upper sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 9
gttagtgccaattctggtgtttagttggccttgcgagttgttcggaggtgcagaagtttgtaacattaaaactgatcacacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG
||  |     ||||| |   ||  ||    ||  |  || || |   ||      | |  |    | || |||         | ||||||| | || || |||||  | |||||||| |||||||||||||||||||| || ||||| ||||| || ||||||||||| || || |||||||||
gtacgcatgcattcttgctctttttt----ttctgttttttttgcgagtc-----gctcttgc--tcaagacttgc----ttttgcagGTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

upper sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 9
gttagtgccaattctggtgtttagttggccttgcgagttgttcggaggtgcagaagtttgtaacattaaaactgatcacacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG
           | |   ||  |  |||  ||      || ||      |||       | |  |   | |  || |      | ||||||| | || || |||||  |||||||||| |||||||||||||||||||| || ||||| ||||| || ||||||||||| || || |||||||||
----------gtacgcatgcattcttgctctc-----ttttttctttttgcgagtcgctcttgctcaagacttgctt-----ttgcagGTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

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|33381492|gb|CF196835.1|CF196835
EST:     CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG                         GTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
genomic: CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAGgttagtgcca ... cacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
EST: gi|58686155|gb|CK074842.1|CK074842
EST:     CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG                         GTCCTNTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTA
genomic: CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAGgttagtgcca ... cacatcgcagGTCCT-TGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTA
EST: gi|58606572|gb|CK034605.1|CK034605
EST:     CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG                         GTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
genomic: CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAGgttagtgcca ... cacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
EST: gi|58687307|gb|CK075994.1|CK075994
EST:     CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG                         GTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
genomic: CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAGgttagtgcca ... cacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
EST: gi|58679602|gb|CK068289.1|CK068289
EST:     CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG                         GTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
genomic: CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAGgttagtgcca ... cacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
EST: gi|58590369|gb|CF988677.1|CF988677
EST:     CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG                         GTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
genomic: CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAGgttagtgcca ... cacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
EST: gi|218498670|gb|FG952679.1|FG952679
EST:     CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG                         GTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
genomic: CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAGgttagtgcca ... cacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
EST: gi|58602991|gb|CK013519.1|CK013519
EST:     CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG                         GTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
genomic: CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAGgttagtgcca ... cacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
EST: gi|58672614|gb|CK061300.1|CK061300
EST:     CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG                         GTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
genomic: CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAGgttagtgcca ... cacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
EST: gi|38469291|gb|CF953422.1|CF953422
EST:     CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG                         GTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
genomic: CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAGgttagtgcca ... cacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
EST: gi|29677190|gb|CB673465.1|CB673465
EST:     CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG                         GTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
genomic: CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAGgttagtgcca ... cacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
EST: gi|58679239|gb|CK067926.1|CK067926
EST:     CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG                         GTCCTTGGAACACCTACAAGGGAGGAAATTA
genomic: CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAGgttagtgcca ... cacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTA
EST: gi|29677191|gb|CB673466.1|CB673466
EST:     CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG                         GTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
genomic: CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAGgttagtgcca ... cacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
EST: gi|58682391|gb|CK071078.1|CK071078
EST:     CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG                         GTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
genomic: CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAGgttagtgcca ... cacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
EST: gi|66918477|gb|CX105325.1|CX105325
EST:     CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG                         GTCCTTGGAACACCTACAAGGGAGGAAATTGAAGATGCATGAATCCAAACT
genomic: CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAGgttagtgcca ... cacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATT-AA-ATGCATGAATCCAAACT
EST: gi|2317500|gb|C22554.1|C22554
EST:     CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAG                         GTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT
genomic: CTCTGTTTCCTGGTGAAAGTGGTGTAGACCAACTTGTGGAAATCATCAAGgttagtgcca ... cacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgagttgttcggaggtgcagaagtttgtaacattaaaactgatcacacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG
                       tttgtaacattaaaa  TA-rich tract