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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG

Basic information

species Oryza sativa
transcript LOC_Os08g02330.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G457231_T01 (Zea mays), 3'ss of exon 7
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaa-aagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG---------------------------------
||| ||  |   | || ||   |  |  |||  | || |||||              ||||||   || ||||   |   | |  |  || | ||||| ||  | |  |   ||  |||   |||||||| || ||||| ||||| ||||||||||||||||| ||||||||||||||||||||||||                                 
gtatgcaaaccttccagaaccaacatgcttgtcttaagttcatggc-----------tcaatg---ttcatgc---tctatttg-atatggtctctaagaaaattggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGGTTTGGTACCTGCACTCATGCTACTACCACTAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G173428_T02 (Zea mays), 3'ss of exon 4
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
          | ||||   |||| | ||   ||||    |  |  | | ||| ||   ||| |   || || |   ||  ||   |    || |  ||||| | |||    ||  |||   |||||||| |||||||| || || |||||||| |||||||||||||||||||||||||||||||||
---------gtatgcaaccttcaggaatcaacata---cttgtgttaagttcatagcccaagg---ttcattcttgtatctg-gtatggtatttaaaaaagtttgccatt-tttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G123866_T01 (Zea mays), 3'ss of exon 10
gtaagctgaatctgcacaattcatgtatttgcataa-atttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
                    |||   ||  |  ||| || ||  |||  |  | | ||||| |     |||  |    |  ||     || |      |||| ||| |    ||  |||   ||| |||| || ||||| ||||| ||||||||||||||||| ||||||||||||||||||||||||
--------------------tcactgatgagggtaatatatccatatccaaccatgtttcagtttg-cttactctctgatatg-gtctctaa-----gaaagttggtcgat-tttctgtgctctgtagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G132286_T01 (Zea mays), 3'ss of exon 4
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtg-tacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
          | ||||   |||| | ||   ||||   ||  || | | ||| |   |||| |   || ||||   |   || ||  |    |    ||||| | |||    ||  |||   |||||||| |||||||| || || |||||||| |||||||||||||||||||||||||||||||||
---------gtatgcaaccttcaggaatcaacata--ctttgttttaagttcatggctcaagg---ttcatgcttgtttctggtatgctctttaaaaaaaagtttgccatt-tttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G349794_T01 (Zea mays), 3'ss of exon 6
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaa--aagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
            |   ||| || | ||    ||  |      |  | | ||| |   ||||||   || ||||   |   | |  |  || | |||||  ||| ||| |    ||  |||   || ||||| || ||||| ||||| ||||||||||||||||| |||||||||||||||||||||| |
-----------gtatgcaaatcttctagaaccaacatgcatgtcttaagttcatggctcaatg---ttcatgc---tctatctg-atatggtctctaagaaagttggtcgat-tttctgtgctctccagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGATG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G398795_T01 (Zea mays), 3'ss of exon 7
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaa--aagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
          | |||| |  |  || |    ||  |   |  |  | | ||| |   ||||||   || ||||   |   | |  |  || | |||||  ||| ||| |    ||  |||   || |||||  | ||||| | ||| ||||||||||||||||| ||||||||||||||||||||||||
---------gtatgcaaaccttctggaac--caacatgcttgtcttaagttcatggctcaatg---ttcatgc---tctatctg-atatggtctctaagaaagttggtcgat-tttctgtgctctacagTCTAACGATGAACATGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G036634_T01 (Zea mays), 3'ss of exon 14
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattctt--gttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
          | ||||   |||| | ||   ||||   ||  || | | ||| |   |||| |   || ||||   |   ||      || | | |||||   |    ||||| ||  ||   |||||||| |||||||| || || |||||||| |||||||||||||||||||||||||||||||||
---------gtatgcaaccttcaggaatcaacata--ctttgttttaagttcatggctcaagg---ttcatgcttgtttctg---gtatgctctttaaaaaaagtttgccatttttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G161649_T01 (Zea mays), 3'ss of exon 3
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtg-tacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
          | ||||   |||| | ||   ||||   ||  || | | ||| |   |||| |   || ||||   |   || ||  |    |    | |   ||||     ||  |||   |||||||| |||||||| || || |||||||| |||||||||||||||||||||||||||||||||
---------gtatgcaaccttcaggaatcaacata--ctttgttttaagttcatggctcaagg---ttcatgcttgtttctggtatgctctttaaaaagagtttggcatt--tttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G166091_T01 (Zea mays), 3'ss of exon 7
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaa--aagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
||| ||  |   | |  || | |  |  |||  | || ||||||             ||||||   || ||||   |   | |  |  || | |||||  ||| ||| |    ||  |||   |||||||| || ||||| ||||| ||||||||||| ||||| ||||||||||||||||||||||||
gtatgcaaaccttccggaactaacatgcttgtcttaagttcattgc-----------tcaatg---ttcatgc---tctatctg-atatggtctctaagaaagttggtcgat-tttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGCACTATCTACTGCACAAACATTGACAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G376619_T01 (Zea mays), 3'ss of exon 6
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaa--aagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
                                                                                           | |||||  ||| |||||    ||  |||   ||| |||| || ||||| ||||| ||||||||||||||||| |||| |||||||||||||||||||
------------------------------------------------------------------------------------------gtatctaagaaagttggccgat-tttctgtgctctgtagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTACACAAACATTGACAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G175541_T01 (Zea mays), 3'ss of exon 1
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaa--aagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAA----CATTGACAAGAAG---------------------------------
||| ||  |   | |  ||   |  |  |||  | || |||||              ||||||   || ||||   |   | |  |  || | |||||  ||| ||| |    ||  |||   || |||||  | ||||| | ||| ||||||||||||||||| |||||||||||    |||||||||||||                                 
gtatgcaaacctttcggaaccaacatgcttgtcttaagttcatggc-----------tcaatg---ttcatgc---tctatatg-atatggtctctaagaaagttggtcgat-tttctgtgctctacagTCTAACGATGAACATGAAATGTGTGCAAGGACTATCTACTGCACAAATTAACATTGACAAGAAGGTTTGGTACCTGCACTCATGCTACTACCACTAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G454261_T01 (Zea mays), 3'ss of exon 1
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
                          |  | |      | |  | ||  | ||  ||  ||   |  |  |     |  || | |   |  |   ||| |  |   |    ||  |||   |||||||| || ||||| ||||| ||||||||||||||||| ||||||||||||||||||||||||
--------------------------acatactattgctaccctgtttctgctgtttcaaactgagatactaaggttgtgt-tgccaatcctacataacatatatacttattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G173428_T04 (Zea mays), 3'ss of exon 5
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG----------------------------------------
          | ||||   |||| | ||   ||||    |  |  | | ||| ||   ||| |   || || |   ||  ||   |    || |  ||||| | |||    ||  |||   |||||||| |||||||| || || |||||||| |||||||||||||||||||||||||||||||||                                        
---------gtatgcaaccttcaggaatcaacata---cttgtgttaagttcatagcccaagg---ttcattcttgtatctg-gtatggtatttaaaaaagtttgccatt-tttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGGTTCCCTACCTACACTCATGCTATACCACTAGGTGTTCAT

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G044246_T02 (Zea mays), 3'ss of exon 5
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaa--aagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
||| ||  |   | |  ||   |  |  |||  | || |||||              ||||||   || ||||   |   | |  |  || | |||||  ||| ||| |    ||  |||   |||||||| || ||||| ||||| ||||||||||||||||| |||||||||||||| |||||||||
gtatgcaaaccttccggaaccaacatgcttgtcttaagttcatggc-----------tcaatg---ttcatgc---tctatctg-atatggtctctaagaaagttggtcgat-tttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G014573_T01 (Zea mays), 3'ss of exon 3
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaa--aagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
          | |||| |  |  || |    ||  |   |  |  | | ||| |   ||||||   || ||||   |   | |  |  || | |||||  ||| ||| |    ||  |||   || ||| | || ||||| ||||| |||||||||||||| || ||||||||||||||||||||||||
---------gtatgcaaaccttctggaac--caacatgcttgtcttaagttcatggctcaatg---ttcatgc---tctatctg-atatggtctctaagaaagttggtcgat-tttctgtgctctccagCCTGACGATGAACGTGAAATGTGTGCAAGGACAATCTACTGCACAAACATTGACAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G324221_T03 (Zea mays), 3'ss of exon 6
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaa--aagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
                   |||    |    |||     |  |  | | ||| |   ||||||   || ||||   |   | |  |  || | |||||  ||| |||      ||  |||   |||||||| || |||||  |||| |||||||| |||||||| ||||||||||||||||||||||||
------------------cttccgaaaccaacatg---cttgtcttaagttcatggctcaatg---ttcatgc---tctatctg-atatggtttctaagaaagttggttgat-tttctgtgctctgcagTCTGACGATGAATGTGAAATGTGTGCTAGGACTATCTACTGCACAAACATTGACAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G044246_T01 (Zea mays), 3'ss of exon 1
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaa--aagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG---------------------------------
||| ||  |   | |  ||   |  |  |||  | || |||||              ||||||   || ||||   |   | |  |  || | |||||  ||| ||| |    ||  |||   |||||||| || ||||| ||||| ||||||||||||||||| |||||||||||||| |||||||||                                 
gtatgcaaaccttccggaaccaacatgcttgtcttaagttcatggc-----------tcaatg---ttcatgc---tctatctg-atatggtctctaagaaagttggtcgat-tttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAGGTTTGGTACCTGCACTCATGCTACTACCACTAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G069102_T03 (Zea mays), 3'ss of exon 4
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaa--aagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
                   |||  | |    |||     |  |  | | ||| |   ||||||   || ||||   |   | |  |  || | |||||  |||||||      ||  |||   |||||||| || ||||| ||||| ||||||||||||||||| ||||||||||||||||||||||||
------------------cttccggaaccgacatg---cttgtcttaagttcatggctcaatg---ttcatgc---tctatctg-atatggtctctaagaaagctggttgtt-tttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G069102_T01 (Zea mays), 3'ss of exon 5
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaa--aagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
          | |||| |  |   | |   | | |   ||  |  | | ||| |   ||||||   || ||||   |   | |  |  || | |||||  |||||||      ||  |||   |||||||| || ||||| ||||| ||||||||||||||||| ||||||||||||||||||||||||
---------gtatgcaaaccttccggaaccg-acatgctt-gtcttaagttcatggctcaatg---ttcatgc---tctatctg-atatggtctctaagaaagctggttgtt-tttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA04G40760.1 (Glycine max), 3'ss of exon 7
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtg----tacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
                    | |||| | | | |   | | |   ||   | |||  |  |  | ||| |    | ||  ||    | || ||  | | |   | ||  |      |  | |      ||||| || |||||  | ||||||||| |||| || ||||| |||||||| ||||||||||||
-------------------gtaatgtttcttctt---tgttagagttgcctattacatttagaagattgaccagagtagctgataatgcatctattttgtctgacctatctaatggtgctatatttctcagTCTGAAGATGAAAGGGAGATGTGTTCAAGAACAATTTATTGCACAAATATTGACAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA06G14030.2 (Glycine max), 3'ss of exon 7
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
                 |||   | |  ||   || | ||   |||||  | | |          |     | |  |     | || ||  |   |   | ||  |   |  |  | |      ||||| || |||||  | ||||||||| |||| || ||||| |||||||| ||||||||||||
---------------gtaatgtttcttctttgttagagttgcctattacatttaaaagatgattgaccagagtagctgataatgcatctctttggtctgacctatctaacggtgctatatttctcagTCTGAAGATGAAAGGGAGATGTGTTCAAGAACAATTTATTGCACAAATATTGACAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G35640.1 (Glycine max), 3'ss of exon 6
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
                   ||  | | ||||  || | ||   |||||  | | |          | |   | |  |     | || ||  |   |   | ||  |      |  | |      ||||| || |||||  | ||||||||| |||| || ||||| |||||||| ||||||||||||
------------------gtttct-tctttgt-tagagttgcctattacatttaaaagatgattgactagagtagctgataatgcatctctttggtctgacctatctaatggtgctatatttctcagTCTGAAGATGAAAGGGAGATGTGTTCAAGAACAATTTATTGCACAAATATTGACAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G49390.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
                       |   ||  ||| |   | ||   |||   |      |||  ||||| |  || ||   | |  | ||| |  |||  |   || | | ||||  |       |||| || ||||||||||||||||| |  |||||| ||||||| || ||||||||||||  |
----------------------gtaagttcacatga---taatggctaaacttggcactaat--aatttttataagtataagcattcttga-gcataatggt--gctctctttctcct-------agTCTGAGGATGAGCGTGAGATGTGCGTTAGGACTGTTTACTGTACCAACATTGACAAGCGG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
                                             | |  | ||  |  |        ||||||||       |    |   | || |            | ||||||    ||||| | || ||||||||||||||||||||||| ||||| ||||| || ||||| |||||||||
--------------------------------------------gtgagattttcctcta-------ctatgcaaagtttctgatggttagcgactgaggaaaatgatttagtcttgtc-tatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT4G10610.2 (Arabidopsis thaliana), 3'ss of exon 5
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgt---tgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
                                 |||  ||  || ||   | | ||  || |   | |   |||||    ||      |    || | | | | |     | || |||   ||     || | || ||||||||||||||||||||||| ||||| |||||||| |||||||||||||||
--------------------------------gtaaggttttttcttgtgtttcatcacattctgact---gcaaagttatggttttttagactcaagaggtttgattttagtcctgtctttgttcttagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv02s0025g02740.t01 (Vitis vinifera), 3'ss of exon 6
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
            ||   || |     |||   ||   ||||||| |  |   ||     | || | |||  |  ||    |   | ||| ||  |   | | |||  |       | | | || |||   || ||||| || |||||||||||||| || |||||||| ||||| ||||| ||||||
-----------gtgagaaactttgccattatgatcgttttcattttccaaaatttgaaaattggagttttggtgaagt--ttctctcctaataacatgatgttggtac-------tttggacttcagAATGAAGATGAACGCGAGATGTGTGCAAGAACAATTTACTGTACAAATATTGATAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
                     |||||   |||   ||    ||   ||   ||||      ||    | |  ||        ||   ||  ||  |   |  |        || | ||  | | ||||| || ||||| ||||| ||||| || |||||||||||||| ||||| ||||| ||||||
--------------------acatgttggtgctagaa----atgggtatagcttagaaacgtgccgatcaaacattgtttactatttcttgtgcttgttaattaaat---gttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S62_224V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatt-tatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
                        | | |||  | |   |    |   ||| ||| |   |||  ||  |     |||||| |  |   |||  |||          |    ||  | |    | ||||| || ||||||||||| ||||||||| |||| || ||||| ||||| ||||||||||||
------------------------ggaattgtttcatacttgcaac-gattgttagtgatatgccatagttcttgaatacg-gctcggatgaattctggc--tctaacttagttactctccattacagTCTGAAGATGAGCGTGAAATGTGTGCACGGACCATCTACTGTACAAATATTGACAAGAAG

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|86899176|gb|CI298078.1|CI298078
EST:     TGCCATCAAAAACTGCGATTGCACCTGTTAACCCAACATTTCTGCCCAGG                         TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATT
genomic: TGCCATCAAAAACTGCGATTGCACCTGTTAACCCAACATTTCTGCCCAGGgtaagctgaa ... ttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATT
EST: gi|86495223|gb|CI137856.1|CI137856
EST:     CCATCAAAAACTGCGATTGCACCTGTTAACCCAACATTTCTGCCCAGG                         TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATT
genomic: CCATCAAAAACTGCGATTGCACCTGTTAACCCAACATTTCTGCCCAGGgtaagctgaa ... ttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATT
EST: gi|86849377|gb|CI297825.1|CI297825
EST:     TGCGATTGCACCTGTTAACCCAACATTTCTGCCCAGG                         TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATT
genomic: TGCGATTGCACCTGTTAACCCAACATTTCTGCCCAGGgtaagctgaa ... ttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATT
EST: gi|29646834|gb|CB651841.1|CB651841
EST:     TGCCATCAAAAACTGCGATTGCACCTGTTAACCCAACATTTCTGCCCAGG                         TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATT
genomic: TGCCATCAAAAACTGCGATTGCACCTGTTAACCCAACATTTCTGCCCAGGgtaagctgaa ... ttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATT
EST: gi|29643786|gb|CB648793.1|CB648793
EST:     TGCCATCAAAAACTGCGATTGCACCTGTTAACCCAACATTTCTGCCCAGG                         TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATT
genomic: TGCCATCAAAAACTGCGATTGCACCTGTTAACCCAACATTTCTGCCCAGGgtaagctgaa ... ttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATT
EST: gi|29646833|gb|CB651840.1|CB651840
EST:     TGCCATCAAAAACTGCGATTGCACCTGTTAACCCAACATTTCTGCCCAGG                         TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATT
genomic: TGCCATCAAAAACTGCGATTGCACCTGTTAACCCAACATTTCTGCCCAGGgtaagctgaa ... ttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATT
EST: gi|86859325|gb|CI278774.1|CI278774
EST:     TGCCATCAAAAACTGCGATTGCACCTGTTAACCCAACATTTCTGCCCAGG                         TCCGATGATGAGCGT-AGATGTGTGCAAGGACTATTTACTGCACAAACATT
genomic: TGCCATCAAAAACTGCGATTGCACCTGTTAACCCAACATTTCTGCCCAGGgtaagctgaa ... ttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATT
EST: gi|218493611|gb|FG968673.1|FG968673
EST:     TGCCATCAAAAACTGCGATTGCACCTGTTAACCCAACATTTCTGCCCAGG                         TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATT
genomic: TGCCATCAAAAACTGCGATTGCACCTGTTAACCCAACATTTCTGCCCAGGgtaagctgaa ... ttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 60 (upstream exon), 75 (downstream exon)
Score: 82

TGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAACATTTCTGCCCAGGgtaagctgaa ... ttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
                    gtctaaa  putative branch site (score: 82)
                                 cccccattcttgtt  putative PPT
                     tctaaaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG