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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtactctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag

Basic information

species Oryza sativa
transcript LOC_Os08g02330.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G349794_T01 (Zea mays), 5'ss of exon 7
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtact-ctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag
|| || ||||| ||||| ||||||||||||||||| |||||||||||||||||||||| ||| || |||  |   ||  | || ||    || | ||| | ||||| ||||| |||| |    ||| || ||          
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGATGgtttggtacc-tgcactcatgctactaccattaggtattcattatg-tcatggttctgt----tttaatacacgcag-----

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G310936_T01 (Zea mays), 5'ss of exon 1
---------------------------------TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtact-ctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag
                                  | || ||||| ||||| ||||||||||||||||| ||| |||||||||||||||||||||| || |||  |    |  | || ||   | | ||||| | || || ||||| |||| |    ||| || ||          
ATGACATATATACTTATTTTCTGTGCTCTGCAGACTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACCGCACAAACATTGACAAGAAGgtttggtacc-tgcattcatgctactacctgtagttattcattctg-tcatggttctgt----tttaatacacgcag-----

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G132286_T01 (Zea mays), 5'ss of exon 5
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtactctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag
|| |||||||| || || |||||||| |||||||||||||||||||||||||||||||||||   ||||  |   ||  | || |     | | | | | || || ||||  |||| |   | |  ||||| ||| |||||
TCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGgttccctacc-tacactcatgctataccactaggtgttcattctg-tcattgttctgttttaatatatgcacttgctacag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G044246_T02 (Zea mays), 5'ss of exon 6
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtact-ctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag
|| || ||||| ||||| ||||||||||||||||| |||||||||||||| ||||||||||| || |||  |   ||  | || ||     | | ||| | || |  ||||| |||| |    ||| || ||          
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAGgtttggtacc-tgcactcatgctactaccactaggtattcattcta-tcatggttctgt----tttaatacacacag-----

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G166091_T01 (Zea mays), 5'ss of exon 8
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtact-ctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag
|| || ||||| ||||| ||||||||||| ||||| |||||||||||||||||||||||||| || |||  |   ||  | || ||     | | ||| | || || ||||| |||| |    ||| || ||          
TCTGACGATGAACGTGAAATGTGTGCAAGCACTATCTACTGCACAAACATTGACAAGAAGgtttggtacc-tgaactcatgctactaccactaggtattcattctg-tcatgattctgt----tttaatacacgcag-----

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G175541_T01 (Zea mays), 5'ss of exon 2
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAA----CATTGACAAGAAGgtatgctacaatttgcttgtact-ctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag----------------------------------------------------------------------------------
||  | ||||| | ||| ||||||||||||||||| |||||||||||    ||||||||||||||| || |||  |   ||  | || ||     | | ||| | || || ||||| || | |   | |  | |||  | |  ||                                                                                   
TCTAACGATGAACATGAAATGTGTGCAAGGACTATCTACTGCACAAATTAACATTGACAAGAAGGTTTGGTACC-TGCACTCATGCTACTACCACTAGgtattcattctg-tcatggttttgttttaatacacgcaggtcactcaagcagatctaaagttattctttgagtccatatgtggtgaggttggtcgttctttactccaaacacaatctcccttctgtatag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G123866_T01 (Zea mays), 5'ss of exon 11
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtact-ctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag
|| || ||||| ||||| ||||||||||||||||| |||||||||||||||||||||||||| || |||  |   ||  | || ||     | | ||| | || || ||||| |||| |    ||| || ||          
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGgtttggtacc-tgcactcatgctactaccactaggtattcattctg-tcatggttctgt----tttaatacacgcag-----

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G175541_T02 (Zea mays), 5'ss of exon 5
------------------------------------TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAA----CATTGACAAGAAGgtatgctacaatttgcttgtact-ctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag
                                    ||  | ||||| | ||| ||||||||||||||||| |||||||||||    ||||||||||||||| || |||  |   ||  | || ||     | | ||| | || || ||||| || | |    ||| || ||          
CTCTAAGAAAGTTGGTCGATTTTCTGTGCTCTACAGTCTAACGATGAACATGAAATGTGTGCAAGGACTATCTACTGCACAAATTAACATTGACAAGAAGgtttggtacc-tgcactcatgctactaccactaggtattcattctg-tcatggttttgt----tttaatacacgcag-----

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G454261_T01 (Zea mays), 5'ss of exon 2
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtact-ctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag
|| || ||||| ||||| ||||||||||||||||| |||||||||||||||||||||||||| || |||  |    |  | || ||     | |||||   || || ||||| |||| |    ||| || ||  |       
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGgtttggtacc-tgcattcatgctactaccactagttatttattgtg-tcatggttctgt----tttaatacacgtag-----

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G069102_T01 (Zea mays), 5'ss of exon 6
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtact-ctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag
|| || ||||| ||||| ||||||||||||||||| |||||||||||||||||||||||||| || |||  |   ||  | || ||     |   ||| | || || ||||| |||| |    ||| || ||          
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGgtttggtacc-tacactcatgctactaccactatgtattcattctg-tcatggttctgt----tttaatacacgcag-----

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G457231_T01 (Zea mays), 5'ss of exon 8
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtact-ctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag------------------------------------------------------------------------------------------------
|| || ||||| ||||| ||||||||||||||||| |||||||||||||||||||||||||| || |||  |   ||  | || ||     | | ||| | || || ||||| |||| |   | |  | | |  | |  ||                                                                                                 
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGGTTTGGTACC-TGCACTCATGCTACTACCACTAGgtattcattctg-tcatgattctattttaatacacgtaggtcactcaagcatatctaaacttattctttgagtcaatatgtggtgaggttggtcgttctttactccaaacacaatctcccttctgtacaactaaaagtttgcag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G376619_T01 (Zea mays), 5'ss of exon 7
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtact-ctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag
|| || ||||| ||||| ||||||||||||||||| |||| ||||||||||||||||||||| || |||  |   ||  | || ||    || | ||| | || || ||||| |||| |    ||| || ||          
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTACACAAACATTGACAAGAAGgtttggtacc-tgcactcatgctactaccattaggtattcattctg-tcatggttctgt----tttaatacacgcag-----

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G161649_T01 (Zea mays), 5'ss of exon 4
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtactctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag
|| |||||||| || || |||||||| |||||||||||||||||||||||||||||||||||   ||||  |   ||  | || |     | | | | | || || ||||  |||| |   | |  ||||| ||| | |||
TCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGgttccctacc-tacactcatgctataccactagctgttcattctg-tcattgttctgttttaatatatgcacttgctgcag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G044246_T01 (Zea mays), 5'ss of exon 2
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtact-ctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag----------------------------------------------------------------------------------
|| || ||||| ||||| ||||||||||||||||| |||||||||||||| ||||||||||| || |||  |   ||  | || ||     | | ||| | || |  ||||| |||| |   | |  |  ||  | |  ||                                                                                   
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAGGTTTGGTACC-TGCACTCATGCTACTACCACTAGgtattcattcta-tcatggttctgttttaatacacacaggtcactcaagcagatctaaagttattctttgagtccatatgtggtgaggttggtcgttctttactgcaaacacaatctcccttctgtatag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G398795_T01 (Zea mays), 5'ss of exon 8
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtact-ctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag
||  | ||||| | ||| ||||||||||||||||| |||||||||||||||||||||||||| || |||  |   ||  | || ||     | | ||| | ||||| ||||| || | |    ||| || |||         
TCTAACGATGAACATGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGgtttggtacc-tgcactcatgctactaccactaggtattcattatg-tcatggttttgt----tttaatacatgcag-----

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G324221_T03 (Zea mays), 5'ss of exon 7
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtact-ctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag
|| || |||||  |||| |||||||| |||||||| |||||||||||||||||||||||||| || |||  |   ||  | || ||     | | ||| | || || ||||| |||| |    ||| || ||          
TCTGACGATGAATGTGAAATGTGTGCTAGGACTATCTACTGCACAAACATTGACAAGAAGgtttggtacc-tacactcatgctactaccactaggtattcattctg-tcatggttctgt----tttaatacacgcag-----

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G014573_T01 (Zea mays), 5'ss of exon 4
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtact-ctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag
 | || ||||| ||||| |||||||||||||| || |||||||||||||||||||||||||| || |||  |   ||  | || ||    || | ||| | ||||| ||||| |||| |    ||| || ||          
CCTGACGATGAACGTGAAATGTGTGCAAGGACAATCTACTGCACAAACATTGACAAGAAGgtttggtacc-tgcactcatgctactaccattaggtattcattatg-tcatggttctat----tttaatacacgcag-----

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G036634_T01 (Zea mays), 5'ss of exon 15
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtactctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag
|| |||||||| || || |||||||| |||||||||||||||||||||||||||||||||||   ||||  |   ||  | || |     | | | | | || ||    |||||  ||   || | ||||| ||| | |||
TCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGgttccctacc-tacactcatgctataccactaggtgttcattctgtcattgttttgttttaatat-atgcacttgttgcag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G173428_T02 (Zea mays), 5'ss of exon 5
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtactctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag
|| |||||||| || || |||||||| |||||||||||||||||||||||||||||||||||   ||||  |   ||  | || |     | | | | | || || ||||  |||| |   | |  ||||| ||| | |||
TCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGgttccctacc-tacactcatgctataccactaggtgttcattctg-tcattgttctgttttaatatatgcacttgctgcag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA06G14030.1 (Glycine max), 5'ss of exon 8
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtactctgtt-tttcgttatcctttatgctcatgtttctttggcatttgatgcatt-tgatacag-----------------------------------------
|| || |||||  | ||||||||| |||| || ||||| |||||||| |||||||||||||||   ||  |||||    |    | |  | | | |       ||||||    || |||  | | || |    |  ||   ||                                         
TCTGAAGATGAAAGGGAGATGTGTTCAAGAACAATTTATTGCACAAATATTGACAAGAAGgtagtttagcatttgaccttttcttataatcttgctggaggaaatgctctgtattttttcacctctgttttgctacgactaagactcataattcttaaaatttccattcttgttccctctgcag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA02G35640.1 (Glycine max), 5'ss of exon 7
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtactctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag
|| || |||||  | ||||||||| |||| || ||||| |||||||| |||||||||||||||   | |  |     | |  |||    ||| || |  ||| || | |  |||  |||  |     ||            
TCTGAAGATGAAAGGGAGATGTGTTCAAGAACAATTTATTGCACAAATATTGACAAGAAGgtagttttccctccctctatcttct----ttcattttgatttttggttaatttttgttgttagggattgag----------

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA04G40760.1 (Glycine max), 5'ss of exon 8
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtactctgtt--tttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag------------------------------------------
|| || |||||  | ||||||||| |||| || ||||| |||||||| |||||||||||||||   ||  |||||    |  |||  |  | | | |       ||||||     | |||   || || |    |  |   |                                           
TCTGAAGATGAAAGGGAGATGTGTTCAAGAACAATTTATTGCACAAATATTGACAAGAAGgtagtttaggatttgacctttttcttataatcttgctggagaaaatgctctgtaatttttcatatctgttttgctacaattatgactcataattcttaaaatttgcattcttgttacctctgcag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G32790.2 (Arabidopsis thaliana), 5'ss of exon 6
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtactctgtttttcgttatcctttatgct-catgtttctttggcatttg---atgcatttgatacag
 | || ||||||||||||||||||||||| ||||| ||||| || ||||| |||||||||||   ||    |       | ||||    ||     | ||| |||    || |  ||||  || |||   ||  |||   || ||
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAGgtg-actctcttgaatcatttctcttaacttaaccgtacttgatgaagtatctccctttcacacttgtgtataaattgcttatag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G49390.2 (Arabidopsis thaliana), 5'ss of exon 7
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtactctgtttttcgtta----tcctttatgctcatgtttctttggcatttgatgcatttgatacag------------------------------------
|| || ||||||||||||||||| |  |||||| ||||||| || ||||||||||||  ||||   | |||||| | |  ||  | |  ||  | |    |  | | |  |         ||  |   | | | ||| || | |                                     
TCTGAGGATGAGCGTGAGATGTGCGTTAGGACTGTTTACTGTACCAACATTGACAAGCGGgta--attcaattttcattcaccatttccttgatgagaatttatctgtttttggaaactgttaactgctaaagtattggagatactaactttcttcaatgtccttttgcttatattttcag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT4G10610.1 (Arabidopsis thaliana), 5'ss of exon 6
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgta-----tgctacaatttgcttgtactctgtttttcgttatcctttatgctcatgtttct---ttggcatttgatgcatttgata-cag
 | || ||||||||||||||||||||||| ||||| |||||||| |||||||||||||||||        ||  |||    | ||   || |       ||| ||  |   | ||||| ||   || || || | | || ||   | |||
ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAGgtgactctcactcgaataaattggtttcctttgccaaactattctgaaacttaatgttgctaactttgc-ttagtttcacttttcaacag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv02s0025g02740.t01 (Vitis vinifera), 5'ss of exon 7
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca-atttgcttgtactc--tgtttttcgttat---------------cctttatgctcatgtttctttggcatttgatgcatttgatacag
   || ||||| || |||||||||||||| || |||||||| ||||| ||||| |||||||||   |  |  |||  || || |   |||  | || | |                 ||| |  |||  |   | | | ||||| |   ||| || |||
AATGAAGATGAACGCGAGATGTGTGCAAGAACAATTTACTGTACAAATATTGATAAGAAGgtactttttatgtttctttatattgaatgtgctccggtgtaggactaggaaacactttttcttttcaaatcaatgttgtatttg-tttgtttaatgcag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgt-actctgtttttcgtt---atcctttatgctcatgtttctttggcatttg---atgcatttgatacag
|| || ||||| ||||| ||||| || |||||||||||||| ||||| ||||| ||||||||||     ||| | ||||| |||     | | |||   | |  | ||    |  | | | |   ||||     |  ||||||| |||
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttgtcacttctagtgtggttgagagcactaattggaaaatctgtatctgatttacttgtttatttgatgcag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S62_224V6.1 (Physcomitrella patens), 5'ss of exon 6
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgct----------acaatttgcttgtactctgtttttcgt------tatcctttatgct-catgtttctttggcatttgatgcatttgatacag--
|| || ||||||||||| ||||||||| |||| || ||||| ||||| ||||||||||||||    |          | |||||  |||| || || |     |       |||| || | || | || || ||||  ||  | |||  ||      |  
TCTGAAGATGAGCGTGAAATGTGTGCACGGACCATCTACTGTACAAATATTGACAAGAAGgtgaagtggagtgaaatagaatttcgttgttctatgctgacgatgagatccatccgttttactgcctgcttttttgcgataagttgctcttctctttgtg

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:     AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
EST: gi|87029144|gb|CI276412.1|CI276412
EST:     AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
EST: gi|86495223|gb|CI137856.1|CI137856
EST:     AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
EST: gi|86849377|gb|CI297825.1|CI297825
EST:     AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
EST: gi|29646834|gb|CB651841.1|CB651841
EST:     AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
EST: gi|29643786|gb|CB648793.1|CB648793
EST:     AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
EST: gi|29646833|gb|CB651840.1|CB651840
EST:     AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
EST: gi|86859325|gb|CI278774.1|CI278774
EST:     AGCGT-AGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
EST: gi|218493611|gb|FG968673.1|FG968673
EST:     AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
EST: gi|86495871|gb|CI138504.1|CI138504
EST:     AGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG                         GTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG
genomic: AGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG

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: 75 (upstream exon), 72 (downstream exon)
Score: 82

TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctaca ... tttgatacagGTCTCTCAGGCAGATGTGAAATTGTTCTTCGAGTCGATATGTGGAGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgtactctgtttttcgttatcctttatgctcatgtttctttggcatttgatgcatttgatacag

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