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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAGgtaagtaaagccttgttatctaattgtctttattgaccatctgacacctttttagaacaccatgctctgatgtgagtgaatattagactattagagtatacttatctgccactagatctcaagactactagctatgtatcag

Basic information

species Arabidopsis thaliana
transcript AT3G54840.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 3
TTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAGgtaagtaaagccttgttatctaattgtctttattgaccatctgacacctttttagaacaccatgctctgatgtgagtgaatattagactattagagtatacttatctgc-cactagatctcaagactactagctatgtatcag
|| ||  |  | || ||||||||||| || |||||||| ||||| ||||| ||||| ||||||||||||||  | || || ||||| | ||  |  |||   |||  | || |   ||||  || | |  | |      |    |||| |    |        |  || || | ||    || |||||| | | ||    || |||                     
TTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattactgttttga-gtctcttagtttcagttgataatgttattcttcaccttagatgcatgattct-tactttcagaagttcgattgttt---taaacttatttcctcaaataatttcag--------------------

upper sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os10g30520.1 (Oryza sativa), 5'ss of exon 3
TTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAGgt-aagtaaagccttg-ttatctaat-tgtctttattgaccatctgacacctttttagaacaccatgctctgatgtgagtgaatattagactattagagtatacttatctgccactagatctcaagactactagctatgtatcag
|| ||  |  | ||||| || |||||||| |||||||| ||||| ||||| ||||| ||||||||||||||| | || || ||||| ||  | |  |||| |||| |  |     |||  ||  ||   |||||    || ||    |   || | || ||  |   ||||  | | |    || |  |||  ||    |||                           
TTGGTATTGCTTGGAGATTCAGGTGTTGGGAAAAGTTGCATTGTTCTTCGCTTTGTCCGTGGTCAGTTTGACCCCACTTCAAAGgtgaaacagacacttgattattttttacaggtttcctgtacagaggacacaccatttgattctcc--ctataatatggct---tattctattctgtttgttttattaaatgaatttag---------------------------

upper sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 4
TTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAGgtaagtaaagccttgttatctaattgtct--ttattgaccatctgacacctttttagaaca---ccatgctctgatgtgagtgaatattagactattagagtatacttatctgccactagatctcaagactactagctatgtatcag
|| ||  |  | |||||||| |||||||| |||||||| ||||| ||||| ||||| ||||||||||||||  |||| || ||||| | | |    || | |||  || | |   | | |||  |  | ||      ||  | ||   |||| | |  |  |   |   | | | |   ||| ||                                              
TTGGTATTGCTGGGAGACTCAGGTGTTGGGAAAAGTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttactgttt-tgatcagatcgacccatgaatgaa-actttactttcggttgcagcatttccattccccaacttatct---tctcaaatggttacag----------------------------------------------

upper sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G35230.3 (Glycine max), 5'ss of exon 3
TTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAGgtaagtaaagccttgttatctaattgtctt-tattgaccatctgacacctttttagaacaccatgctctgatgtgagtgaatattagactattagagtat-acttatctgcc--actagatctcaagactactag-ctatgtatcag---
 | ||||| ||||| || ||||||||||||||||| |||||||| || |||||||| ||||||||||||||  | ||||||||||||| || |    |||||| || |  | || | || |   | | |     ||||     |  ||  | |      |   ||||||    | ||    | | | ||||       | | | ||| |    |  ||| || ||||       
CTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatata----tgttatttagtacttttatttttattttttaatgtaattttttt-taatatagtttatgacaaaaaaatattgtcgtcttgatatgttaattattccatggaattgttcttatatgttttagactttgtaatgtaag

upper sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 3
TTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAGgtaagtaaagccttgttatctaattgtctttattg-accatctgacac--ctttttagaacaccatgctctgatgtgagtgaatattagactattagagtatacttatctgccactagat-ctcaagactactag-ctatgtatcag---
 | ||||| ||||| || ||||||||||| ||||| |||||||| || |||||||| ||||||||||||||  | ||||||||||||| || |    ||||   |   |   ||||||  |   | | | |    ||||   || |   |  | |||| | | |   | || | || ||   ||  | |  ||       |  | || |    |  ||| || ||||       
CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatata----tgttgcttcggtacttttattttattttttaatataatttttcttaatatggt-ttatgatataaat---tttttgtctttttatgttaattattccatggaaattttcttatatgttttagactctgtaatgtaag

upper sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 3
TTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAGgtaagtaaag--ccttgttatctaattgtctttattgaccatctgacacctttttagaacaccatgctctgatgtgagtgaatattagactattagagtatacttatctgccactagatctcaagactactagctatgtatcag---------------------------------------
 | ||| | || || || ||||||||||| ||||| |||||||| ||||| ||||| ||||| ||||||||| ||||||| |||||||| ||    | | | ||| || |      |    |   | |    || |||||  | |  |   |||| |   |     | ||   | | | || | |    |||   |     ||   ||    |       | | |||                                        
CTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGTTTTGTTCGTGGCCAGTTTGACCCTACATCCAAGgtaagaaatatacatagctatatattatgtgatgcacattttttttttcccttttattatattaaattctgtt-caaccttgttttgtgccaatgga-tgttagcatcaatcctctcatgcaaaatacatggatgttatttcatgatagatttacttagattggttgatcttaataacttcag

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|164114252|gb|ES140566.1|ES140566
EST:     CCTTCGATTTGTACGTGGTCAGTTTGACGCAACATCTTAAG                         GTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTC
genomic: CCTTCGATTTGTACGTGGTCAGTTTGACGCTACATC-TAAGgtaagtaaag ... tatgtatcagGTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTC
EST: gi|124794348|gb|EH884027.1|EH884027
EST:     TACGTGGTCAGTTTGACGCTACATCTAAG                         GTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCT
genomic: TACGTGGTCAGTTTGACGCTACATCTAAGgtaagtaaag ... tatgtatcagGTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCT
EST: gi|19875441|gb|AU236272.1|AU236272
EST:     GTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG                         GTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCT
genomic: GTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAGgtaagtaaag ... tatgtatcagGTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCT