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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaatcttatgatgagaactttgtaatatgttaaccaatgatacaaaaggatcgtatctgacacttaaaatcatttattgcagATTTTCAATGGTGTGTTCTTGAAGGTCAACAAGGCAACCATTAACATGCTTCGCCGTGTTGAACCCTATGTAACCTATGG

Basic information

species Arabidopsis thaliana
transcript AT3G13580.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 3
----gtaacaatcttatgatgagaactttgtaatatgtt-aaccaatgatacaaaaggatcgtatctgacacttaaaatcatttattgcagATTTTCAATGGTGTGTTCTTGAAGGTCAACAAGGCAACCATTAACATGCTTCGCCGTGTTGAACCCTATGTAACCTATGG
    ||     | | |  || |      || |   |||| ||   |||||| |  |   ||  ||     |   ||  | | || |||||||| || ||||| |||||||||||||||||||| || |||||||||||||| ||| | ||||| || |||||  | |||||
gtgggtgtggttttcacaatcatttgaatgca-cgtgttgaaattatgatatagtactgtca-attgaggaaaaaatgttaatt-ttgcagATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG

upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 3'ss of exon 4
gtaacaatcttatgatgagaactttgtaatatgttaaccaatg-atacaaaaggatcgtatctgacacttaaaatcatttat--tgcagATTTTCAATGGTGTGTTCTTGAAGGTCAACAAGGCAACCATTAACATGCTTCGCCGTGTTGAACCCTATGTAACCTATGG
||     | | |    |    ||| | |||  || |||   ||  |||    |  |  || ||      | || |  || ||  | ||||| ||||||||||| ||| | ||||| ||||||||||||||||||||||| ||| | ||||| || |||||  | |||||
gttggtttatgaaccagttttcttagaaatgcgtgaactcttgcgtacgctggtgtattaactttgtgcttaattgtttgattctacagATCTTCAATGGTGTCTTCCTCAAGGTTAACAAGGCAACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG

upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 4
gtaacaatcttatgatgagaactttgtaatatgttaaccaatgatacaaaaggatcgtatctgacacttaaaatcatttattgcagATTTTCAATGGTGTGTTCTTGAAGGTCAACAAGGCAACCATTAACATGCTTCGCCGTGTTGAACCCTATGTAACCTATGG
       | |    || |     |||  ||    | |     |||       ||    |   |||| ||||  | |||| |  ||||| |||||||| |||||| |||| ||||||||||| |||||||||||||||||| | ||||| || |||||  | |||||
--gtgggtttgccaattacgttcttgctattgaattatggccgattgtttgtgaa---actggacatttaatttaattttt--cagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG

upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G094051_T06 (Zea mays), 3'ss of exon 4
-----gtaacaatcttatgatgagaactttgtaatatgttaaccaatgatacaaaaggatcgtatctgacacttaaaatc-atttattgcagATTTTCAATGGTGTGTTCTTGAAGGTCAACAAGGCAACCATTAACATGCTTCGCCGTGTTGAACCCTATGTAACCTATGG--------------------
      | ||     | || |   |   ||| | |      |  | | ||       ||| || | | | ||| || ||   ||||||  |||| ||||||||||||||| | || ||||||||||| || ||||||||||| ||| | ||||| || |||||  | |||||                    
gtgtgttcactgatgtctgtttttacaattgcattgctgctatta-taattttgtctgattgtttgtaaaactgaacatttgtttattttagATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTACGCAGGGTTGAGCCATATGTTGCATATGGGTAAGTTTTCTAGCTGATTT

upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G094051_T03 (Zea mays), 3'ss of exon 4
-----gtaacaatcttatgatgagaactttgtaatatgttaaccaatgatacaaaaggatcgtatctgacacttaaaatc-atttattgcagATTTTCAATGGTGTGTTCTTGAAGGTCAACAAGGCAACCATTAACATGCTTCGCCGTGTTGAACCCTATGTAACCTATGG
      | ||     | || |   |   ||| | |      |  | | ||       ||| || | | | ||| || ||   ||||||  |||| ||||||||||||||| | || ||||||||||| || ||||||||||| ||| | ||||| || |||||  | |||||
gtgtgttcactgatgtctgtttttacaattgcattgctgctatta-taattttgtctgattgtttgtaaaactgaacatttgtttattttagATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTACGCAGGGTTGAGCCATATGTTGCATATGG

upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ20182 (Selaginella moellendorffii), 3'ss of exon 3
gtaacaatcttatgatgagaactttgtaatatgttaaccaatgatacaaaaggatcgtatctgacacttaaaatcatt-tattgcagATTTTCAATGGTGTGTTCTTGAAGGTCAACAAGGCAACCATTAACATGCTTCGCCGTGTTGAACCCTATGTAACCTATGG
               | |   | |||| | | | |   | ||  |  ||   | ||   ||||||  | |   || || | ||  |||| |||||||| |||||| ||||||| |||||||||||||| ||||||||     | || || || || || || || ||
--------------gtaaattccttgtga-aagctg--cgattgtgaaacgagttc---tctgactatcacgttctttcttttatagATCTTCAATGGGGTGTTCATGAAGGTGAACAAGGCAACCATGAACATGCTCAAGAGAGTCGAGCCGTACGTGACTTACGG

upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ23123 (Selaginella moellendorffii), 3'ss of exon 3
gtaacaatcttatgatgagaactttgtaatatgttaaccaatgatacaaaaggatcgtatctgacacttaaaatcatt-tattgcagATTTTCAATGGTGTGTTCTTGAAGGTCAACAAGGCAACCATTAACATGCTTCGCCGTGTTGAACCCTATGTAACCTATGG
               | |   | |||| | |  |       |||||| |        | ||| ||  | | | || || | ||  |||| |||||||| |||||| ||||||| |||||||||||||| ||||||||     | || || || || || || || ||
--------------gtaaattccttgtgaaagttgcgattgtgatacgagt------tctcttactatcacattctttcttttatagATCTTCAATGGGGTGTTCATGAAGGTGAACAAGGCAACCATGAACATGCTCAAGAGAGTCGAGCCGTACGTGACTTACGG

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|124962655|gb|EL037043.1|EL037043
EST:     CCATTGACCCAAAGACAAAGAAGATTTTGCAACTTTTGCGTTTAAGACAG                         ATTTTCAATGGTGTGTT
genomic: CCATTGACCCAAAGACAAAGAAGATTTTGCAACTTTTGCGTTTAAGACAGgtaacaatct ... tttattgcagATTTTCAATGGTGTGTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttaaccaatgatacaaaaggatcgtatctgacacttaaaatcatttattgcagATTTTCAATGGTGTGTTCTTGAAGGTCAACAAGGCAACCATTAACATGCTTCGCCGTGTTGAACCCTATGTAACCTATGG
                                  acttaaaatcatttat  TA-rich tract