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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtataccaagaagcctttgattgagtattatgcacagtttctcttggttgtgtaagattttcatctgtcttgattgtttgaatagTGGTGGCCTGGTGGTTTGGGAAAAGTTTCTACTCATGCTGTTGTTTACGCTCGTCTCATAACTAACGGAAAAGACTACGGTATCCATG

Basic information

species Arabidopsis thaliana
transcript AT4G16760.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G16760.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 4
-------------------------gtaagtataccaagaagcctttgattgagtattatgcacagtttctcttg-gttgtgtaagattttcatctgtcttgattgtttgaatagTGGTGGCCTGGTGGTTTGGGAAAAGTTTCTACTCATGCTGTTGTTTACGCTCGTCTCATAACTAACGGAAAAGACTACGGTATCCATG
                              | ||  |||| ||      |    | | ||    | |||||      |  |||   ||  |      | ||       ||   |||||||||||||||| |||||||||| ||| |||||||| ||||| || |||||||| |||||| | ||||| |||||||| || ||||
gtaatactcctatctactcttcctctcttatctattaagatgctacatttcttctttaatttggaatttcttcaatatcttgttgcatggttcatgattttatccccatgtgcagTGGTGGCCTGGTGGCTTGGGAAAAGCTTCCACTCATGCAGTTGTGTATGCTCGTCTGATAACTGAAGGAAAGGACTACGGCATACATG

upper sequence: AT4G16760.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------gtaagtataccaagaagcctttgattgagt-attatgcacagtt-tctcttggt--------tgtgtaagatttt---catctgtcttgattgtttgaatagTGGTGGCCTGGTGGTTTGGGAAAAGTTTCTACTCATGCTGTTGTTTACGCTCGTCTCATAACTAACGGAAAAGACTACGGTATCCATG
                                                | | |         | |||  ||| || | | |   || || | ||||| |        |||  |  ||||    ||||| |||| || ||| |   |||||||||||||||| ||||| |||| ||| |||||||| || || || ||||| || |||||| | ||||| ||||| ||||| ||||
gtaaagtcctgtgaatcaactacctccattttgatttattttaaaaccattcttttcctttccttttttttgtgttactttagccatttgtatcttgttcaaaatcttgtccacaatttgttacatctatcttcat-gttgg--cagTGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATG

upper sequence: AT4G16760.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 2
-----gtaagtataccaagaagcctttgattgagtattatgcacagtttctcttggttgtgtaagattttcatctgtcttgattgt------ttgaatagTGGTGGCCTGGTGGTTTGGGAAAAGTTTCTACTCATGCTGTTGTTTACGCTCGTCTCATAACTAACGGAAAAGACTACGGTATCCATG
      || ||    |     |   |   || | ||        |  |||   | | |   || ||||||  | | || | ||| |       | |||||||||||||||||||  |||| ||||| || || |||||||||||||| || || ||||||||| | ||  | ||| | ||  | ||||
tttgcatacgtggttctttgtggactatttttaataccgaagttatcttcaaataggttcttatgatttttttttttccttattttattattctaaatagTGGTGGCCTGGTGGACTGGGTAAAGTATCCACACATGCTGTTGTTTATGCACGGCTCATAACTGATGGTCAGGACCATGGAGTGCATG

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|116424738|gb|EG467330.1|EG467330
EST:     CCAAGACTGATGAGTTTGTAATTCACACTCCAACTCAGACTGCATCCAAA                         TGGTGGCCTGGTGGTTTGGGAAAAGTTTCTACTCATGCTGTTGTTTACGCT
genomic: CCAAGACTGATGAGTTTGTAATTCACACTCCAACTCAGACTGCATCCAAAgtaagtatac ... gtttgaatagTGGTGGCCTGGTGGTTTGGGAAAAGTTTCTACTCATGCTGTTGTTTACGCT
EST: gi|164078180|gb|EL991557.1|EL991557
EST:     GTTTGTAATTCACACTCCAACTCAGACTGCATCCAAA                         TGGTGGCCTGGTGGTTTGGGAAAAGTTTCTACCCATGCTGTTGTTTACGCT
genomic: GTTTGTAATTCACACTCCAACTCAGACTGCATCCAAAgtaagtatac ... gtttgaatagTGGTGGCCTGGTGGTTTGGGAAAAGTTTCTACTCATGCTGTTGTTTACGCT
EST: gi|124897175|gb|EH973389.1|EH973389
EST:     CCAACTCAGACTGCATCCAAA                         TGGTGGCCTGGTGGTTTGGGAAAAGTTTCTACTCATGCTGTTGTTTACGCT
genomic: CCAACTCAGACTGCATCCAAAgtaagtatac ... gtttgaatagTGGTGGCCTGGTGGTTTGGGAAAAGTTTCTACTCATGCTGTTGTTTACGCT
EST: gi|125276427|gb|EL290512.1|EL290512
EST:     TTTGTAATTCACACTCCAACTCAGACTGCATCCAAA                         TGGTGGCCTGGTGGTTTGGGAAAAGTTTCTACTCATGCTGTTGTTTACGCT
genomic: TTTGTAATTCACACTCCAACTCAGACTGCATCCAAAgtaagtatac ... gtttgaatagTGGTGGCCTGGTGGTTTGGGAAAAGTTTCTACTCATGCTGTTGTTTACGCT
EST: gi|116424736|gb|EG467328.1|EG467328
EST:     CCAAGACTGATGAGTTTGTAATTCACACTCCAACTCAGACTGCATCCAAA                         TGGTGGCCTGGTGGTTTGGGAAAAGTTTCTACTCATGCTGTTGTTTACGCT
genomic: CCAAGACTGATGAGTTTGTAATTCACACTCCAACTCAGACTGCATCCAAAgtaagtatac ... gtttgaatagTGGTGGCCTGGTGGTTTGGGAAAAGTTTCTACTCATGCTGTTGTTTACGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcacagtttctcttggttgtgtaagattttcatctgtcttgattgtttgaatagTGGTGGCCTGGTGGTTTGGGAAAAGTTTCTACTCATGCTGTTGTTTACGCTCGTCTCATAACTAACGGAAAAGACTACGGTATCCATG
                                     tcttgat  putative branch site (score: 4)
                      taagatttt  TA-rich tract