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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagataagttgaagtattttaacgttttcatatgtggaaatgaagtggtttttagaaaatgttttaatatgtattttcatggttatgtatgtagCCTGGTCCGGATTCTATTGGTATCGTAGCTGTTTCACGCAACTGCAGTGGAATAGCAGCACGTGCCTGTGGCCTCGTGAGTTTAGAACCCATGAAG

Basic information

species Arabidopsis thaliana
transcript AT1G30490.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 4
gtagataagttgaagtattttaacgttttc--atatgtggaaatgaagtggtttttagaaaatgttttaat---atgtattttcatggttatgta--tgtagCCTGGTCCGGATTCTATTGGTATCGTAGCTGTTTCACGCAACTGCAGTGGAATAGCAGCACGTGCCTGTGGCCTCGTGAGTTTAGAACCCATGAAG
|||    | | |  |||    ||   | |    ||||| ||  |    |     ||      | ||||  |   ||  | |   |||   || |   |  |||||||||||||||| ||||| ||| | |||||||| | ||| ||||||||  |||||||||| || || ||||| |||||  | || ||||  |||
gtaatgtattcgttgtacaagaaaactgtgcagtatgttgattttctctttccattcatgttttttttgttcaaatcaactgaaatgaaaatttgattacagCCTGGTCCGGATTCCATTGGAATCATCGCTGTTTCGCACAATTGCAGTGGCGTAGCAGCACGAGCTTGCGGCCTGGTGAGCCTTGAGCCCACAAAG

upper sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 4
gtagataagttgaagtattttaacgttttcatatgtggaaatgaagtggtttttagaa---aatgttttaatatgtattttcatggttatgtatgt---agCCTGGTCCGGATTCTATTGGTATCGTAGCTGTTTCACGCAACTGCAGTGGAATAGCAGCACGTGCCTGTGGCCTCGTGAGTTTAGAACCCATGAAG
              ||| | |||   |  || | |    |||   |||  |||   |    | | ||||      |   || | |||    | |||   |||||||||||||||| ||||| ||| | |||||||| | ||| || |||||  |||||||||| || || ||||| |||||  | || ||||  |||
--------------gtaatgtaattatcgcagaaggcagaattgtgtgtgtttattacttcagttttttggagaattacttaaaggtggaatttgttacagCCTGGTCCGGATTCCATTGGAATCATCGCTGTTTCGCACAATTGTAGTGGCGTAGCAGCACGAGCTTGCGGCCTTGTGAGCCTTGAGCCCACAAAG

upper sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 3
gtagataagttgaagtattttaacgtttt-catatgtgga-aatgaagtggtttttagaaaa-tgttttaatatgt--------atttt---catggttatgtatgtagCCTGGTCCGGATTCTATTGGTATCGTAGCTGTTTCACGCAACTGCAGTGGAATAGCAGCACGTGCCTGTGGCCTCGTGAGTTTAGAACCCATGAAG
||     | |||   | ||  | ||| |   |  |||  | |||| | |    |   ||||| | |  | |||| |        |||     |  |||  ||  |  ||||||||||||||||  |||| ||| | |||||||| | ||||||||| ||  |||||||||| || || ||||| |||||  | || ||||  |||
gtgatgtacttgttttcttacatcgtgtagtacttgtatacaatgcaatatcgtggcgaaaactatgctgatatctctgacctgattccaaacgcggtgctgattacagCCTGGTCCGGATTCCGTTGGAATCATCGCTGTTTCGCACAACTGCAGCGGCGTAGCAGCACGAGCTTGCGGCCTTGTGAGCCTCGAGCCCACAAAG

upper sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G178102_T01 (Zea mays), 3'ss of exon 4
gtagataagttgaagtattttaacgttttcatatgtggaaatgaagtggtttttagaaaatgttttaatatgtatttt---catggttatgtatgtagCCTGGTCCGGATTCTATTGGTATCGTAGCTGTTTCACGCAACTGCAGTGGAATAGCAGCACGTGCCTGTGGCCTCGTGAGTTTAGAACCCATGAAG
||| ||    |    | | |  |   | |  ||     | |||  |  |    |        | |   |     |||    | || |  ||  || ||||||||||||||||  |||| ||| | |||||||| | ||||||||| ||  |||||||||| || || ||||| |||||  | || ||||  |||
gta-atgtacttgtttttctagatagtgtgctaccctaatatggtgatgcacctgatgttgatatctctgaccgtttcaaacgtgatactgattgcagCCTGGTCCGGATTCCGTTGGAATCATCGCTGTTTCGCACAACTGCAGCGGCGTAGCAGCACGAGCTTGCGGCCTTGTGAGCCTTGAGCCCACAAAG

upper sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 4
--gtagataagttga-agtattttaacgt-----tttcatatgtggaaatgaagtggtttttagaaaatgttttaatatgtattttcatggttatgtatgtagCCTGGTCCGGATTCTATTGGTATCGTAGCTGTTTCACGCAACTGCAGTGGAATAGCAGCACGTGCCTGTGGCCTCGTGAGTTTAGAACCCATGAAG
  ||     | |  | | |  ||   | |     || | |   |  ||   | ||  || |  ||  || ||||       |||||    ||  |   ||||||||||||||||||||||||| ||||| |||||||| |||||||| |||||  |||| ||| | ||||||||||| |||||  | || ||||  |||
gtgtgacctattcaataattcttcttcatggtcattgcttgcataaaacatatgtatttgtatgattatattttgcctctcattttttctgtctt-cgtgtagCCTGGTCCGGATTCTATTGGAATCGTTGCTGTTTCCCGCAACTGTAGTGGTGTAGCGGCAAGAGCCTGTGGCCTTGTGAGCCTTGAGCCCACAAAG

upper sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G13640.1 (Glycine max), 3'ss of exon 4
gtagataagttgaagtattttaacgttttcatatgtggaaatgaa----gtggtttttagaaaatgttttaatatgtattttcatggttat-----gtatgtagCCTGGTCCGGATTCTATTGGTATCGTAGCTGTTTCACGCAACTGCAGTGGAATAGCAGCACGTGCCTGTGGCCTCGTGAGTTTAGAACCCATGAAG
|||      ||  | |||| | |  |  |  | | || |  |  |     |   |||  || | |||| |  | ||| | ||||| || ||      |  |||||||||||||||||| ||||| |||||||||||||| |||||||| |||||  | |||||||| ||||| ||||| |||||  | || ||||  |||
gtatgccctttttaatattcttaattgcttgtgtttgtatgtatatttcataaatttgtgatattgttgttgtgtgtttgttcattgtgattttcaatgagtagCCTGGTCCGGATTCCATTGGAATCGTAGCTGTTTCCCGCAACTGTAGTGGCGTGGCAGCACGAGCCTGCGGCCTTGTGAGCCTGGAGCCCACTAAG

upper sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 4
------------------gtagataagttgaagtattttaacgttttcatatgtggaaatgaagtggtttttagaaaatgttttaatatgtattttcatggttatgtatg-----tagCCTGGTCCGGATTCTATTGGTATCGTAGCTGTTTCACGCAACTGCAGTGGAATAGCAGCACGTGCCTGTGGCCTCGTGAGTTTAGAACCCATGAAG
                   |   | |      || ||||  | || | || | || | |     |   | || |  |||||| |  | | | | || || |  || |        ||||||||||||||||||||||| ||||| |||||||| |||||||| |||||  | |||||||| ||||| ||||| |||||  |||| ||||  |||
gtaatgccccgtttaataatctttgatgcttggttttttttctttcttatgtttgtataattcataaatatttgttaatgttgttgtgtttttgttaattgcaatttgcaatgaatagCCTGGTCCGGATTCTATTGGAATCGTTGCTGTTTCCCGCAACTGTAGTGGCGTGGCAGCACGAGCCTGCGGCCTTGTGAGCCTAGAGCCCACTAAG

upper sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G30000.1 (Glycine max), 3'ss of exon 4
gtagataagttgaagtattttaacgttttcatatgtggaaatgaagtggtttttagaaaatgttttaatatgtattttcatggttatgtatgtagCCTGGTCCGGATTCTATTGGTATCGTAGCTGTTTCACGCAACTGCAGTGGAATAGCAGCACGTGCCTGTGGCCTCGTGAGTTTAGAACCCATGAAG
     || |    | |  || |  ||  |    ||   ||||  | |||| |    |  || ||||      | |||||    |||   |||||||||||||||||||||||||| || || |||||||| |||||||| |||||  |||| ||| | ||||||||||| |||||  |||| ||||  |||
----gtatgacctacttcttcatggtcattgcttgcataaatatattggtat---aattatattttgcctcattttttctgtctta---atgtagCCTGGTCCGGATTCTATTGGAATTGTTGCTGTTTCCCGCAACTGTAGTGGCGTAGCGGCAAGAGCCTGTGGCCTTGTGAGCCTAGAGCCCACAAAG

upper sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 4
gtagataagttgaagtattttaacgttttcatatgtggaaatgaagtggtttttagaaaatgttttaatatgtattttcatggttatgtatgtagCCTGGTCCGGATTCTATTGGTATCGTAGCTGTTTCACGCAACTGCAGTGGAATAGCAGCACGTGCCTGTGGCCTCGTGAGTTTAGAACCCATGAAG
    | ||  |     |  ||    | || |  |     | |    |    ||     | |     ||| |     |   | | | |  |||||||||||||||||||||||||| ||||| |||||||| |||||||| |||||  |||||||||| |||||||||||||||||| ||||||||| ||||
--gtacaatctctttcagcttcctttctttaatttcaccagttgctttaccttgtagcagttcccaaatgtaaccatcttttgatttccatgtagCCTGGTCCGGATTCTATTGGAATCGTTGCTGTTTCCCGCAACTGTAGTGGGGTAGCAGCACGAGCCTGTGGCCTCGTGAGTCTAGAACCCACGAAG

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|116415557|gb|EG458149.1|EG458149
EST:     GCAAGGCTACAGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAG                         CCTGGTCCGGATTCTATTGGTATCGTAGCTGTTTCACGCAACTGCAGTGGA
genomic: GCAAGGCTACAGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAGgtagataagt ... atgtatgtagCCTGGTCCGGATTCTATTGGTATCGTAGCTGTTTCACGCAACTGCAGTGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaagtggtttttagaaaatgttttaatatgtattttcatggttatgtatgtagCCTGGTCCGGATTCTATTGGTATCGTAGCTGTTTCACGCAACTGCAGTGGAATAGCAGCACGTGCCTGTGGCCTCGTGAGTTTAGAACCCATGAAG
                      ttttaat  putative branch site (score: 3)
         tttttagaaaatgttt  TA-rich tract