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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgttcttgctataatgaaatggggaattcttaaatactagatgatagaaacatttgatcaaattgtgtttgtagcctgataggtcgtattgtttatcagACAGGTCCTGTTATTTATCGCAGCCGGACTGTGTTTGAGGATGCAACTCCAGATATTGTTAGGGATTTCTTCTGGGATGATGAGTTTCGACCTAAATGGG

Basic information

species Arabidopsis thaliana
transcript AT4G14500.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g08760.2 (Oryza sativa), 3'ss of exon 1
--gtgttcttgctataatgaaatggggaat--tcttaaatactagatgatagaaacatttgatcaaattgtgtttgtagcctgataggtcgtattgtttatcagACAGGTCCTGTTATTTATCGCAGCCGGACTGTGTTTGAGGATGCAACTCCAGATATTGTTAGGGATTTCTTCTGGGATGATGAGTTTCGACCTAAATGGG
   |  | |   |  ||||||     |  |  | | |   | |  ||   | | |  ||  |    |   |  |  | | |||||   |    ||| || | ||   || ||| | || ||  | || || ||| | ||||||||||| ||||| ||  ||||||| |||||||||||||||||||| ||||| |  || ||||
atttcctgtcttttcaatgaatctacgtttgatgtgaccaaatcaatagcatataggttatagtgcaacat-ctaatggactgatc--ttcctttgcttgt-agGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG

upper sequence: AT4G14500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G121223_T02 (Zea mays), 3'ss of exon 3
gtgttcttgctataatgaaatggggaattcttaaatactagatgatagaaacatttgatcaaattgtgtttgtagcctga---taggtcgtat-tgtttatcagACAGGTCCTGTTATTTATCGCAGCCGGACTGTGTTTGAGGATGCAACTCCAGATATTGTTAGGGATTTCTTCTGGGATGATGAGTTTCGACCTAAATGGG
      ||   | | || | |      |   | |  |||| ||| |  |      | ||  | |||| |   || |||||   ||  |   ||   ||||| ||   || ||| | || ||  ||||||| ||| | ||||||||||| ||||| ||  | ||||| |||||||||||||||| ||| ||||| |  || ||||
-aacagttagaagattgcagtaaaatctgtgtcatgactaaatgttttac---cataatatatttgtatacatatcctgagtttattttaaatacatttattagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACTCCTGAACTGGTTAGAGATTTCTTCTGGGATGGTGATTTTCGTCTAAAGTGGG

upper sequence: AT4G14500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G01030.1 (Glycine max), 3'ss of exon 2
gtgttcttgctataatgaaatggggaattc-ttaaatactagatg-atagaaacatttgatcaaattgtgtttgtagcctgata--ggtcgt--attgtttatcagACAGGTCCTGTTATTTATCGCAGCCGGACTGTGTTTGAGGATGCAACTCCAGATATTGTTAGGGATTTCTTCTGGGATGATGAGTTTCGACCTAAATGGG
     |   ||||  |||  ||   | ||  || | | ||   || ||    || || ||| | |      |      |||||   || | |  ||   ||| ||||||||||||    |||| || ||  | ||||| ||||| ||||||||||||||  | || ||||||||||||||||||||||| ||||| ||||||||||
----accatctatgttga--tgattatttgatttatttctttttgtatttccaccttagattagaaatatatcaccatctgatgttggacatggatctgttaacagACAGGTCCTACAGTTTACCGTAGTAGAACTGTCTTTGATGATGCAACTCCAGAGTTGGTGAGGGATTTCTTCTGGGATGATGACTTTCGTCCTAAATGGG

upper sequence: AT4G14500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G44500.1 (Glycine max), 3'ss of exon 2
-------gtgttcttgctataatgaaatggggaattcttaaat----actagatgatagaaacatttgatcaaattgtgtttgtagcctgataggtcgtattgtttatcagACAGGTCCTGTTATTTATCGCAGCCGGACTGTGTTTGAGGATGCAACTCCAGATATTGTTAGGGATTTCTTCTGGGATGATGAGTTTCGACCTAAATGGG
        || | ||| | || |  | |      || ||  ||    ||   |   |||||| ||   ||||  |  |||| |   ||||         |||  ||| ||||||||||||  | ||||  | ||  | ||||| || || ||||||||||||||  | || ||||||||||||||||||||||| ||||| ||||||||||
accatctatgctgttgat-tatttgatttatttctttttgtatttccaccttagattagaaatataccatcatctgatgttgg--acctgg--------atttgttaacagACAGGTCCTACTGTTTACTGTAGTAGAACTGTCTTCGATGATGCAACTCCAGAGTTGGTGAGGGATTTCTTCTGGGATGATGACTTTCGTCCTAAATGGG

upper sequence: AT4G14500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0020g04870.t01 (Vitis vinifera), 3'ss of exon 2
----gtgttcttgctataatgaaatgggga-attcttaaatactagatgatagaaacatttgatcaaattgtgtttgtagcctgataggtcgtattgtttatcagACAGGTCCTGTTATTTATCGCAGCCGGACTGTGTTTGAGGATGCAACTCCAGATATTGTTAGGGATTTCTTCTGGGATGATGAGTTTCGACCTAAATGGG
    ||||   ||      || | || | | | | || ||| ||      |  | ||    ||| |||||   || ||| ||    | |  || || |||||||||  || ||   | | ||||| ||| | ||||| ||||||||||||||||| ||  | ||||| |||||||||||||||||||||||| ||||||||||||
gtgtgtgtgtgtgtgtgtgtgtattgtgcataattttcaattct---cattgtagactgaagataaaatt-cattagtaaccgataatggtgt-ttctttatcagAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCCGAGGTGGTTAGAGATTTCTTCTGGGATGATGAGTTTAGACCTAAATGGG

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|86072297|gb|DR368054.1|DR368054
EST:     TAAGACTACTCCAAATATGAGCTACCCAG-CTTGGCGTCATGAGCCTGAG                         ACAGGTCCTGTTA
genomic: TAAGACTACTCCAAATATGAGCTACC-AGGCTTGGCGTCATGAGCCTGAGgtaatctaag ... tgtttatcagACAGGTCCTGTTA
EST: gi|164229586|gb|ES040733.1|ES040733
EST:     CTACCAGGCTTGGCGTCATGAGCCTGAG                         ACAGGTCCTGTTATTTATCGCAGCCGGACTGTGTTTGAGGATGCAACTCCA
genomic: CTACCAGGCTTGGCGTCATGAGCCTGAGgtaatctaag ... tgtttatcagACAGGTCCTGTTATTTATCGCAGCCGGACTGTGTTTGAGGATGCAACTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaaacatttgatcaaattgtgtttgtagcctgataggtcgtattgtttatcagACAGGTCCTGTTATTTATCGCAGCCGGACTGTGTTTGAGGATGCAACTCCAGATATTGTTAGGGATTTCTTCTGGGATGATGAGTTTCGACCTAAATGGG
                             gcctgat  putative branch site (score: 4)
                                          tattgtttat  TA-rich tract