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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgatgtcttgaaactattggttgagcataaaagatcagtgtttaagtggtcgatgaggtagattttggttctgatccctgaacttttgttgtgtgtagTTCGATCATTTGGAACTGAAGGAAGGAAAAAAGATGGTCCACAAGTTCCTCCAAGTGACAAAGTTTACGAGTACATATTGTTCCGTGGAACTGATATCAA

Basic information

species Arabidopsis thaliana
transcript AT1G26110.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G26110.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G11300.1 (Glycine max), 3'ss of exon 1
-attgatgtcttgaaactattgg-ttgagcataaaagatcagtgtttaagtggtcgatgaggtagattttggttctgatccctgaacttttgttgtgtgtagTTCGATCATTTGGAACTGAAGGAAGGAAAAAAGATGGTCCACAAGTTCCTCCAAGTGACAAAGTTTACGAGTACATATTGTTCCGTGGAACTGATATCAA
        | | || | | |||  ||||   ||  |  | |   | |      || ||| | | |||||  |   |||| | |    |||| |||| |||||| ||||| |||||||| |||||||||||||| ||||| |||||| | |||||| ||||||| ||||| ||||| ||| | |||||||| ||||| |||||
tgcaacaatgtggatattgttgccttgattttaccacctaaacatgtttactatc-atgggttggatttgtggagtgatgcttttgttttttttgt-tgtagTGCGATCTTTTGGAACAGAAGGAAGGAAAAAGGATGGCCCACAAATCCCTCCAGGTGACAAGGTTTATGAGTATATACTTTTCCGTGGGACTGACATCAA

upper sequence: AT1G26110.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G17050.1 (Glycine max), 3'ss of exon 1
-----at-tgatgtcttgaaactattggttgagcataaaagatcagtgtttaagtggtcgatgaggtagattttggttctgatccctgaacttttgttgtgtgtagTTCGATCATTTGGAACTGAAGGAAGGAAAAAAGATGGTCCACAAGTTCCTCCAAGTGACAAAGTTTACGAGTACATATTGTTCCGTGGAACTGATATCAA
     || |||  | ||| | || |   ||   |     | |    ||||||     || | ||| | ||||   |   |||| | |    ||||  | | |||||| ||||| |||||||| |||||||||||||| ||||| | |||| |||||||| |||||||  |||| ||||| ||| | |||||||| ||||| |||||
caaccatgtgaattattgcagctttgaattttaccacctaaa--gatgttta--ctatc-acgagttggattggtggagtgatgcttttgttttttgtct-tgtagTGCGATCTTTTGGAACAGAAGGAAGGAAAAAGGATGGCCTACAAATTCCTCCAGGTGACAAGATTTATGAGTATATACTTTTCCGTGGGACTGACATCAA

upper sequence: AT1G26110.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G11320.2 (Glycine max), 3'ss of exon 1
-attgatgtcttgaaactattggtt-gagcataaaagatcagtgtttaagtggtcgatgaggtagattttggttctgatccctgaacttttgttgtgtgtagTTCGATCATTTGGAACTGAAGGAAGGAAAAAAGATGGTCCACAAGTTCCTCCAAGTGACAAAGTTTACGAGTACATATTGTTCCGTGGAACTGATATCAA
        | | || | |  || || ||   ||  |  | |   | |      || ||| | | ||||   |   |||| | |    ||||  ||| |||||| || || |||||||| |||||||||||||| ||||| |||||| | ||||| |||||||| ||||| ||||| ||| | |||||||| ||||| |||||
tgcaacaatgtggatattgctgctttgattttaccacctaaacatgtttactatc-atgggctggattggtggagtgatgcttttgttttttgtgt-tgtagTGCGGTCTTTTGGAACAGAAGGAAGGAAAAAGGATGGCCCACAAATCCCTCCCAGTGACAAGGTTTATGAGTATATACTTTTCCGTGGGACTGACATCAA

upper sequence: AT1G26110.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv01s0011g02820.t01 (Vitis vinifera), 3'ss of exon 1
-attgatgtcttgaaactattggttgagcataaaagatcagtgtttaagtggtcgatgaggtagattttggttctgatccctgaacttttgttgtgtg-tagTTCGATCATTTGGAACTGAAGGAAGGAAAAAAGATGGTCCACAAGTTCCTCCAAGTGACAAAGTTTACGAGTACATATTGTTCCGTGGAACTGATATCAA
 ||| || || ||    || |   ||    |   |  | | |||  |  | ||  |  |   |   ||   || |  |     | ||  |||    ||  |||  | ||||| || || |||||| | || || |||||||| ||||| |||||||||||||||||||| || |||||  | || ||||||| ||| |||||
tatt-atttcatgtttatacttactgttt-tgtcaagtaattgtcaacctagtgtaaaaaaaatggttccttttttctaatctatctcctgtcacatggcagTAAGGTCATTCGGTACAGAAGGACGAAAGAAGGATGGTCCCCAAGTCCCTCCAAGTGACAAAGTTTATGAATACATCCTATTTCGTGGAAGTGACATCAA

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|301501034|gb|HO206574.1|HO206574
EST:     GATCCTTTACAATATTAATACAGATGAATCCAGTATCGGACTTCAAAACG                         TTCGATCATTTGGAACTGAAGGAAGGAAAAAAGATGGTCCACAAGTTCCTC
genomic: GATCCTTTACAATATTAATACAGATGAATCCAGTATCGGACTTCAAAACGgtacgatccg ... ttgtgtgtagTTCGATCATTTGGAACTGAAGGAAGGAAAAAAGATGGTCCACAAGTTCCTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtggtcgatgaggtagattttggttctgatccctgaacttttgttgtgtgtagTTCGATCATTTGGAACTGAAGGAAGGAAAAAAGATGGTCCACAAGTTCCTCCAAGTGACAAAGTTTACGAGTACATATTGTTCCGTGGAACTGATATCAA
                         ttctgat  putative branch site (score: 3)
                                       cttttgtt  putative PPT
               tagatttt  TA-rich tract