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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagaatcagatcttggggttttattagtttgatctgttgtgactcaaggatgattatgtaattatatgagtttacttttttcttgtttgttttgtgtagCCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCACTTGGTTGATAAGCTTATGGAAAATGAGAAGAATGAG

Basic information

species Arabidopsis thaliana
transcript AT5G59290.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 2
--acagaatcagatcttggg-gttttattagtttgatctgttgtgactcaaggatgattatgtaattatatgagtttacttttttcttgtttgttttgtgtagCCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCACTTGGTTGATAAGCTTATGGAAAATGAGAAGAATGAG
  | | |    ||| |||   |    | |   ||  ||||   | ||| ||   |  ||      || | | |    || ||| | |  ||  ||     ||| | || ||||| ||||||||  | ||||||||||| ||||||||||||||| | |||||||   | ||||||||||| || ||||||
ttataaacagggattttgtctgaaagaatcccttagtctgc-ataacttaatttttcttgatgccttgtttaa-ccaacatttctttcattc-ttgaccatagTCTAACATGAGAATCTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTTGATAGATTGATGGAAAATGAAAAAAATGAG

upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 3
acagaatcagatcttggggttttattagtttgatctgttgtgactcaaggatgattatgtaattatatgagtttactt-----ttttcttgtttgttttgtg-tagCCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCACTTGGTTGATAAGCTTATGGAAAATGAGAAGAATGAG
      |  |    || || |||   ||    | || || ||  | |       || | |  |  |      ||  ||     | |||||   |  ||  |  ||| |||| ||||| |||||| |  ||||||||||||| |||||||| |||||||| ||||| |   | ||||||||||| || ||||||
------tttgtgaatgtggcttttgcagaagcaactattttgcatgagcctcttttttcttgtcttgatgccttgtttaccagtattctttcattcttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG

upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 3
acagaatcagatcttggggttttattagtt-tgatctgttgtgactcaaggatgattatgtaattatatgagtttacttttttcttgtttgttttgtgtagC---CCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCACTTGGTTGATAAGCTTATGGAAAATGAGAAGAATGAG
    |||   || |||   ||  |  ||     || |    | |  |     |  || | |   |   |  ||||||   | | |  ||  || |   || |   |||| ||||| |||||| |  ||||||||||||| |||||||| |||||||| ||||| |   | ||||||||||| || ||||||
---caattgaatattgcttttgcagaagcaactattttgcataagcctctttttcttgtattgatgcctt-gtttaccagtatttctttcattcttgataacagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG

upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 2
--acagaatcagatct-tggggttttattagtttgatctgttgtgactca-aggatgattatgtaattatatgagtttacttttttcttgtttgttttgtgtagCCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCACTTGGTTGATAAGCTTATGGAAAATGAGAAGAATGAG
    |  |||| ||   ||       || | |    |   |  | |||   |  ||  |||  |||||   |    | | |  ||||    ||| |    | || |||||||||| || ||| || ||||||||||||| ||||||||||| || ||||| || ||||| ||||||||||| |||||||||
tccaatcatcacattcatgccaacacatcattgcactagatcattacttttattatctttaactaattcc-tacagtaattcctttcactcttgatg---gcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG

upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------------------------acagaatcagatcttggggtttta---ttagtttgatctgttgtgactcaaggatgattatg---taattatatgagtttacttttttcttgt-ttgttttgtgt-agCCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCACTTGGTTGATAAGCTTATGGAAAATGAGAAGAATGAG
                                                                                  |  || | | | ||      |     ||    || | | ||   | |   | ||  |  ||    | |  | |   ||||  | |||   || || ||  || | || | || ||||||||||||||| | ||||||||||| ||||| || ||||||||||| || | ||| |||||| | |  |  || || 
gtaagcacgcaaatcaattcttggccagacctaattggtggaagttatgtagtccaggtttaaaacggtggttgtgattcatcgtaaactgttattactacctccagctttaactgcttttttagaagttgtgcatcgtcgtgactcagtcttgttgatttaaatatttgaggtatttttccgtttcagGCGAAGATGAGGATCTTGATCACAGGAGGAGCTGGATTCATCGGGTCTCACTTGGTCGACAGGCTCATGGAAGAGGGCACAAACGAA

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|86047698|gb|DR343453.1|DR343453
EST:     CAAAGCCTCCTCCTTCTCCTTCTCCTCTCCGCAATTCCAAGTTTTGTCAG                         CCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCAC
genomic: CAAAGCCTCCTCCTTCTCCTTCTCCTCTCCGCAATTCCAAGTTTTGTCAGgtaaaatctt ... ttttgtgtagCCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCAC
EST: gi|222357254|gb|GH717964.1|GH717964
EST:     CAAAGCCTCCTCCTTCTCCTTCTCCTCTCCGCAATTCCAAGTTTTGTCAG                         CCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCAC
genomic: CAAAGCCTCCTCCTTCTCCTTCTCCTCTCCGCAATTCCAAGTTTTGTCAGgtaaaatctt ... ttttgtgtagCCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCAC
EST: gi|125053678|gb|EL124682.1|EL124682
EST:     CCTCCTCCTTCTCCTTCTCCTCTCCGCAATTCCAAGTTTTTGTCAG                         CCCAATATGAGGATCTTGATCTCTGGAGGAAGCTGGCTTCATTGGTTCTC
genomic: CCTCCTCCTTCTCCTTCTCCTCTCCGCAATTCCAAGTTTT-GTCAGgtaaaatctt ... ttttgtgtagCCCAATATGAGGATCTTGATCTCTGGAGGA-GCTGGCTTCATTGGTTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaggatgattatgtaattatatgagtttacttttttcttgtttgttttgtgtagCCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCACTTGGTTGATAAGCTTATGGAAAATGAGAAGAATGAG
                          tttacttttttcttgt  CT-rich tract
        attatgtaattatatg  TA-rich tract