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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgttgccagattcatatccttggataatgtttttggtccattagttctcaagactttcacatcctaattagttttgttttgtttatctctcagGTCTTCGGAATTCCTAAGGAACACAGGAAATCTAAGCCTTACCATGACCATGTATTTGTCTTTTCAATTGTTGATGAGCATATATGGTTCCGAAATTACC

Basic information

species Arabidopsis thaliana
transcript AT1G52930.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G52930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G51310.1 (Glycine max), 3'ss of exon 4
---------gttgttgcc-agattcatatccttggataatgtttttggtccattagttctcaagactttcacatcctaattagttttgttttgtttatctctcagGTCTTCGGAATTCCTAAGGAACACAGGAAATCTAAGCCTTACCATGACCATGTATTTGTCTTTTCAATTGTTGATGAGCATATATGGTTCCGAAATTACC
          ||  || | | | |  | ||  |   | ||| | |||  | | || |      || | | ||      | ||  ||| |||  |||||   |||| | || | ||  || ||||| ||||| ||  ||||||||| |||||| || || ||||| || ||||| |||||||| |||||||||||||| |||||||
catgcatgttttcctgtctacaattttctctatttctgatgctcttgtccaagtactgtatttgattattactgatatacta--tttctttcttttat---tcagATATTTGAAACACCAAAGGACCACAGAAAGGCTAAGCCTTTCCATGATCACGTTTTTGTTTTCTCAATAGTTGATGACCATATATGGTTCCGGAATTACC

upper sequence: AT1G52930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G28320.2 (Glycine max), 3'ss of exon 5
gttgttgccagattcatatcct-tggataatgtttttggtccattagttctcaa--gactttcacatcctaattagttttgttttgtttatctctc------agGTCTTCGGAATTCCTAAGGAACACAGGAAATCTAAGCCTTACCATGACCATGTATTTGTCTTTTCAATTGTTGATGAGCATATATGGTTCCGAAATTACC
   ||| |  |  || | |||| |  | ||| || |   |   |  | |||     || |     ||  | |||| |  || | | ||| | ||||      || | || | ||  || ||||| ||||| ||  | ||||||| |||||| || || ||||| || ||||| |||||||| |||||||||||||| ||||| |
---gttccatgcatcttttcctgtctacaattttctgtatttctatgctcttggccgagtactgtatt-tgattattgctgatatatttctttctcttcttcagATATTTGAAACACCAAAGGACCACAGAAAGGCCAAGCCTTTCCATGATCACGTTTTTGTTTTCTCAATAGTTGATGACCATATATGGTTCCGGAATTATC

upper sequence: AT1G52930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G12700.2 (Glycine max), 3'ss of exon 6
gttgttgccagattcatatccttggataatgtttttggtccattagttctcaagacttt-caca-tcctaattagt-----tttgttttgtttatctctcagGTCTTCGGAATTCCTAAGGAACACAGGAAATCTAAGCCTTACCATGACCATGTATTTGTCTTTTCAATTGTTGATGAGCATATATGGTTCCGAAATTACC
  || |   | | || | |||  |  || ||| | |||   ||||  |   || ||||  |||| |  | |||| |     | |  | | | | ||| |||| | || | ||  || ||||| |  || |   ||||||| | |||||| || || ||||| || ||||| |||||||| ||||||||||| || |||||||
tatgatatgatactcttgtcc--gagtactgtatctgggtgattaaatggtaaaacttcacacaattttgattattgctaatatactatttctttctttcagATATTTGAAACACCAAAGGACCTAAGAAGGACTAAGCCATTCCATGATCACGTTTTTGTTTTCTCAATAGTTGATGACCATATATGGTTTCGGAATTACC

upper sequence: AT1G52930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0005g04550.t01 (Vitis vinifera), 3'ss of exon 4
gttgttgccagattcatatccttggataatgtttttggtccattagttctca---agactttcacatcctaattagtt--ttgttttgtttatctc--tcagGTCTTCGGAATTCCTAAGGAACACAGGAAATCTAAGCCTTACCATGACCATGTATTTGTCTTTTCAATTGTTGATGAGCATATATGGTTCCGAAATTACC
  | |||| ||   ||  | ||  ||| || ||  |  || ||| |     |   |   |||  | || | || ||||    | ||| ||| | |   | || | || |||| ||| ||||| ||||||||| |||| ||||| ||||| ||||| ||||  || ||| ||| |||||| |||||||||||||| || ||||
tattttgctagg--caccttctaagattatcttgctcatctatttgcctatatataagttttatcctcttgataagttgacaggttttttttttttggttagATATTTGGAACTCCGAAGGAGCACAGGAAAGCTAAACCTTATCATGATCATGTCTTTGCTTTCTCACTTGCTGATGATCATATATGGTTCCGGAACTACC

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|124884304|gb|EH963206.1|EH963206
EST:     TTTTGATAAAGATGCGCACTGGAAACTCTTGAAGGAGATGCTTACTCAG                         GTCTTCGGAATTCCTAAGGAACACAGGAAATC
genomic: TTTTGATAAAGATGCGCACTGGAAACTCTTGAAGGAGATGCTTACTCAGgttgttgcca ... tatctctcagGTCTTCGGAATTCCTAAGGAACACAGGAAATC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattagttctcaagactttcacatcctaattagttttgttttgtttatctctcagGTCTTCGGAATTCCTAAGGAACACAGGAAATCTAAGCCTTACCATGACCATGTATTTGTCTTTTCAATTGTTGATGAGCATATATGGTTCCGAAATTACC
                       tcctaat  putative branch site (score: 2)
                                      ttttgtttatctctc  putative PPT
                          taattagttttgtttt  TA-rich tract