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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgggtgttggttttgctatagtttaaagcctttgggatgattaaaacatcagtatactgatagtttttcttgtctttttatacatgttttgcatgtctagGATGCTTTGAAGAACATTTTGACTATTTTCGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCT

Basic information

species Arabidopsis thaliana
transcript AT4G13730.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G13730.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g68010.3 (Oryza sativa), 3'ss of exon 5
gttgggtgttggttttgctatagtttaaagcctttgggatgattaaaacatcagtatactgatagtttttcttgtctttttatacatgttttgcatgtctagGATGCTTTGAAGAACATTTTGACTATTTTCGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCT
                        | ||  ||  |       |  |||||    | | || | |      | || ||  | |||  |  |    |   | ||||  || |||| || ||  ||| ||| || |||||| ||||| | || ||  | |||||||||||||||||||| || ||||||||| | ||||   | |
-----------------------gtgaactccactatctaagtctaaacagagttctgctcagaaa----cctgactgatcataggtcatcctta---ccagGAATCTCTGAAAAATATACTGATTATCTTTGCAAAGCTGAATGCCGGAATACGTTATGTACAAGGGATGAATGAAATTTTGGCACCTCTCTTCTTTGTGT

upper sequence: AT4G13730.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G022308_T02 (Zea mays), 3'ss of exon 6
gttgggtgttggttttgctatagtttaaagcctttgggatgattaaaacatcagtatactgatagtttttcttgtctttttatacatgttttgcatgtctagGATGCTTTGAAGAACATTTTGACTATTTTCGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCT
  | |||||      ||  || |  | |    |||    |  | |    | || | | |    |||||||||  |        | ||||||||  | |||||||  |  | |||   ||  | || || || ||||| |||||||| || || |||||||||||||| ||||||||| | ||||||||| | |  ||  | |
-gtaggtgtgttccctgacatgggatcactttttttttgttgtcag--taacattgttc----agtttttctaatgca-----atatgttttg--tttctagGAGTCACTAAAGCGTATACTTACAATATTTGCAAAATTGAATCCGGGTATAAGATATGTACAAGGAATGAATGAGGTTTTGGCACCTCTCTATTATGTTT

upper sequence: AT4G13730.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G068392_T02 (Zea mays), 3'ss of exon 5
gttgggtgttggttttgctatagtttaaagcctttgggatgattaaaacatcagtatactgatagtttttcttgtctttttatacatgttttgcatgt-ctagGATGCTTTGAAGAACATTTTGACTATTTTCGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCT
                  || |  |  | ||  |  |  |  | |||    |||| |  | | |    |   ||   |||||    | | ||       | ||||  ||||||| ||  |  ||   || || || ||| ||||| |||| || |||||||||||||||||||||||  | ||||||||  | ||||   | |
-----------------gtaaatctccacgcactctgagt--tcaaa----cagtgttgtcagatccctgtctgatcttttacctttttattattctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT

upper sequence: AT4G13730.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G11760.1 (Glycine max), 3'ss of exon 5
gttgggtgttggttttgctatagtttaaagcctttgggatgattaaaacatcagtatactgatagttt---ttcttgtctttttatacatgttttgc-------atgtctagGATGCTTTGAAGAACATTTTGACTATTTTCGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCT
     || ||   |||  | |   || ||   | |   |   |  ||     ||| |  |  | |  |     ||||  |  ||||   | |||| |       || |  |||| ||||||||||| || || | |||||| |||||||| || || ||  | |||||||| ||||| ||||||||||||||||| ||| | |||||| | |
-----gtttttcctttatt-tgtcttgaaatttatacaa-actccaagttcaagtctttttcttgagtgaacccttgattaattattactatttttcgggggggattttcagGAGGCTTTGAAGAATATATTAATTATTTTTGCAAAGTTAAACCCGGGTGTAAGATATGTGCAAGGAATGAATGAGATATTGGCTCCTCTATTCTACGTGT

upper sequence: AT4G13730.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G28660.1 (Glycine max), 3'ss of exon 5
gttgggtgttggttttgctatagtttaaagcc-----tttgggatgattaaaacatcagtatactgatagtttttcttgtctttttatacatgttttgcatgtctagGATGCTTTGAAGAACATTTTGACTATTTTCGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCT
||    | || || |||  ||   |  || |      ||   |    ||    ||| |      ||||  || || ||    ||||   |  |    |||| |  |||| ||||||||||| || || | |||||| |||||||| || || ||| |   |||||| ||||| ||||||||||||||||| ||| | |||||  | |
gtcctttatttgtcttgaaattcatccaaactccaaattcaagtcttttctgccatgaaccctttgat--ttattattactatttttcgcgggggg-gcattttcagGAGGCTTTGAAGAATATATTAATTATTTTTGCAAAGTTAAACCCAGGCGTACAATATGTGCAAGGAATGAATGAGATATTGGCTCCTCTATTCTATGTGT

upper sequence: AT4G13730.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G36520.1 (Glycine max), 3'ss of exon 5
gttgggtgttggttttgctatagtttaaagcctttgggatgattaaaacatcagtatactgatagtttttcttgtcttttta---tacatgttttgca---tgtctagGATGCTTTGAAGAACATTTTGACTATTTTCGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCT
          | | || || || |||  |   ||    ||  | |||     |  |     ||  ||||||||| | ||||    | ||  |||| |    | |  |||| ||||| |||| ||| || | |||||| |||||||||||  | || || |||||||| ||||||||||||||  ||||||| ||| | |||||  | |
----------gttcttcctctattttttaatttt----attttcaaattcataccaactcaatcctttttcttgccattttgactttcaacttttccggatttttcagGAGGCTTTAAAGACCATATTAATTATTTTTGCAAAGTTGAACTCAGGTATAAGATATGTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT

upper sequence: AT4G13730.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 5
gttgggtgttggttttgctatagtttaaagcctttgggatgattaaaacatcagtatactgatagtttttcttgtctttttatacatgttttgcatgtctagGATGCTTTGAAGAACATTTTGACTATTTTCGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCT
          |  | || | |   || | || |  |   ||||  ||||||||                | |   |   ||| |    |  || || |  |||||||||||| |||||| |||| | | || |||||||||||||| || || |||||||| |||||||||||||| || ||||| ||| | |||||  | |
----------gtatgtgttgttacttgaggcatgagacttgatacaaacatca------------cccatttgaccaaattaaatggatcctgtat-ttcagGATGCTTTGAGGAACATATTGATTGTGTTTGCAAAGTTGAATCCGGGTATAAGATATGTGCAAGGGATGAATGAAATTTTGGCGCCTCTATTCTATGTAT

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|86076731|gb|DR372488.1|DR372488
EST:     CAGATATGCACTTTTTCTCTGGGGATTCAGCAGTTGCAAAATCTAATCAG                         GATGCTTTGAAGAACATTTTGACTATTTTCGCAAAGTTGAATCCTGGCATC
genomic: CAGATATGCACTTTTTCTCTGGGGATTCAGCAGTTGCAAAATCTAATCAGgttgggtgtt ... gcatgtctagGATGCTTTGAAGAACATTTTGACTATTTTCGCAAAGTTGAATCCTGGCATC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatcagtatactgatagtttttcttgtctttttatacatgttttgcatgtctagGATGCTTTGAAGAACATTTTGACTATTTTCGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCT
         tactgat  putative branch site (score: 2)
                             tttttatacatgtttt  TA-rich tract