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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catattttaagtgtcaattatttagttgacaatggtagctagattacttcatttgcacctctcttgaaggtgacttctatatgttcaatgtgtttcacagTCTGGACCTGATGAAAGAAGCATTCCGGGGAACACAGTAGCAGTTCAAGCAGATATGCCATTCAGTGGTCTTACAACTTTTGGGACTGCCTTTTTGTCAA

Basic information

species Arabidopsis thaliana
transcript AT3G20290.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 10
-catattttaagtgtcaattatttagttgacaatgg-tagct--agattacttcatttg---cacctctcttgaaggtgacttct-----atatgttcaatgtgtttcacagTCTGGACCTGATGAAAGAAGCATTCCGGGGAACACAGTAGCAGTTCAAGCAGATATGCCATTCAGTGGTCTTACAACTTTTGGGACTGCCTTTTTGTCAA
  |  || ||  ||   ||   | | ||  |  ||  || ||   | ||  |  |  |     | |||   |||   | |||||      |||  | |  |   |    ||||||||||||||||||||| |||| || || |||||| | || || |||||||| |||||||  |||||  |  || |||||||||| || ||| | ||||
gtaggttctatatggagatgtgtcaatttgctttgcctaacttttgtttgttctacctaacatatctccactgatcttcacttcccaatgatacatcctctcactactgcagTCTGGACCTGATGAAAGATGCATCCCTGGAAACACAATTGCCGTGCAAGCAGACATGCCATATAGTGGCTTGTCATCTTTTGGGACAGCATTTCTATCAA

upper sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA18G10150.1 (Glycine max), 3'ss of exon 10
---cat--attttaagtgtcaattatttagttgacaat--ggtagctagattacttcatttgcacctctcttgaaggtgacttctatatgttcaatgtgtttcacagTCTGGACCTGATGAAAGAAGCATTCCGGGGAACACAGTAGCAGTTCAAGCAGATATGCCATTCAGTGGTCTTACAACTTTTGGGACTGCCTTTTTGTCAA
   |||   | |||||| | |  | || |  ||| | |   ||||  | |||| ||  | |||   | | |   || | | |   |||  ||   ||| || || |||||||||||||||||||||||||||| || || ||  | || || |||||||| |||||||| |||||||||||||||||||| ||  | |||||||| |
tagcattagtattaagtttaatatgttgaaatgatagttatgtagggaaattaattgttgtgctagtttttaagagctaatt---atagttt---tgt-ttacatagTCTGGACCTGATGAAAGAAGCATTCCTGGCAATACTATTGCTGTCCAAGCAGACATGCCATTTAGTGGTCTTACAACTTTTGGTACATCATTTTTGTCCA

upper sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA02G46350.2 (Glycine max), 3'ss of exon 10
catattttaagtgtcaattatttagttgacaatggtagctagattacttcatttgcacctctcttgaaggtgacttctatatgttcaatg----tgtttcacagTCTGGACCTGATGAAAGAAGCATTCCGGGGAACACAGTAGCAGTTCAAGCAGATATGCCATTCAGTGGTCTTACAACTTTTGGGACTGCCTTTTTGTCAA
 ||  |||   |   |||  |||| |  |  | |  | || ||  |  | | ||     |   ||     |  ||||||  |    || |    || |  |||||||||| ||||||| |||||| |||| || || || || || || |||||||| |||||||| |||||||||||||||||||| || || ||||||||||
aattattttcttaataatcctttaatctagta-gtcatcttgaaaaaatgagttat---tgcattagttttatcttctaactagcaaaagatactgatatacagTCTGGATCTGATGAGAGAAGCGTTCCTGGAAATACTGTTGCTGTCCAAGCAGACATGCCATTTAGTGGTCTTACAACTTTTGGCACAGCATTTTTGTCAA

upper sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv19s0090g01130.t01 (Vitis vinifera), 3'ss of exon 10
-catattttaagtgtcaatt--atttagttgacaatggtagctagattacttcatttgcacctctcttgaaggtgacttctatatgttcaatgtgtttcacagTCTGGACCTGATGAAAGAAGCATTCCGGGGAACACAGTAGCAGTTCAAGCAGATATGCCATTCAGTGGTCTTACAACTTTTGGGACTGCCTTTTTGTCAA
   | |||||  | | | ||  ||||  || |   |  |     |   |  |          | | || |   | |||     ||  |   | | |   |||||||||||||||||||||||| ||||| || |||||| | || ||||||||||| ||||| | ||||||||| ||||||||||| || || |||||||| |
ggcttttttactttttagtttgatttttttaaatttttttctctgtccatctttcccaatatttttttcatcttcactcactaatcctgcttttat---acagTCTGGACCTGATGAAAGAAGTATTCCTGGAAACACAATTGCTGTTCAAGCAGACATGCCTTACAGTGGTCTGACAACTTTTGGAACGGCATTTTTGTCCA

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|164216542|gb|ES186962.1|ES186962
EST:     TATTGGACCAGAGCCGACTACTGACAGATTTGTTGTTGTCATG                         TCTGGACCTGATGAAAGAAGCATTCCGGGGAACACAGTAGCAGTTCAAGC
genomic: TATTGGACCAGAGCCGACTACTGACAGATTTGTTGTTGTCATGgtatgttagt ... tgtttcacagTCTGGACCTGATGAAAGAAGCATTCCGGGGAACACAGTAGCAGTTCAAGC
EST: gi|124763269|gb|EH853399.1|EH853399
EST:     TCATATTGGACCAGAGCCGACTACTGACAGATTTGTTGTTGTCATG                         TCTGGACCTGATGAAAGAAACATTCCGGGGAACACAGTAGCAGTTCAAGCA
genomic: TCATATTGGACCAGAGCCGACTACTGACAGATTTGTTGTTGTCATGgtatgttagt ... tgtttcacagTCTGGACCTGATGAAAGAAGCATTCCGGGGAACACAGTAGCAGTTCAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttcatttgcacctctcttgaaggtgacttctatatgttcaatgtgtttcacagTCTGGACCTGATGAAAGAAGCATTCCGGGGAACACAGTAGCAGTTCAAGCAGATATGCCATTCAGTGGTCTTACAACTTTTGGGACTGCCTTTTTGTCAA
                             ttctatat  TA-rich tract