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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtagtcctcttacatagcattgttcttatgaatgtttcacagaagatagttcacggtttgatttagactcattcaaacactcttctaattttctgatattgttatttcccagCCTCATCCGGATGTGAAGCCTATGGCATATGCAAACAACTTTCTCAGGATGTTCAACTAACCAGCAAAAAGCTTCTTCTACTCAAAATGCTATTCTAAAG

Basic information

species Arabidopsis thaliana
transcript AT2G42810.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G42810.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G126435_T01 (Zea mays), 3'ss of exon 12
gtgagtgtagtcctcttacatagcattgttcttatgaatgtttcacagaagatagttcacggtttgatttagactcattcaaacactcttctaattttctgatattgttatttcccagCCTCATCCGGATGTGAAGCCTATGGCATATGCAAACAACTTTCTCAGGATGTTCAACTAACCAGCAAAAAGCTTCTTCTACTCAAAATGCTATTCTAAAG-
          |   |||  ||    ||  | |||    | |||      |  |  ||  |   | ||| |   || ||| |     | | |    || ||| | |    || |  ||||| ||||| ||||||||||| |||||||||||||| ||||| |||||||||||  | | ||  | | | | |  | |    |   |||  |  ||  | | 
---------atatccttttatcatgttcctgttaaacttctttgcaccgatttgattagcaactggatat---ctgattgagggggtttac--gcttgctggtgt----atcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATGTTTCAATGAC-GGAATATAACAACATTGTTTAGCAATTTTTATCAGATGA

upper sequence: AT2G42810.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G126435_T02 (Zea mays), 3'ss of exon 11
----gtgagtgtagtcctcttacatagcattgttcttatgaatgtttcacagaagatagttcacggtttgatttagactcattcaaacactcttctaattttctgatattgttatttcccagCCTCATCCGGATGTGAAGCCTATGGCATATGCAAACAACTTTCTCAGGATGTTCAACTAACCAGCAAAAAGCTTCTTCTACTCAAAATGCTATTCTAAAG
    |    |  | |   |||  ||    ||  | |||    | |||      |  |  ||  |   | ||| |   || ||| |     | | |    || ||| | |    || |  ||||| ||||| ||||||||||| |||||||||||||| ||||| |||||||||||  | | ||  | | | | |  | |    |   |||            
gttggctctttgaatatccttttatcatgttcctgttaaacttctttgcaccgatttgattagcaactggatat---ctgattgagggggtttac--gcttgctgGTGT----ATCTTGCAGCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATGTTTCAATGAC-GGAATATAACAACATTGTTTAGCAAT------------

upper sequence: AT2G42810.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 12
gtgagtgtagtcctcttacatagcattgttcttatgaatgtttcacagaagatagttca--cggtttgatttagactcattcaaacactcttctaattttctgatattgtt-atttcccagCCTCATCCGGATGTGAAGCCTATGGCATATGCAAACAACTTTCTCAGGATGTTCAACTAACCAGCAAAAAGCTTCTTCTA---CTCAAAATGCTATTCTAAAG
                     |  | | ||||  || || | | || | | ||  ||||  | || | || |||  |            ||| |   |   | || ||||| | |   ||||| || || ||||| || ||||||||||||||||||||||| ||| ||||||||   |||     | | ||||   |  |   ||  || ||| | |    | 
--------------------aacaaattttctggtgcat-tatgactgcatatctttcaatctgtgttatatagggttgacattctttccttgtgtctggtttattttgttgaatatgcagCCACACCCTGATGTCAAACCTATGGCATATGCAAACAACTTCCTCCGGATGTTCTCATAATT--TATACAGCTGACTAGAAGCCTAGAACTGCCAATTGTTA-

upper sequence: AT2G42810.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 6
gtgagtgtagtcc-tcttacatagcattgttcttatgaatgtttcacagaagatagttcacggtttgatttagactcattcaaacactcttctaattttctgatattgttatttcccagCCTCATCCGGATGTGAAGCCTATGGCATATGCAAACAACTTTCTCAGGATGTTCAACTAACCAGCAAAAAGCTTCTTCTACTCAAAATGCTATTCTAAAG
||||||    |   | ||    |  ||  ||||  | ||| ||      ||  | ||| |  | | | || | |    |  ||    || ||| ||||  |  | |  | |  |  ||||| || || ||||||||||| ||||| ||||| || ||||||||| ||||||||   | |   |   |  ||   || ||    || |  |  | || | 
gtgagtagcctgtgttttctgaaagatccttctgctaaattttgt---caacttggtttatagat-ggttaaaa---gtgtaacttgtcctcttatttctttttgtgatgaaattgcagCCACACCCTGATGTGAAGCCAATGGCGTATGCCAATAACTTTCTCCGGATGTTCTCTTGATTGGTGTACCGCCAGTTGTATGTCAATTTTTTCTATACAA

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|164085770|gb|ES066050.1|ES066050
EST:     TGAAGCTCCTGATATGAAGCCAAACATTGTTACATTCTCAGCAGTG                         CCTCATCCGGATGTGAAGCCTATGGCATATGCAAACAACTTTC
genomic: TGAAGCTCCTGATATGAAGCCAAACATTGTTACATTCTCAGCAGTGgtgagtgtag ... tatttcccagCCTCATCCGGATGTGAAGCCTATGGCATATGCAAACAACTTTC
EST: gi|125235765|gb|EL249850.1|EL249850
EST:     GTTTTGAAGCTCCTGATATGAAGCCAAACATTGTTACATTCTCAGCAGTG                         CCTCATCCGGATGTGAAGCCTATGGCATATGCAAACA
genomic: GTTTTGAAGCTCCTGATATGAAGCCAAACATTGTTACATTCTCAGCAGTGgtgagtgtag ... tatttcccagCCTCATCCGGATGTGAAGCCTATGGCATATGCAAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatttagactcattcaaacactcttctaattttctgatattgttatttcccagCCTCATCCGGATGTGAAGCCTATGGCATATGCAAACAACTTTCTCAGGATGTTCAACTAACCAGCAAAAAGCTTCTTCTACTCAAAATGCTATTCTAAAG
                                            ttatttccc  CT-rich tract
                            taattttctgatattg  TA-rich tract