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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccccccaacattctttttctgcaccatagtagctgagatttcgtgtcccatgtctctgtgttgtggtactgactagttttatgtgctctgaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTCTTTGTTGCAAGTCTCCTACAAAGGCGGCTCATGATGATTGTTGACAAAC

Basic information

species Arabidopsis thaliana
transcript AT4G27720.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g02380.1 (Oryza sativa), 3'ss of exon 6
gtaagtccccccaacattctttttctgcaccatagtagctgagatttcgtgtcccatgtctctgtgttgtggtactgactagttttatgtgctctgaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTCTTTGTTGCAAGTCTCCTACAAAGGCGGCTCATGATGATTGTTGACAAAC
||||||      ||  |  | || ||| | |  |     |||   |||   ||   ||  |   |       ||     |  || | ||   | || |||| ||||||||||||||||| ||||||||||| ||||| || |||||||||||  | ||     |||| || || ||||| ||| |  ||  ||||  ||
gtaagtg-----aaagtgttcttactgaatctca-----tga---ttctaatctgttgatttccttcaaaaataacatttttttctgtgaattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTCTTCATGGCGGCAATCCTGCAGAGACGGCTAATGGTTGTTTCTGACCTAC

upper sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 6
--------gtaagtccccccaacattctttttct--------------gcacca--tagtagctgagatttcgtgtcccatgtctctgtgtt---gtggtactgactagttttatg-tgctctgaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTCTTTGTTGCAAGTCTCCTACAAAGGCGGCTCATGATGATTGTTGACAAAC
         ||| |||  |     || |||||                 |||||   || |  ||  | | |       |      | |||    ||   | | |  |     ||| || |||| |||| ||||||||||| ||||| ||||||||||| |||||  | || ||||| ||  | |||    || | || |||||||| ||| |  |   |||    |
gtaagtagctaaatccaacttctgtttttttttctttatgaaaataacacaccaacaagcaaatgcaaatgcaaaaaaaaaagacatttgtcccagtaacattaatcatacaaatgatgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTTTTCATGGCAGCAATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCC

upper sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G051189_T01 (Zea mays), 3'ss of exon 1
-------gtaagtccccccaacattctttttctgcaccatagta--gctgagatttcgtgt-cccatgtctctgtgttgtggtactgactagttt-----tatgtgctctgaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTCTTTGTTGCAAGTCTCCTACAAAGGCGGCTCATGATGATTGTTGACAAAC
       |  | |||| |   ||     | | | | |  ||||   ||||  |     | |    |  | || |       |||  |  | | ||      |||  || || |||| ||||||||||||||||| ||||||||||| ||||| || |||||||||||  | |||    || | || || ||| | ||| |              
gtaaggagccattccctctcccaactactatgttctctttagttgtgctggcaagaattatatagaaatatcagcacacaagtaacggtttgcttgtggacatggtctttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGGATGTGTTCTATCTTCCTCTTCATGGCAGCCATCTTGCAGAGACGGTTGATGGTT-------------

upper sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 6
-------gtaagtccccccaacattctttttctgcaccatagta--gctgagatttcgtgt-cccatgtctctgtgttgtggtactgactagttt-----tatgtgctctgaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTCTTTGTTGCAAGTCTCCTACAAAGGCGGCTCATGATGATTGTTGACAAAC
       |  | |||| |   ||     | | | | |  ||||   ||||  |     | | |  |  | || |       |||  |  | |  |      |||  || || |||| ||||||||||||||||| ||||||||||| ||||| || |||||||||||  | |||    || | || || ||||| ||| |  |   |||  || 
gcaaggagccattccctctcccaactactatgttctctttagttgtgctggcaagaattatacagaaatatcagcacacaagtaacgctttgcctgtggacatggtctttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGGATGTGTTCTATCTTCCTCTTCATGGCAGCAATCTTGCAGAGACGGCTGATGGTTGTCTCTGATCAAG

upper sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G077669_T01 (Zea mays), 3'ss of exon 6
gtaagtccccccaacattctttttctgcaccatagtagctgagatttcgtgtcccatgtctctgtgttgtggtactgactagttttatgtgctctgaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTCTTTGTTGCAAGTCTCCTACAAAGGCGGCTCATGATGATTGTTGACAAAC
|||||    |    | |  |      |||  |   || | || || ||    | |  ||  |  | |    ||   |||  |||    ||  | || |||| || |||||||||||||| |||||||| || ||||| || |||||||||||  | |||    || | || || ||||| ||| |  |    ||   ||
gtaaggagtcattccctcgtccaatggcaagaatata-cagaaatatcagcacacgagtaacactttgcctgtg--gac--gtt----gtcttttgcagGTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTCTTCATGGCAGCAATCTTGCAGAGACGGCTGATGGTTGTCTCGGATCTAC

upper sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 6
gtaagtccccccaacattctttttctgcaccata-gtagctgagatttcgt-gtcccatgtctctgtgttgtggtactgactagttttatgtgctct----gaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTCTTTGTTGCAAGTCTCCTACAAAGGCGGCTCATGATGATTGTTGACAAAC
||| ||  | | ||  | ||  |||   || ||  |        |    || ||   || |   | ||     |   |||||| || | | |  |||    | ||||  |||||||||||||||| || |||||||| |||||||| || ||||| || || ||  || || | |||||||| || ||| |||||   || || |
gtatgttacac-aatctactacttcaatacaatgcgcgatcttaacagtgtagtagtattttcttatgcgtgtgctttgactaattgtgtattttcttggtgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCGGATAAGC

upper sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G13760.1 (Glycine max), 3'ss of exon 6
gtaagtccccccaacattctttttctgcaccatagtagctgagatttcgtgtcccatg----tctctgtgttgtggtactgactagttttatgtgctct----gaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTCTTTGTTGCAAGTCTCCTACAAAGGCGGCTCATGATGATTGTTGACAAAC
||| ||  |    ||| |||  | || ||    | |   |||| || |   | |  |     | |||    | ||||  |||||| || | | |  |||    | ||||  |||||||||||||||| || |||||||| |||||||| || ||||| || || ||  || || | |||||||| || ||| |||||   || || |
gtatgttac----acaatctactacttcaatgcaatgcttgagcttaccaatgcagtagtattttcttatctctggttttgactaattgtgtattttctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCCGATAAGC

upper sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 6
gtaagtccccccaaca-ttctttttctgcaccatagtagctgagatttcgtgtcccatgtctctgtgttgt--ggtactgactagttttatgtgctctgaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTCTTTGTTGCAAGTCTCCTACAAAGGCGGCTCATGATGATTGTTGACAAAC
 |          ||   ||  || |||  |||||||  | | |  | ||     |     |||| |         || ||  | ||| |      | ||||||| |||||||| || ||||| ||||||||||| ||||||||||| ||||||||||| ||||  ||  | |||||| ||||||||||||||   || |  |
-tgtactgttttaatggtttcttctcttaaccatag-ggataatttatctctctctgctcctctctaacactaaatattggtttgttcttccctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCAACACTGTTGCAAAGGAGGCTCATGATGATTTCAGAGAGCC

upper sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 6
--gtaagtccccccaacattctttttctgcaccatagtagctgagatttcgtgtcccatgtctctgtgttgtggtactgactagttttatgtgctctgaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTCTTTGTTGCAAGTCTCCTACAAAGGCGGCTCATGATGATTGTTGACAAAC
   ||  |       | |   | |     |  |   ||        | | |||  |  |   ||||| |  |  || |   |  |  |||||  | ||||||| ||||||||||| ||||| ||||||||||| ||||||||||| ||||||||||| |||  | || | ||||||||||||||| |||||| ||||||  
ccttattttggatatagaccatgtgaagacttctatgtgctccttctctggtgatcgttccttctgtttcttaatagttgtttttggtatgt-ttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCATCTATCTTGCAAAGGCGGCTCATGGTGATTGCTGACAAGT

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|124899872|gb|EH974490.1|EH974490
EST:     TTCCGCATTCCTCTGAATATCTTTGTCTGCGTTGTATTGTACAAT                         GTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGC
genomic: TTCCGCATTCCTCTGAATATCTTTGTCTGCGTTGTATTGTACAATgtaagtcccc ... tgctctgaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGC
EST: gi|47830344|gb|CK120028.1|CK120028
EST:     ACTTTTTCCGCATTCCTCTGAATATCTTTGTCTGCGTTGTATTGTACAAT                         GTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTC
genomic: ACTTTTTCCGCATTCCTCTGAATATCTTTGTCTGCGTTGTATTGTACAATgtaagtcccc ... tgctctgaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTC
EST: gi|86083914|gb|DR379673.1|DR379673
EST:     ACTTTTTCCGCATTCCTCTGAATATCTTTGTCTGCGTTGTATTGTACAAT                         GTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTC
genomic: ACTTTTTCCGCATTCCTCTGAATATCTTTGTCTGCGTTGTATTGTACAATgtaagtcccc ... tgctctgaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgtgtcccatgtctctgtgttgtggtactgactagttttatgtgctctgaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTCTTTGTTGCAAGTCTCCTACAAAGGCGGCTCATGATGATTGTTGACAAAC
                            tactgac  putative branch site (score: 1)
                                   tagttttat  TA-rich tract