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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtagaaaatcttgttgccccttttagattttacttcctgttttgcttctctgtctattgtgatggttctgtgttttgtttctcattgtcctcattgaagaatgtatgatggtaacaaaatttttgtatcttttatcagATGAGAAGATAGCACTATTGGGTGCTATCCAGTCGCTCTTTGAAGGATCTATGTATACTTTTGTATTCCTCTGGACTCCTGCTCTAAGTCCGAACGATGA

Basic information

species Arabidopsis thaliana
transcript AT4G27720.1
intron # 4
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 4
lower sequence: GRMZM2G067638_T01 (Zea mays), 3'ss of exon 4
gtgagtagaaaatcttgttgccccttttagattttacttcctgttttgcttctctgtctattgtgatggttctgtgttttgtttctcattgtcctcattgaagaatgta--tgatggtaacaaaatttttgtatcttttatcagATGAGAAGATAGCACTATTGGGTGCTATCCAGTCGCTCTTTGAAGGATCTATGTATACTTTTGTATTCCTCTGGACTCCTGCTCTAAGTCCGAACGATGA
                                               |    | || |   |||  | | |  |    | | ||     |    | | |||   ||  |  ||| |   |   || || || |  ||    |||| |||||||| ||| |  | || || || |||||  | ||||| ||||| ||||||||||| || ||||| |||||||||||||| || || || |||||
-----------------------------------------------gtaggtttggcc--tgtcctagcttaggaaatggctt---gataaatttagtgagttataaaattgacgtggaaggaacttgtgaaattt----cagACGAGAAGATTGCATTGCTTGGAGCCATACAGTCATTGTTTGAGGGATCAATGTATACTTTCGTTTTCCTGTGGACTCCTGCTCTGAGCCCAAAGGATGA

upper sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 4
gtgagtagaaaatcttgttgccccttttagattttacttcctgttttgcttctctgtctattgtgatggttctgtgttttgtttctcattgtcctcattgaagaatgtatgatggtaacaaaatttttgtatcttttatcagATGAGAAGATAGCACTATTGGGTGCTATCCAGTCGCTCTTTGAAGGATCTATGTATACTTTTGTATTCCTCTGGACTCCTGCTCTAAGTCCGAACGATGA
                               | ||| |   || | |  |  | | |  ||     | ||  ||| || |  |||  ||||| ||     |     ||    || | || | ||| || | |  ||   ||||||| || |||||  |  |||||||||| ||||| ||||||||||| || ||||| || ||||| || || |||||||||||  | || || || |||||
-------------------------------tcttattctgtgatcttttattttattcatctc--ttgtcttgtattcttgttcatattgtacttcccaa-----gttcattgtttactacattctt-tgtgctt---cagATGAAAAAATAGCCTTGCTGGGTGCTATACAGTCTCTCTTTGAAGGTTCAATGTACACCTTTGTGTTTCTGTGGACTCCTGCATTGAGCCCAAATGATGA

upper sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G13760.2 (Glycine max), 3'ss of exon 4
gtgagtagaaaatcttgttgccccttttagattttacttcctgttttgcttctctgtctattgtgatggttctgtgttttgtttctcattgtcctcattgaagaatgtatgatggtaacaaaatttttgtatcttttatcagATGAGAAGATAGCACTATTGGGTGCTATCCAGTCGCTCTTTGAAGGATCTATGTATACTTTTGTATTCCTCTGGACTCCTGCTCTAAGTCCGAACGATGA
                              ||| |  |  |  || |  || |   ||| ||||        ||| || |  |||  ||||| ||     |     ||    |  | ||   ||| ||      |   |||||||| ||||||||  |  ||||||| || ||||| ||||||||||| || ||||| || ||||| || || |||||||||||  | || || || |||||
---------------------------cttattctgttatcatttatttttattcatctcttgt------cttgtattcttgttcatattgtacttcccaa-----gttcattttttactgcattctt----tctgcctcagATGAAAAGATAGCCTTGCTGGGTGCCATACAGTCTCTCTTTGAAGGTTCAATGTACACCTTTGTGTTTCTATGGACTCCTGCATTGAGCCCAAATGATGA

upper sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtagaaaatcttgttgccccttttagattttacttcctgttttgcttctctg-tctattgtgatggttctgtgttttgtttctcattgtcctcattgaagaatgtatgatggtaacaaaatttttgtatcttttatcagATGAGAAGATAGCACTATTGGGTGCTATCCAGTCGCTCTTTGAAGGATCTATGTATACTTTTGTATTCCTCTGGACTCCTGCTCTAAGTCCGAACGATGA
                                | || || || | || ||||| || | |||| |    | |  |   ||| ||| | ||| || |  |      || | | ||  |   |   ||  |||       |||||||||||| |||||| |  ||||||| || ||||| || |||||||| || ||||| || ||||| ||||| |||||||||||| | |||||||| || ||
-------------------------------atatattttctttctttcttctttgatttattttatatgcttggaagtttcttttttattttcttttt------at-tttaatattgttatgtttcatgtg-----gatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA

upper sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtagaaaatcttgttgccccttttagattttact-tcctgttttgcttctctgtctattgtgatggttctgtgttttgtttctcattgtcctcattgaagaatgtatgatggtaacaaaatttttgtatcttttatcagATGAGAAGATAGCACTATTGGGTGCTATCCAGTCGCTCTTTGAAGGATCTATGTATACTTTTGTATTCCTCTGGACTCCTGCTCTAAGTCCGAACGATGA
                            |   ||| || |||   |  | || ||  ||| ||        | |    ||| || |||     | |  ||| ||  |      | |||  |   ||  |||   |     |||||||||| || ||  |  ||||||| || |||||| | |||||||| || |||||||||||||| ||||||||||||||||||||||| || || || ||
---------------------------cattgtttgctatcccaatgggtttatccatctgtttcctcatcttttcagttttttcctc-----ctttcttggagctt------tagtattatgtttcatgtggtt-----cagATGAGAAAATTGCGTTGCTGGGTGCAATTCAGTCGTTGTTTGAAGGCTCAATGTATACTTTTGTGTTCCTCTGGACTCCTGCTCTAAGCCCAAATGAAGA

upper sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S8_271V6.1 (Physcomitrella patens), 3'ss of exon 4
---------gtgagtagaaaatcttgtt---gccccttttagattttacttcctgttttgctt--ctctg-----tctattgtgatggttctgtgttttgtttctcattgtcctcattga--------agaatgtatgatggtaacaaaattt--ttgtatcttttat----cagATGAGAAGATAGCACTATTGGGTGCTATCCAGTCGCTCTTTGAAGGATCTATGTATACTTTTGTATTCCTCTGGACTCCTGCTCTAAGTCCGAACGATGA
          ||||| | | |  |  ||   || |    |   |  ||||| |       | |   ||||     |  |   | |||  |    |||| ||       ||      ||||        | | |   | | | |       | |  |||| ||  | |     |||||||||||||||| || |||||||| ||||||||  | ||||| || || ||||| || ||||| ||||||||||| || ||  | || || |||||| |
gtaagattgatgagttgtagacatatttcaagctctgactgattcatacttacgaccaaacatagttctgaaagtttcaaattaatgtgtgctcgtttggtactgagatggaggatttgagatcagccaaagtaagtcacgatgctgggttgtgattgtgtcactgaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCA

upper sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S18_8V6.2 (Physcomitrella patens), 3'ss of exon 4
------------------------------------gtgagtagaaaatcttgttgccccttttagattttact--tcctgttttgcttctctgtctatt---gtgatggttctgtgttttgtttctcattgtcctcattgaagaatgtatgatggtaacaaaatttttgtatctt--ttatcagATGAGAAGATAGCACTATTGGGTGCTATCCAGTCGCTCTTTGAAGGATCTATGTATACTTTTGTATTCCTCTGGACTCCTGCTCTAAGTCCGAACGATGA
                                     |  | |    ||  |   |  |   | || ||  |    || |||||   |  | | | || |   ||  ||    | ||||  |   |   ||     |||  | ||||   | ||  |        || ||| | |   ||  ||||||||||||| ||  | |||||||| |||||||| || ||||||||||| |||||||| ||||||||||| ||||| || ||  | || || |||||| |
gtgagaacttaagtgcttatggacgagtttcaagacatttgcacttcattctcgcggtcaaatgaggttgcaaaggtcttgtttctatcatttatttacttaagtactgtgcttttgttcggcaccaagttcgtggcatgtaggaattcttaattctggtctccattgtgtctttggattgacagATGAGAAGATTGCTTTGTTGGGTGCCATCCAGTCCCTGTTTGAAGGATCCATGTATACGTTTGTATTCCTTTGGACACCAGCCTTGAGCCCTAACGATCA

upper sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S44_143V6.1 (Physcomitrella patens), 3'ss of exon 4
----------gtgagtaga-aaatcttgttgccccttttagattttacttcctgttttgcttctc----tgtctattgtgatggttctgtgttttgtttctcattgtcctcattgaagaatg--tatgatggtaacaaaatt---------tttgtatcttttat----cagATGAGAAGATAGCACTATTGGGTGCTATCCAGTCGCTCTTTGAAGGATCTATGTATACTTTTGTATTCCTCTGGACTCCTGCTCTAAGTCCGAACGATGA
           ||  | ||  |||||    |    | || |  ||       |  ||     |      | | |||  | ||| ||  |  || | |||||| | | |     ||   | ||  | | ||  |   | ||||          |||||  | ||      ||||||| ||||| || || |||||||||||||| ||  | || ||||| || |||||||| ||||| ||||||||||| || ||  | |||||  | ||| |
gtaagatcaaatgtcttgacgaatctgagcgtaattcttcgtcttccacaagtacttaaacacatatggtttgtatcttaatgctttagatttctatttctcctggacgcttgtgtgcagtgattgtaatattgtgagaattgggatcttacttgtaaatgttgctatgcagATGAAAAGATTGCTCTTTTGGGTGCTATCCAATCCTTGTTCGAAGGTTCCATGTATACATTTGTTTTCCTCTGGACACCAGCATTGAGTCCTTATGATCA

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|125062675|gb|EL130934.1|EL130934
EST:     CAAGGACTTGCTTACCCAGTTCAGAGGTGCTGCAGTGGCCATTGCCTCTG                         ATGAGAAGATAGCACTATTGGGTGCTAT
genomic: CAAGGACTTGCTTACCCAGTTCAGAGGTGCTGCAGTGGCCATTGCCTCTGgtgagtagaa ... cttttatcagATGAGAAGATAGCACTATTGGGTGCTAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtcctcattgaagaatgtatgatggtaacaaaatttttgtatcttttatcagATGAGAAGATAGCACTATTGGGTGCTATCCAGTCGCTCTTTGAAGGATCTATGTATACTTTTGTATTCCTCTGGACTCCTGCTCTAAGTCCGAACGATGA
                         tggtaac  putative branch site (score: 2)
                                    tttttgtatctttt  putative PPT
                            taacaaaatttttgta  TA-rich tract