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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagatctctttcactggatatgattggctttcttgtgattgaatatggatttgtttgattatgttcgaaatgatgtgttttttctattatagGTTTTGTTAGGAACAGACTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTG

Basic information

species Arabidopsis thaliana
transcript AT4G13430.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 4
gtaaagatctctttcactggatatgattggctttcttgtgattgaatatggatttgtttgattatgttcgaaatgatgtgttttttctattat--agGTTTTGTTAGGAACAGACTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTG
          ||| || || || ||         ||  ||   |||| |||  | |||| || | |   | | | |  || |     | || |  ||||| |  | || || || || || || || | ||||||||| ||||| |||||||| || || ||||||||||||||||| ||||||||| | |||||||
-------gtacttccagtgaatgtg---------ctaatgcaggaatctgg--tggtttcat-aggacaggattaacctgctccaattgttgtctagGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAATTTGCAACTGGAATTGGAAACACTGATGCTGGTTTTGTGATGGGCACTG

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 5
gtaaagatctctttca-ctggatatgattggctttcttgtgattgaatatggatttgtttgattatgttcgaaatgatgtgttttttctattatagGTTTTGTTAGGAACAGACTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTG
      | ||   | |  |    |||    | |  | |||||||| |   | |  |||| |       |   |||  | |    || ||||  |||||| |  | || || || || || || || | ||||||||| |||||||||||||| || || ||||||||||||||||||||||||||| | |||||||
----gtaccttgctgagttttccatgtacaggtcacctgtgattgta---gaacatgttgggaagcact---aatcttctccaattgctatc-tagGTTCTCCTGGGTACTGATTCTCATACGTGCAATGCTGGAGCCTTTGGTCAATTTGCAACCGGAATTGGAAACACTGATGCAGGTTTTGTGATGGGCACTG

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G010044_T02 (Zea mays), 3'ss of exon 4
gtaaagatctctttcactggatatgat-tggctttcttgtgattgaatatggatttgtttgattatgttcgaaatgatgtgttttttctattatagGTTTTGTTAGGAACAGACTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTG
      | ||     | |   |  | |   |||  | |||||||| | ||    |||  ||    |  |  |  || |    ||| | |    |||||| | || || || || || || || || | ||||||||| |||||||| ||||| || || || |||||||||||||||||||||||||| |||||||
----gtaccttgccgagtctttcagctacagctcgcctgtgattggacata---ttgggtggcgttaattaacctgctccaatttctgt----tagGTTCTCTTGGGCACTGATTCTCATACATGCAATGCTGGAGCTTTTGGTCAGTTTGCAACTGGAATCGGAAACACTGATGCAGGTTTTGTGTTGGGCACTG

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 5
gtaaagatctctttcactggatatgattggctttcttgtgattgaatatgg---atttgtttga------ttatgttcgaaatgatgtgttttttctattat----agGTTTTGTTAGGAACAGACTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTG
       | |  ||   |  | | | ||   ||| || |  |  |  || |   ||||||||||      ||  ||||    |    |  ||| ||| |||     ||||| | ||||| || || || ||||||||||||||||||||||||||||||||||||||||||||||| || |||||||| || |||||| | || ||||
------gtttgcttagtttaacaagtttttttttattatagtgaagcattgttcatttgtttgacagaagtttggttcctcctttgctaatttctctgttacctgcagGTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGTAATACTGATGCCGGCTTTGTGCTGGGAACTG

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 5
gtaaagatctctttcactggatatgattggctttcttgtgattgaatatgg---atttgtttga------ttatgttc--gaaatgatgtgttttttctattat----agGTTTTGTTAGGAACAGACTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTG
     | || |||    |    |   ||   ||| || |  |  | ||| |   ||||||||||      ||  ||||  |   || |   || | ||| |||     ||||| | ||||| || || || |||||||||||||||||||||||||| |||||||||||||||||||| || |||||||| || |||||| | || ||| 
----ggttcgcttagtttaaccagtttttattttattatagtgaagtattgttcatttgtttgacagaagtttggttcctgctttgctaatttctctctgttacctgcaGGTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGCCAATTTGCTACAGGGATTGGTAATACTGATGCTGGCTTTGTGCTGGGAACT-

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 5
gtaaagatctctttcactggatatgattggctttcttgtgattgaatatggatttgtttgattatgttcgaaatgatgtgttttttctattatagGTTTTGTTAGGAACAGACTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTG
    |  | ||| | |    |  | |   |   | ||   |||  | ||  |   |||| |         | ||| | || |   |  || |||||| ||||| || || || || |||||     | |||||||||||||| || ||||| |||||  |||| ||||||||||||| |||||| ||||| || |
--gtaagtttctgttaacaaagctaa---gacatgttaaaatttgaaatctacaggtttca--------aagatgttctgatcacttgataatagGTCTTGTTTGGTACTGATTCTCACACCACATCAGCTGGAGCATTTGGCCAGTTTGCCACAGGAGTTGGTAACACTGATGCAGCTTTTGTATTAGGGACAG

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 3'ss of exon 5
gtaaagatctctttcactggat-atgattggctttcttgtgattgaatatggatttgt-ttgattatgttcgaaatgatgtgttttttctattatagGTTTTGTTAGGAACAGACTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTG
      || ||| |  |   || ||  ||   | | ||   |||   ||    ||| | || |  ||  | |     |  | |    | | | | ||||  || | || || ||||| ||||| ||||||||||| |||||||| || |||||||| || || || ||||| ||||| |||||||| || |||||||
--gtgcatttctcttgccaaatcattttttaatctgtt-caattttttaatcctttatattcacaatacttgttg-aacctttacactttctcacagGTCCTGCTGGGTACTGACTCCCACACATGTACTGCTGGGGCATTTGGCCAGTTTGCTACTGGAATAGGTAACACCGATGCTGGTTTTGTATTGGGCACTG

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 3'ss of exon 5
gtaaagatctctttcactggatatgatt---ggctttcttgtgattgaatatggatttgtttg-attatgttcgaaatgatgtgttttttctattatagGTTTTGTTAGGAACAGACTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTG
    | || ||| |  |    |    ||      | | ||   | |   |||   ||| | || |  |   | |        | | |    | | | ||||  | ||||| || ||||| ||||| ||||||||||| |||||||| || || ||||| || || || ||||||||||| | ||| || ||||||||||
--gtacatttctcttgccaagtcctttttcaaaatctatttaaactttttatatctttatatgcacaacacttgttgaaccctatatacattctcacagGTCCTCTTAGGTACTGACTCCCACACATGTACTGCTGGGGCATTTGGCCAGTTCGCTACTGGAATAGGTAACACTGATGCTGCTTTCGTATTAGGCACTG

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S227_66V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------gtaaagatctctttcactggatatgattggctttcttgtg-attgaatatggatttgtttgattat------gttcgaaatgat-gtgttttttctat-tatagGTTTTGTTAGGAACAGACTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTG
                                       |||  |     | |  || | |   ||  ||   |  ||  |    || |  | || || |||| |      |||  | | ||| |||  ||   |     |||||| | || || ||||| || |||||||| | ||||||||| |||||||| ||||| |||||||| || |||||||||||||| ||| |  | ||||| |
gtatttgttacggaagttttcgttactgtcgaatatgccgtagtgcataatgttgctcgttgacatatgcagccccgtctaccacatttacagtttttggatttttcgcaagttaaatacgatcgtggcttcaatgggcgtagGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAGTTTGCAACAGGGATCGGTAACACTGATGCAGGCTTTATTATGGGCACCG

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ32611 (Selaginella moellendorffii), 3'ss of exon 4
gtaaagatctctttcactggatatgattggctttcttgtgattgaatatggatttgtttgattatgttcgaaatgatgtgttttttctattatagGTTTTGTTAGGAACAGACTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTG
                                    || |  |||   | ||| | ||  |||  ||  || | | |    || || |  | |||||| | || ||||| ||||| || ||||| ||||||||||| ||||| ||||| ||||| || || |||||||| ||||| |||||  |  | || ||||
-----------------------------------gtgagtctgatatttgatgtcttgtattgcgtgagagacggttcagttgttgt-ctctagGTTCTTTTTGGAACTGACTCGCATACTTGCACTGCTGGAGCGTTTGGACAATTCGCTACTGGAATAGGAAACACCGATGCTGGTTTCATCATGGGAACTG

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ16664 (Selaginella moellendorffii), 3'ss of exon 2
gtaaagatctctttcactggatatgattggctttcttgtgattgaatatggatttgtttgattatgttcgaaatgatgtgttttttctattatagGTTTTGTTAGGAACAGACTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTG
                                    || |  |||   | ||| | ||  |||  ||  || | | |    || || |  | |||||| | || ||||| ||||| || ||||| ||||||||||| | ||| ||||| ||||| || || |||||||| ||||| |||||  |  | || ||||
-----------------------------------gtgagtctgatctttgatgtcttgtattgcgtgagagacggttcagttgttgt-ctctagGTTCTTTTTGGAACTGACTCGCATACTTGCACTGCTGGAGCGTCTGGACAATTCGCTACTGGAATAGGAAACACCGATGCTGGTTTCATCATGGGAACTG

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|124795951|gb|EH885630.1|EH885630
EST:     GTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAG                         GTTTTGTTAGGAAC
genomic: GTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAGgtaaagatct ... tctattatagGTTTTGTTAGGAAC
EST: gi|124979374|gb|EL052433.1|EL052433
EST:     GTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAG                         GTTTTGTTAGGAACAGACTCACACACTTGT
genomic: GTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAGgtaaagatct ... tctattatagGTTTTGTTAGGAACAGACTCACACACTTGT
EST: gi|124752085|gb|EH842215.1|EH842215
EST:     TGTTTGCCATGTTGCACTTGCACAAGAAGGTCAATTGCAGGCCAGGAGAG                         GTTTTGTTAGGAACA
genomic: TGTTTGCCATGTTGCACTTGCACAAGAAGGTCA-TTGCAGGCCAGGAGAGgtaaagatct ... tctattatagGTTTTGTTAGGAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgaatatggatttgtttgattatgttcgaaatgatgtgttttttctattatagGTTTTGTTAGGAACAGACTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTG
               gtttgat  putative branch site (score: 5)
                                        ttttttctatt  putative PPT
                                      tgttttttctattata  TA-rich tract