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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttttggtcggaacagttctcaaaatttaatatttagccttaaggctctgaaatctaataatagatcaatatgtgaagGTTAAATGGAGCTATATTGTTGGAGATGCTTAGAGGAAGAAGACTTGTCTTTGTGGGTGATTCACTAAATAGGAACATGTGGGAATCTCTGGTTTGTATT

Basic information

species Arabidopsis thaliana
transcript AT5G06700.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G06700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g10560.1 (Oryza sativa), 3'ss of exon 1
----------gttagttttggtcggaa-cagttctcaaaatttaatatttagccttaaggc-tctgaaatctaataataga-tcaatatgtgaagGTTAAATGGAGCTATATTGTTGGAGATGCTTAGAGGAAGAAGACTTGTCTTTGTGGGTGATTCACTAAATAGGAACATGTGGGAATCTCTGGTTTGTATT
          |||| |   |   | || || || |    | ||  ||||    ||||  || |   |   ||||| |||   |   ||| | | | || |||  | ||    ||||||||| ||| || || | |||||| || || || ||||||||||| |||||||||||||||||||| ||||| || || 
gtgaggaaaagttactagagcaggcaatcaattttggtgaatttttattccatcttagtgcataacatgcctaattatattcttgttatatta-gATTGAATCCAACTGATATGTTGGAGAGGCTGAGGGGGAAAAGACTGGTTTTCGTTGGTGATTCACTTAATAGGAACATGTGGGAATCCCTGGTCTGCATC

upper sequence: AT5G06700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g53380.1 (Oryza sativa), 3'ss of exon 1
gttagttttggtcg---gaacagttct-caaaatttaatatttagccttaaggctctgaaatctaataat--agatcaat-atgt-----gaagGTTAAATGGAGCTATATTGTTGGAGATGCTTAGAGGAAGAAGACTTGTCTTTGTGGGTGATTCACTAAATAGGAACATGTGGGAATCTCTGGTTTGTATT
|| ||||  |       || ||  |||     ||| | |  || |  ||     |   | | || | |||  || || || ||||       || || ||      |    ||||||||| ||| || || |  || || || ||||| |||||||| || || ||||||||||||||||| |||||||| || 
gtgagttgagactacttgagcaactctgttttattcagttcttggtgtttcatgtgacacagctgaaaattcagttccatgatgttcataacagATTGAACCCGAGTGACATGTTGGAGAGGCTGAGGGGGAAGAGGCTGGTGTTTGTCGGTGATTCGCTCAACAGGAACATGTGGGAATCCCTGGTTTGCATC

upper sequence: AT5G06700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G033805_T01 (Zea mays), 3'ss of exon 1
-----gttagttttggtcggaacagttctcaaaatttaat-atttagccttaag---gctctgaaatctaataa-tagatcaatatgtga----agGTTAAATGGAGCTATATTGTTGGAGATGCTTAGAGGAAGAAGACTTGTCTTTGTGGGTGATTCACTAAATAGGAACATGTGGGAATCTCTGGTTTGTATT
     | ||   ||  | |||||| | |      |||||| ||||    | ||    | | || ||| |   || |  ||   | ||| |    || || ||   | |     ||||||||| ||| ||||||| |||||| || || || |||||||| || |||||||||||||||||||| || || ||||||
gtgaggataaggttact-ggaacaatgcaatggttttaattatttcatttcaatcttggtttgtaatttgtcaagttcatgtttgtgtcatttcagATTGAACCCAACCGATATGTTGGAGAGGCTGAGAGGAAAAAGACTGGTGTTCGTTGGTGATTCGCTCAATAGGAACATGTGGGAATCCCTTGTGTGTATT

upper sequence: AT5G06700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM5G843892_T01 (Zea mays), 3'ss of exon 1
---------------------------gttagttttggtcggaacagttctcaaaatttaatatttagccttaaggctctgaaa-tctaataatag-atcaatatgtgaagGTTAAATGGAGCTATATTGTTGGAGATGCTTAGAGGAAGAAGACTTGTCTTTGTGGGTGATTCACTAAATAGGAACATGTGGGAATCTCTGGTTTGTATT
                               | ||| ||     ||        | ||   | ||  || ||     | ||||| | || |  |   |||  | ||| | | || ||   | ||    ||||||||| ||| || || |  || || || |||||||||||||| || || ||||||||||||||||| ||| ||||||| 
gtgagaaaggtttatactgcaacaactacgcggtttagttactgcaccaaatgcagttctgtgtt--gctttttttttttgaaagtttagttctgtcatctgtgtgtta-gATTGAACCCAACTGATATGTTGGAGAGGCTGAGGGGGAAGAGGCTGGTGTTTGTGGGTGATTCGCTCAACAGGAACATGTGGGAATCCCTGATTTGTATC

upper sequence: AT5G06700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G165961_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------gttagtt-ttggt-cggaacagttctcaaaatttaatatttagccttaaggctctgaaatctaataatagatcaatatgtga-agGTTAAATGGAGCTATATTGTTGGAGATGCTTAGAGGAAGAAGACTTGTCTTTGTGGGTGATTCACTAAATAGGAACATGTGGGAATCTCTGGTTTGTATT
                                                       ||||||| ||||   |  |||  |       | |  |  ||    |||| | | | |  |||   |   |       | ||  ||||| ||   | ||    ||||||||| ||| || || |  || || || ||||| |||||||| || || ||||||||||||||||| ||| ||||||| 
gtgagaaaaaaagtacttcaacaactgcgccgttttggtgaattcaatagttatagttagttattggcgtgtgacaaatgcagttctgtgttgctttattttaaagttattagttctgtcacctgtgttgcttatgttagGTTGAACCCAACTGACATGTTGGAGAGGCTGAGGGGGAAGAGGCTGGTGTTTGTCGGTGATTCGCTCAACAGGAACATGTGGGAATCCCTGATTTGTATA

upper sequence: AT5G06700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0007g06680.t01 (Vitis vinifera), 3'ss of exon 1
-------------gttagttttggtcggaacagttc--tcaaaatttaatatttagccttaaggctctgaaatctaat--aatagatcaat-atgtgaagGTTAAATGG-AGCTATATTGTTGGAGATGCTTAGAGGAAGAAGACTTGTCTTTGTGGGTGATTCACTAAATAGGAACATGTGGGAATCTCTGGTTTGTATT
             ||   |||     | ||| | ||  || |  || | |   | |  ||    |  |||  |  | |   ||  ||  ||    |  ||||| ||||| ||  |||| ||||||  || | || ||||  ||||| || |||||||| ||||| || |||||||| |||||||||||||||||||| || 
atcctgttgtgttgtatttttataatgaaactgatccatctagtttaagttcctgggtttgttccagtgatgttgatttagatgaattgattgcattcagGTTGAATGGGAGTCATAT-GTTGGAACTGTTGAGGGGAAAGAGACTGGTTTTTGTGGGGGATTCTCTCAATAGGAATATGTGGGAATCTCTGGTTTGCATA

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|125298652|gb|EL312737.1|EL312737
EST:     AAAGATTTCCAGAAATTGAAGTGGAAACCTAAGAAATGTAGTTTACCAAG                         GTTAAATGGAGCTATATTGTTGGAGA
genomic: AAAGATTTCCAGAAATTGAAGTGGAAACCTAAGAAATGTAGTTTACCAAGgttagttttg ... atatgtgaagGTTAAATGGAGCTATATTGTTGGAGA
EST: gi|164093269|gb|ES052298.1|ES052298
EST:     AAAGATTTCCAGAAATTGAAGTGGAAACCTAAGAAATGTAGTTTACCAAG                         GTTAAATGGAGCTATATTGTTGGAGATGCTTAGAGGAAGAAGACTTGTCTT
genomic: AAAGATTTCCAGAAATTGAAGTGGAAACCTAAGAAATGTAGTTTACCAAGgttagttttg ... atatgtgaagGTTAAATGGAGCTATATTGTTGGAGATGCTTAGAGGAAGAAGACTTGTCTT
EST: gi|164136565|gb|EL969980.1|EL969980
EST:     AAAGATTTCCAGAAATTGAAGTGGAAACCTAAGAAATGTAGTTTACCAAG                         GTTAAATGGAGCTATATTG
genomic: AAAGATTTCCAGAAATTGAAGTGGAAACCTAAGAAATGTAGTTTACCAAGgttagttttg ... atatgtgaagGTTAAATGGAGCTATATTG
EST: gi|164153246|gb|EL999708.1|EL999708
EST:     AAGATTTTCCAGAAATTGAAGTGGAAACCTAAGAAATGTAGTTTACCAAG                         GTTAAATGGAGCTATATTG
genomic: AAGA-TTTCCAGAAATTGAAGTGGAAACCTAAGAAATGTAGTTTACCAAGgttagttttg ... atatgtgaagGTTAAATGGAGCTATATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttaatatttagccttaaggctctgaaatctaataatagatcaatatgtgaagGTTAAATGGAGCTATATTGTTGGAGATGCTTAGAGGAAGAAGACTTGTCTTTGTGGGTGATTCACTAAATAGGAACATGTGGGAATCTCTGGTTTGTATT
                             atctaat  putative branch site (score: 3)
                           aaatctaataatagat  TA-rich tract