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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatacctcaaaattccatcttccacagctgatattaatccagattgagaatgcacaagagtcatgctgaaaacctcttcaatatctgcagGATAATGTGCGGAATCAGCTGATCCAGTTCGAGTTGCTTCTGACGACTGCAACGTTTGTTGTAGCCATATTTGGGGTCGTTGCTGGGATCTTTGGGATGA

Basic information

species Arabidopsis thaliana
transcript AT1G16010.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os06g44150.1 (Oryza sativa), 3'ss of exon 4
-----gtaatacctcaaaattccatcttccacagctgatattaa-tccagattgagaatgcacaagagtcatgctgaaaacctcttca----------atatctgcagGATAATGTGCGGAATCAGCTGATCCAGTTCGAGTTGCTTCTGACGACTGCAACGTTTGTTGTAGCCATATTTGGGGTCGTTGCTGGGATCTTTGGGATGA
       |  | |||    | || || |||| | |||  || |  ||   ||   | || ||   |    || |  |     | | ||           |   | ||||| ||||| ||||| || |||||||| |||||  |  | || || |||||||| |||||||| ||||| ||||| || ||||||||||| ||||||||||
gtaaatcagcatctctct-taccctcatccata-ctgccatcacctcttcatcctgcatacaatgggcctataccaacttattttccatggctttgttgtgctttcagGACAATGTTCGGAACCAACTGATCCAATTCGAACTTTTACTCACAACTGCAACATTTGTTGTCGCCATTTTTGGAGTGGTTGCTGGGATATTTGGGATGA

upper sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G170326_T01 (Zea mays), 3'ss of exon 5
--------------gtaatacctcaaaattccatcttccacagctgatattaatccagattg-agaatgcacaagagtcatgctgaaaacctcttcaatatctgc--agGATAATGTGCGGAATCAGCTGATCCAGTTCGAGTTGCTTCTGACGACTGCAACGTTTGTTGTAGCCATATTTGGGGTCGTTGCTGGGATCTTTGGGATGA
               | ||||        |      |   ||  | |  || || ||  |   | | |||      ||  |  |  |      ||| |||| | |  |||| || |||||||| |||||||||||||| |||||||| || ||||||||||| |||||||| ||||| ||||| || ||||||||||| ||||||||||
gtacgtcgacatattttatactctgcttatttgggatatgcatatcaggtttatgcatttcccatactgctggtctgtgttatttgacttgagttccatatgttcctagGACAACGTGCGGAACCAGCTGATCCAGTTTGAGTTGCTCCTAACGACTGCAACATTTGTTGTGGCCATTTTTGGAGTGGTTGCTGGGATATTTGGGATGA

upper sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G108477_T01 (Zea mays), 3'ss of exon 4
gtaatacctcaaaattccatcttccacagct--gatattaat-ccaga--ttgagaat-----gcacaagagtcatgctgaa-------aacctcttcaatatctgcagGATAATGTGCGGAATCAGCTGATCCAGTTCGAGTTGCTTCTGACGACTGCAACGTTTGTTGTAGCCATATTTGGGGTCGTTGCTGGGATCTTTGGGATGA
||| | ||   | |||  ||  ||   |     ||||| |||  ||||  ||  | ||      |||    |   ||   ||        || |     || |    |||| ||||||||||| |||||||||||||| || ||||| || ||||| ||||| |||||||| ||||| || || || ||||||||||| || |||||||
gta-tgccagcatattttatgctctctattcgggatatgaatatcagagtttatgcatttctcacactgctggtctgtgtaacttatttgactttccatatgttcctagGACAATGTGCGGAACCAGCTGATCCAGTTTGAATTGCTGCTAACGACCGCAACATTTGTTGTGGCCATTTTCGGAGTGGTTGCTGGGATATTCGGGATGA

upper sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G064467_T01 (Zea mays), 3'ss of exon 4
----------------gtaatacctcaaaattccatcttccacagctgatattaatccagattgagaatgcacaagagtcatgctgaaaacctcttcaatatctgcagGATAATGTGCGGAATCAGCTGATCCAGTTCGAGTTGCTTCTGACGACTGCAACGTTTGTTGTAGCCATATTTGGGGTCGTTGCTGGGATCTTTGGGATGA
                || | | ||       |   | | | |  |  |  |   |    |  || ||  || |      ||||| | |    ||        |||||||||| || ||||| ||||||||||| |||||| |||| ||||| || || ||||| || || ||||| || ||||| ||  | ||| | || || ||||
tctctggcctatttgtgtgacaacttgtgcccctgccctgcccccccca-gtcgtttgtaacagaaaaaacaaag-----atgctcacagatgct--ggctgttgcagGATAACGTCCGGAACCAGCTGATCCAATTCGAGCTGCTCCTGACCACCGCCACGTTCGTGGTGGCCATCTTCGGGGTGGTCTCGGGGGTTTTCGGCATGA

upper sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S423_14V6.1 (Physcomitrella patens), 3'ss of exon 4
---gtaatacctcaaaattccatcttccacagctgatattaatcca--gattgagaatgcacaa----gagtcatgctgaaaacctcttcaatatctgcagGATAATGTGCGGAATCAGCTGATCCAGTTCGAGTTGCTTCTGACGACTGCAACGTTTGTTGTAGCCATATTTGGGGTCGTTGCTGGGATCTTTGGGATGA
    |  |   ||   |||   | ||    |  | || |  |   |    |  ||||    ||      | |  ||  |   |    |    | ||  ||||| ||||||||||||||||||||||| || ||| |  | || || || ||||| |||||  | ||||| | | | || || || ||  | ||||| ||||
atttttctttttctttatttt-ttttttgaatttaatctgcacgtactagtgaagaagatgcagtgctaatttttgtggctgatgggtatgttttcaacagGACAATGTGCGGAATCAGCTGATCCAATTTGAGCTTTTGCTCACAACAGCAACATTTGTGTTGGCCATCTATAGTGTGGTGGCAGGTGTGTTTGGAATGA

upper sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ37468 (Selaginella moellendorffii), 3'ss of exon 5
gtaatacctcaaaattccatcttccacagctgatattaatccagattgagaatgcacaagagtcatgctgaaaacctcttcaatatctgcagGATAATGTGCGGAATCAGCTGATCCAGTTCGAGTTGCTTCTGACGACTGCAACGTTTGTTGTAGCCATATTTGGGGTCGTTGCTGGGATCTTTGGGATGA
                                          || | |    |   ||   ||  | || ||    ||||   |     |||||| |||| ||||||||||| || ||||||||| |  ||||||| || |||||||||||  | ||  | | | |  || ||||||| || ||||| ||||
---------------------------------------gtaagctcgtctttctccacatgtgttactaaag---tcttgggtg---acagGATCATGTTCGGAATCAGCTTATTCAGTTCGAGCTCATTCTGACCACGGCAACGTTTGTGATGGCGTTCTATAGCATCATTGCTGGCATTTTTGGTATGA

upper sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ33960 (Selaginella moellendorffii), 3'ss of exon 5
gtaatacctcaaaattccatcttccacagctgatattaatccagattgagaatgcacaagagtcatgctgaaaacctcttcaatatctgcagGATAATGTGCGGAATCAGCTGATCCAGTTCGAGTTGCTTCTGACGACTGCAACGTTTGTTGTAGCCATATTTGGGGTCGTTGCTGGGATCTTTGGGATGA
                                          || | |    |   |    ||  | || ||    ||||   |     |||||| |||| ||||||||||| || ||||||||| |  ||||||| || |||||||||||  | ||  | | | |  || ||||||| || ||||| ||||
---------------------------------------gtaagctcgtttttctccccatgtgttactaaag---tcttgggtg---acagGATCATGTTCGGAATCAGCTTATTCAGTTCGAGCTCATTCTGACCACGGCAACGTTTGTGATGGCGTTCTATAGCATCATTGCTGGCATTTTTGGTATGA

upper sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ36513 (Selaginella moellendorffii), 3'ss of exon 5
gtaatacctcaaaattccatcttccacagctgatattaatccagattgagaatgcacaagagtcatgctgaaaacctcttcaatatctgcagGATAATGTGCGGAATCAGCTGATCCAGTTCGAGTTGCTTCTGACGACTGCAACGTTTGTTGTAGCCATATTTGGGGTCGTTGCTGGGATCTTTGGGATGA
                  |  ||||  ||  | | |  |||||   |      |     ||   ||| |       | || |   ||  ||||| |||||| |||| ||||||||||||||||||||||| || ||||| || ||||| || || || || ||||| ||  |||| ||  | || |||||||
----------------gtactttccg-agaagttgtcgatccaaggtttttcggtttttgatcgatggtctttgg-ttttgatcgtc--cagGACAATGTGAGGAACCAGCTGATCCAGTTCGAGTTGCTGCTCACGACCGCGACGTTCGTGGTGGCGATTTTTGGCGTGATTGCGGGTGTTTTCGGGATGA

upper sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ18545 (Selaginella moellendorffii), 3'ss of exon 5
gtaatacctcaaaattccatcttccacagctgatattaatccaga--ttgagaatgcacaagagtcatgctgaaaacctcttcaatatctgcagGATAATGTGCGGAATCAGCTGATCCAGTTCGAGTTGCTTCTGACGACTGCAACGTTTGTTGTAGCCATATTTGGGGTCGTTGCTGGGATCTTTGGGATGA
                                 || |  || |||  |||   || ||      |   | |    | |  |    | | | ||||| |||||| |||| |||||||||||||| |||||||| || ||||| || ||||| || || || || ||||| ||  |||| ||  | || |||||||
--------------------------------gtacttttcgagaagttgtcgatccaaggtttttcggtttttgatcgatggtctttgtccagGACAATGTGAGGAACCAGCTGATCCAGTTTGAGTTGCTGCTCACGACCGCGACGTTCGTGGTGGCAATTTTTGGCGTGATTGCGGGTGTTTTCGGGATGA

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|164002138|gb|ES015898.1|ES015898
EST:     GACACTGAAGATTTCATTAACATTCAACTG                         GATAATGTGCGGAATCAGCTGATCCAGTTCGAGTTGCTTCTGACGACTGCA
genomic: GACACTGAAGATTTCATTAACATTCAACTGgtaatacctc ... atatctgcagGATAATGTGCGGAATCAGCTGATCCAGTTCGAGTTGCTTCTGACGACTGCA
EST: gi|124740418|gb|EH831580.1|EH831580
EST:     AAGATTTCATTAACATTCAACTG                         GATAATGTGCGGGATCAGCTGATCCAGTTCGAGTTGCTTCTGACGACTGCA
genomic: AAGATTTCATTAACATTCAACTGgtaatacctc ... atatctgcagGATAATGTGCGGAATCAGCTGATCCAGTTCGAGTTGCTTCTGACGACTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatccagattgagaatgcacaagagtcatgctgaaaacctcttcaatatctgcagGATAATGTGCGGAATCAGCTGATCCAGTTCGAGTTGCTTCTGACGACTGCAACGTTTGTTGTAGCCATATTTGGGGTCGTTGCTGGGATCTTTGGGATGA
 tattaat  putative branch site (score: 2)
                                         ttcaatat  TA-rich tract