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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaactgcatcttttgaatgctattcttgaaaacttgtttggacttctagatgaaaagaaaattcgtttgaaaatgactcaatcattcggtgtttgttatgcttgacttgcagGCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTACTCCAGTTATGGTTAGTGTTGCCAAATCCTTCGATGCTCCAATTAAG

Basic information

species Arabidopsis thaliana
transcript AT2G03120.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os05g36070.2 (Oryza sativa), 3'ss of exon 7
gtaagaactgcatcttttgaatgctattcttgaaaacttgtttggacttctagatgaaaagaaaattcgtttgaaaatgactcaatcattcggtgtttgttatgcttgacttgcagGCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTACTCCAGTTATGGTTAGTGTTGCCAAATCCTTCGATGCTCCAATTAAG
              |    |||   | ||    | | |||| |  ||  |   ||      ||   |  ||      | |||      |   ||| |  |     || | |  |||   ||||| |||||||||||||| |||||||| ||||| |||||||||||||| ||||||||||| || || ||||||||||| |||
-----------gcttgcgaaattaaagtcc---atatttgtatacaccaccgtattgtgtaaagcatttttaatttgtaacttttgtgtatcgtggtattcccttttaatt--cagAGCGGACTCTTTTTCTATGATATTTTCTGGGTCTTCTTCACTCCAGTTATGGTCAGTGTTGCCAAGTCATTTGATGCTCCAATAAAG

upper sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g02530.3 (Oryza sativa), 3'ss of exon 6
gtaagaactgcatcttttgaatgctattcttgaaaacttgtttggacttctagatgaaaagaaaattcgtttgaaaatgactcaatcattcggtgtttgttatgcttgacttgcagGCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTACTCCAGTTATGGTTAGTGTTGCCAAATCCTTCGATGCTCCAATTAAG
        |  || | | |||  |||||    |   |||| |     || || || |  |  || ||     |   |||  |||      |||  |||  | |  |||| |  ||||| || || |||||||||||||| |||||||||||||| ||||| |||||||| |||||||| ||||| || ||||| || || |||
---cctgttatatttgtagaa-actattgc--actgcttgctgtactttgtaaatcactattaagttgtaacgcttatgtatca------cgggatttccttt--ttgatt--cagGCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATGGTCAGTGTTGCAAAATCATTTGATGCACCGATAAAG

upper sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G044348_T04 (Zea mays), 3'ss of exon 7
gtaagaactgcatcttttgaatgctattcttgaaaacttgtttggacttctagatgaaaagaaaattcgtttgaaaatgactcaatcattcggtgtttgttatgcttgacttgcagGCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTACTCCAGTTATGGTTAGTGTTGCCAAATCCTTCGATGCTCCAATTAAG
     || ||   ||      |||  ||   ||  |  ||  |    || |       ||  | |||| | || |||||       ||||     ||  || | |||   || ||||  ||||| ||| | ||||| || |||||||| ||||| |||||||||||||| ||||| || ||||| |||||||||||||| |||
---gtaattggggctagcccttgcattttgagagcatctgaattattttatgttcattaattacattcatatgtaaatg-------cattt----ttccttttcctt--tttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG

upper sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G150251_T01 (Zea mays), 3'ss of exon 7
gtaagaactgcatcttttgaatgctattcttgaaaacttgtttggac-ttctagatgaaaagaaaattcgtttgaaaatgactcaatcattcg---gtgtttgttatgcttgacttgcagGCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTACTCCAGTTATGGTTAGTGTTGCCAAATCCTTCGATGCTCCAATTAAG
                      | |  | |     ||||||||  || || |    |  ||  |   ||  || |  || ||      ||  |   |   ||||  |  |  | || ||||  ||||| ||| | ||||| || |||||||| ||||| |||||||||||||| ||||| || ||||| || |||||||| || |||
--------------------gagttgatttcttctacttgtttcaacattgtgccagtgaatcattctctgttcattattacatgcatatgtgaatgcaattgtccttttccatttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAG

upper sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G08620.2 (Glycine max), 3'ss of exon 7
gtaagaactgcatcttttgaatgctattcttgaaaacttg--tttggacttctagatgaaaagaaaattcgtttgaaaatgactcaatcattcggtgtttgttatgcttga--cttgcagGCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTACTCCAGTTATGGTTAGTGTTGCCAAATCCTTCGATGCTCCAATTAAG
                    |  |  || || |||  |      |   ||| |   || | |      || |||       |     || ||   | | |   || | ||    || ||||| || |||||| | ||||| || |||||||||||||| |||||||| |||||||| ||||| ||||| || ||||||||||| |||
--------------------agtcagttattaaaagatcaaacatatgcttttcattgtataattctctctttttgtttcaatatggtctttgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTTAGCGTTGCAAAATCATTTGATGCTCCAATAAAG

upper sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 7
gtaagaactgcatcttttgaatgctattcttgaaaactt--gtttggacttctagatgaaaagaaaattcgtttgaaaatgactcaatcattcggtgtttgttatgcttga--cttgcagGCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTACTCCAGTTATGGTTAGTGTTGCCAAATCCTTCGATGCTCCAATTAAG
                 | | | |  || || |||  ||  |  |   ||| |   || | |     ||  |||    |  |    ||| ||   | | |   || | ||    || ||||| || |||||| | ||||| || |||||||||||||| || ||||| ||||| || ||||| ||||| || ||||||||||| |||
-----------------ttagt-cagttattaaaagattaagcatatgcttttcattgtataactccttttttttttca--atatgatctttgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG

upper sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 7
gtaagaactgcatcttttgaatgctattcttgaaaacttgtttggacttctagatgaaaagaaaattcgtttgaaaatgactcaatcattcggtgtttgt-tatgcttgacttgcagGCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTACTCCAGTTATGGTTAGTGTTGCCAAATCCTTCGATGCTCCAATTAAG
              ||        |||| |||    ||  | |  |   ||        |   | || ||||| |  |  || | | |||       ||  ||     || |||||||||||||| ||| | |||||||| |||||||| ||||| |||||||| ||||| |||||||| || |||||||||||||| ||||||
--------------ttgatgccagtatttttgtcc-ctcatatctatgcctgttcctgcattcagtttgtttgtactt--ctaagtgatttttgacatgggtacttgcgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG

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|116442939|gb|EG485531.1|EG485531
EST:     GAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTG                         GCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTACTCCAGTTATG
genomic: GAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTGgtaagaactg ... tgacttgcagGCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTACTCCAGTTATG
EST: gi|124947402|gb|EL023243.1|EL023243
EST:     GAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTG                         GCAGGACTATTTTT
genomic: GAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTGgtaagaactg ... tgacttgcagGCAGGACTATTTTT
EST: gi|125304424|gb|EL318509.1|EL318509
EST:     GAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTG                         GCAGGACTATTTT
genomic: GAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTGgtaagaactg ... tgacttgcagGCAGGACTATTTT
EST: gi|164089581|gb|EL994182.1|EL994182
EST:     GAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTG                         GCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTA
genomic: GAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTGgtaagaactg ... tgacttgcagGCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTA
EST: gi|125192206|gb|EL207160.1|EL207160
EST:     GAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTG                         GCAGGACTTATTTTTCTATGATATCTTCTGGGTTTTC
genomic: GAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTGgtaagaactg ... tgacttgcagGCAGGACT-ATTTTTCTATGATATCTTCTGGGTTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaattcgtttgaaaatgactcaatcattcggtgtttgttatgcttgacttgcagGCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTACTCCAGTTATGGTTAGTGTTGCCAAATCCTTCGATGCTCCAATTAAG
                                          gcttgac  putative branch site (score: 4)
        tttgaaaat  TA-rich tract