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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgcgtttttttttcttttctctttcatgattattattattattattattattattattggtacttgttttctattgttgaaattgatagtaatgtttaacttatatgtcaatatttttctttgtagAGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATA

Basic information

species Glycine max
transcript GLYMA08G01800.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 13
gtactgcgtttttttttcttttctctttcatgattattattattattattattattattattggtacttgttttctattgttgaaattgatagtaatgtttaacttatatgtcaatatttttctttgtagAGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATA
                                    |   | || |||  ||    ||   |||||   | ||     |||  ||||  ||  ||||  ||| |||     |||||        ||  ||  ||  | |||  ||||| ||||||  |||||||||| ||||||||||| | |||||||||||| |||||||||||||||||||| || ||||| || ||
-----------------------------------gtatatttttttacaatggaaatc--tggtataagcttatctgtgtgcaaataaattctaatacttatctt-----tcaat--------ttacagCTGAGGTTTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTA

upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os06g36080.1 (Oryza sativa), 3'ss of exon 11
----------gtactgcgtttttttttcttttctctttcatgattatt-attattattattattattattattggtacttgttttctattgttgaaattgatagtaatgtttaacttatatgtcaatatttttctttgtagAGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATA
             |  |  ||   |    ||| |  | | | | | || |||||  | ||| |    |  |   ||||     || |   ||   ||   | |||     || | || ||| |  ||   |||||   |||| ||  |||||||||| | ||||||| | ||| |||| ||||||||||| || ||||||||||| ||||| |||||||||||||| || || || |||||
gtaagaataaaagcgacacttaagtgaaatttgttgtgctttagtgttgattatactaattgtccagagaa--agtaccgaaattttgcagtgctaacatacagtttatgttcatttgtatattcat---tttctggctagATGAGGTATTCAAGGAAATTCAACCACTAATTAGATCAGTTCTTGATGGCTATAATGTTTGTATTTTTGCGTATGGTCAAACTGGATCAGGGAAAACATA

upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 13
gtactgcgtttttttttcttttctctttcatgattattattattattattattattattattggtacttgttttctattgttgaaattgatagtaatgtttaacttatatgtcaatatttttctttgtagAGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATA
                              |   ||||| ||  |  |  | | | ||||  |  |      || |    |  |  |  | | |  |    | ||| ||| |  |||  |  |     ||  ||| | |||   || |  ||||| |||||| |||| ||||||||||| | ||||||||| || ||||| ||||| |||||||| || ||||| |||||
-----------------------------gtatatattagtaagagcaggaatttaattaaagaaaaaaaaatt-tggcatacagttgaacattgctcacaagcttttat-ttgataactcac-----agCTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATA

upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G062034_T01 (Zea mays), 3'ss of exon 4
gtactgcgtttttttttcttttctctttcatgattattattatt--attattattattattattggtacttgttttctattgttgaaattgatagtaatgtttaacttatatgtcaatatttttctttgtagAGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATA
       ||  |  |  | ||    |   |  ||   | || ||  ||   | | |||  |||  |||||  |    ||    |||  |  |||  | | |||  | ||| | ||  | || ||  || ||||     | ||||| || | ||  ||| | ||| |||| ||||||||||| ||||||||||| || ||||| |||||||||||||| || ||||| ||| |
-------gtgctaatgacattgaaataaaaatatatcttttgtttaatctatttaattgctataagtactcataaaatagcactgagtt--ata-cattttttgtcatatctttctttcttgtttgttatagATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA

upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G124883_T01 (Zea mays), 3'ss of exon 4
gtactgcgtttttttttcttttctctttcatgattattattattattattattattattattggtacttgttttctattgttgaaattg-atagtaatgtttaacttatatgtcaatatt--tttctttgtagAGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATA
                               |  |||  | | | |||    | |||||| ||||   |  | |  | | |  || ||| ||  |    | |  || | |      | ||   |  |||  ||  ||  |||||   || |  |||||  ||||  |||| |||||||||||||  ||||| || || ||||| |||||||||||||| || |||||||| ||
-------------------------------gtatatcttaactcttaagtatgttattaatggt--ctaatctaaaatttaaaagttgtatcattggatattgctcacaaagttttcttacctaatttccagCTGAGGTATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTA

upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G323622_T01 (Zea mays), 3'ss of exon 4
gtactgcgtttttttttcttttctctttcatgattattattattattattattattattattggtacttgttttctattgttgaaattg-atagtaatgtttaacttat--atgtcaatatttttctttgtagAGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATA
                                        ||| ||  | | |||  ||| |||| |    | |  | | |  || ||| ||| |    | | ||| |   |  |   |    |  |||  ||  ||| |||||   || |  || ||  ||||  |||| |||||||||||||  ||||| || || ||||| |||||||||||||| || |||||||| ||
---------------------------------------gtat-atcttaagtat-gttaatggtgc--aatctaaaatttaaaagttgtataattgaatattactcaccaagttttcttgcctaatttccagTTGAAGTATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTA

upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 13
lower sequence: AT5G41310.1 (Arabidopsis thaliana), 3'ss of exon 11
gtactgcgtttttttttcttttctctttcatgattattattattattattattattattattggtacttgttttctattgttgaaattgatagtaatgtttaacttatatgtcaatatttttctttgtagAGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATA
                                       ||        |   | |  | ||  | | | | |   | |||  |  ||   | |  |  |||| | |||||    ||| | |   || ||||||| | |||   || |||| |||  ||||||||||  |||||||||| |||||||| ||||||||||||||||| || || || || |||||||| ||
--------------------------------------gttcaagcctcttccacttattttatttcatatatgaaaatgtatagttttggacttgtaattaattaatatg----tatatatgcgtgcagAGGAAGTTTTCTTAGATACTCGACCTATGATTCGATCCATTCTTGATGGCTACAATGTATGTATATTTGCTTATGGCCAGACGGGTTCTGGAAAGACTTA

upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 13
lower sequence: AT1G63640.1 (Arabidopsis thaliana), 3'ss of exon 13
gtactgcgtttttttttcttttctctttcatgattattattattattattattat-tattattggtacttgttttctattgttgaaattgatagtaatgtttaacttatatgtcaatatttttctttgtagAGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATA
                                 ||   |    | |   | |||| |||| || |   || |  |||||  |        ||| | || || |  |  |   ||  | || |  | |||||||||  | |||   || |||| |||||| ||||||||  |||||||||| || ||||||||||||||||| |||||||| ||||| || ||||| || ||
--------------------------------gtttaaacctctttccctcttatgtattgttagcgttt-tcctctataat--------ata-tgatattcatatcctgaatc--tgttatcttatgtagAGGAGGTTTTCTTAGATACTCGACCATTAATTCGATCCATTCTTGATGGCTATAATGTTTGTATATTTGCCTATGGTCAGACTGGTTCTGGAAAAACTTA

upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv02s0025g03480.t01 (Vitis vinifera), 3'ss of exon 14
---------gtactgcgtttttttttcttttctctttcatgattattat-tattattattattattattattggtacttgttttctattgttgaaattgatagtaatgtttaacttatatgtcaatatttttctttgt-agAGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATA
          ||     |||| | ||      | |||| | |||  ||| |  |   |||  ||||    || | |    |||  ||     ||| ||   | |  |  |    |||| |||  |||  ||   || | ||||||  ||||    |||||||||||||| ||||||||||| |||||||| |||||||| ||||||||||| ||||||||||||||||| ||||| || ||
gttatcttcttataatattttatatttggccttgtttctttatttgtatatcctcagatttctattccacttagcatgcttttgttaggaaagaacttttaact--tactacctttatttgtatatacattgtgttatcagAGGAGGTATTTTTAGACACTCAACCATTAATTCGATCTGTACTTGATGGATACAATGTCTGTATATTTGCCTATGGTCAAACTGGCTCTGGAAAAACCTA

upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ19920 (Selaginella moellendorffii), 3'ss of exon 8
gtactgcgtttttttttcttttctctttcatgattattattattattattattattattattggtacttgttttctattgttgaaattgatagtaatgtttaacttatatgtcaatatttt-tctttgtagAGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATA
                                                                              |  | ||  |     ||| || |   | || | | ||  |  | | |||| |||  || |||||  ||| ||||| |||||||| || || ||||||||||| ||||| || ||||| ||||| ||||||||||| ||||||||||| || ||
-----------------------------------------------------------------------------gtagtaaagcttccgttaaagtct---tgatgtataaacttgatatgtttgcagAACAAGTATTCCTGGATACTCAGCCATTGATACGGTCAGTTCTTGATGGTTACAACGTGTGTATTTTTGCGTATGGTCAAACAGGCTCGGGAAAAACGTA

upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ12333 (Selaginella moellendorffii), 3'ss of exon 8
gtactgcgtttttttttcttttctctttcatgattattattattattattattattattattggtacttgttttctattgttgaaattgatagtaatgtttaacttatatgtcaatatttt-tctttgtagAGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATA
                                                                              |  | ||  |     ||| || |   | || |   ||  |  | | |||| |||  || |||||  ||| ||||| |||||||| || || ||||||||||| ||||| || ||||| ||||| ||||||||||| ||||||||||| || ||
-----------------------------------------------------------------------------gtagtaaagcttccgttaaagtct---tgatgtagaaacttgctatgtttgcagAACAAGTATTCCTGGATACTCAGCCATTGATACGGTCAGTTCTTGATGGTTACAACGTGTGTATTTTTGCGTATGGTCAAACAGGCTCGGGAAAAACGTA

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|208091383|gb|GD885872.1|GD885872
EST:     TCGCAAGCTTTTTAAATTTAATAAGGTTTTCGGTCAAGCAACAAGTCAAG                         AGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGT
genomic: TCGCAAGCTTTTTAAATTTAATAAGGTTTTCGGTCAAGCAACAAGTCAAGgtactgcgtt ... ttctttgtagAGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgttgaaattgatagtaatgtttaacttatatgtcaatatttttctttgtagAGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATA
                      gtttaac  putative branch site (score: 3)
                                        tatttttcttt  putative PPT
                  taatgtttaacttata  TA-rich tract