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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacatctttggaaaagaaattataacacattagtattactgattatatacagaggcttttcttggttttggttggtcaattcagtatgctaaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG

Basic information

species Glycine max
transcript GLYMA10G42250.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 6
gtatacatctttggaaaagaaattataacacattagtattactgattatatacagaggcttttcttggttttggttggtcaattcagtatgctaaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG
                                                |   |  | ||||  |    | ||  |   |   ||     ||||   |||||    |      ||| ||      |||  | | |||||||||||||||||||||| ||||||||||| || || |||||||||||||| || ||||||||||| || || |||||||||
-----------------------------------------------gtgggccaacgcttaaccaaatattattaactggttttctgctgctg--tttattcccagcaaactaacttgcc---aactgcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTTATTATGGGAATGGCCCCGGTCTTGGGAAAG

upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 6
gtatacatctttggaaaagaaattataacacattagtattactgattatatacagaggcttttcttggttttggttggtcaattcagtatgctaaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG
                                                         |  | | |  |  |||      || |   |    ||  |   ||||| |  ||||  |  |  |           |   ||||||| ||||||||||| ||||||||||| || || |||||||| || || || |||||||||||||| || |||||||||
---------------------------------------------------------gtgtgtttaagcattgcacaaacactattgagctctgcaccaatattcagtggtt--aacttgtgccttttgtactcatagGAATTATCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCATCGGTTATTATGGGAATGGCTCCTGTATTGGGAAAG

upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 6
gtatacatctttggaaaagaaattataacacattagtattactgattatatacagaggcttttcttggttttggttggtcaattcagtatgctaaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG
                                                      | |||    |    || | |     || |||  |  ||||  ||| |  | |  |  |||| |  |   ||    | | | |||||||||||||||||||| || |||||||| || || ||||| || ||||| || |||||||||||||| ||  ||||||||
---------------------------------------------------gtgggggcaaagc--aattattgaacaccatttcgtt--gctatttttcttctgagtgaattaactcatgccaagtg-catctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG

upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 6
gtatacatctttggaaaagaaattataacacattagtattactgattatatacagaggcttttcttggttttggttggtcaattcagtatgctaaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG
                                              |   | || || |  || || |||||| |  |  | ||   | | || | |    ||| ||  ||| | | |  ||| |      |||  ||||||||||||||||||| || |||||||| || || ||||| || ||||| || |||||||||||||| ||  ||||||||
---------------------------------------------gtgggtgcaaag-caattattcgttttgtt--gctatttt--ttttctgagt--gaattaactagttcatgctaattgca------tttatagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAG

upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 6
gtatacatctttggaaaagaaattataacacattagtattactgattatatacagaggcttttcttggttttggttggtcaattcagtatgctaaatttatatttac-aggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG
                                      |      |||   | || |  ||   ||  | ||         |  ||  || ||   |   | ||| | | | |||    || | || | ||    | ||||||| |||||||| ||||||||||| ||| | ||||| ||||| ||||| |||||||||||||||||||| ||||| |||
-------------------------------------gtacacacttaagaagagtgtgttgatttcatattatgcaaaggac-caaaatact--gtcggtgtttgctaagctta---cctataaatctacac--gtagGAATTATCATCAGACTCTTCTCAGCACGTCAGATCTGCATTGGCATCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG

upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 5
gtatacatctttggaaaagaaattataacacattagtattactgattatatacagaggcttttcttggttttggttggtcaattcagtatgctaaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG
                                     ||   | |    || ||   | ||| |  | |  |    |   |     ||||  |   |  ||||| || | |     ||| |   ||       || ||||  | |||||||| ||||||||||||||| | ||||| ||||| ||||| |||||||||||||||||||| ||||| |||
---------------------------------gtacatgcttaagagaattcaattgttttccaagttccttacagaaaatcaacgtatagttgttgcatatt-actgat---gattcctcttaatgctacctgtagGAGCTATCATCAGACTCTTCTCAGCATGTCAGATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG

upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatacatctttggaaaagaaattataacacattagtattactgattatatacagaggcttttcttggttttggttggtcaattcagtatgctaaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG
                                                       | |  |   |   || |   |   | | |   |          | | |    |  ||    | | |    |    | | ||||||||| ||||| ||||||||||| |||||||| |||||| | ||||||||||||||||| ||||||||  |  | || |||
-----------------------------------------------------gtaagactccttaaattctatataaacgagttgtttgatgtcccctgtctcgtaatattctgatacatactgatg--tctggcagGAATTATCATCGGATTCTTCTCAACATGTCCGCTCTGCTCTAGCTTCAGTAATAATGGGGATGGCTCCTATCCTTGGGAAG

upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 5
gtatacatctttggaaaagaaattataacacattagtattactgattatatacagaggcttttcttggttttggttggtcaattcagtatgctaaatttatatttacaggtttaagttctttgaaacaac-ttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG
||   ||  |||   |||  | |            || |  |||  | |||| |  | ||  | ||| |   |      | ||| ||  |  |       | || |    | | | |  || |  |   | ||||| |||||||||||| |||||| || ||||||||||| ||||| |||||||||||  |||||||||||||||| || || ||||||
gtgctcacgtttattaaaagagt------------gtttctctgtat-tatataatgtctccttttgttcacgaacttactattgagc-taatgtgcacctgttgagctttctcaatatttggtgatgtcattttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTTTTAATGGGAATGGCTCCCGTCTTAGGAAAG

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|207759469|gb|GD731252.1|GD731252
EST:     GGATTTTAAATCCAGATCTTTCAATTCAGCATATTCTTTCTTGTGTGAAG                         GAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTA
genomic: GGATTTTAAATCCAGATCTTTCAATTCAGCATATTCTTTCTTGTGTGAAGgtatacatct ... acttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTA
EST: gi|151407658|gb|EV277473.1|EV277473
EST:     CCAGATCTTTCAATTCAGCATATTCTTTCTTGTGTGAAG                         GAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTA
genomic: CCAGATCTTTCAATTCAGCATATTCTTTCTTGTGTGAAGgtatacatct ... acttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTA
EST: gi|254331030|gb|GR842295.1|GR842295
EST:     GGATTTTAAATCCAGATCTTTCAATTCAGCATATTCTTTCTTGTGTGAAG                         GAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTA
genomic: GGATTTTAAATCCAGATCTTTCAATTCAGCATATTCTTTCTTGTGTGAAGgtatacatct ... acttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTA
EST: gi|7926502|gb|AW832528.1|AW832528
EST:     GGATTTTAAATCCAGATCTTTCAATTCAGCATATTCTTTCTTGTGTGAAG                         GAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTA
genomic: GGATTTTAAATCCAGATCTTTCAATTCAGCATATTCTTTCTTGTGTGAAGgtatacatct ... acttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTA
EST: gi|26057519|gb|CA800433.1|CA800433
EST:     GGATTTTAAATCCAGATCTTTCAATTCAGCATATTCTTTCTTGTGTGAAG                         GAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTA
genomic: GGATTTTAAATCCAGATCTTTCAATTCAGCATATTCTTTCTTGTGTGAAGgtatacatct ... acttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagtatgctaaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG
      tgctaaa  putative branch site (score: 2)
                                              cttttgc  putative PPT
         taaatttatatttaca  TA-rich tract