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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacatctttggaaaagaaattataacacattaatattactgattatatacagaggctttccttggttttggtttgtcaattcagtaggataaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCACAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG

Basic information

species Glycine max
transcript GLYMA20G24790.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 6
gtatacatctttggaaaagaaattataacacattaatattactgattatatacagaggctttccttggttttggtttgtcaattcagtaggataaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCACAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG
                                                |   |  | ||||  |    | ||  ||      ||   |        |||||    |      ||| ||      |||  | | |||||||||||||||||||||| || |||||||| || || |||||||||||||| || ||||||||||| || || |||||||||
-----------------------------------------------gtgggccaacgcttaaccaaatatta-ttaactggttttctgctgctg-tttattcccagcaaactaacttgcc---aactgcatctgcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTTATTATGGGAATGGCCCCGGTCTTGGGAAAG

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 6
gtatacatctttggaaaagaaattataacacattaatattactgattatatacagaggctttccttggttttggtttgtcaattcagtaggataaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCACAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG
                                                      | |||    |    || | |     || |||  |  | ||  ||| |  | |  |  |||| |  |   ||    | | | |||||||||||||||||||| || |||||||| || || ||||| || ||||| || |||||||||||||| ||  ||||||||
---------------------------------------------------gtgggggcaaagc--aattattgaacaccatttcgtt--gctatttttcttctgagtgaattaactcatgccaagtg-catctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 6
gtatacatctttggaaaagaaattataacacattaatattactgattatatacagaggctttccttggttttggtttgtcaattcagtaggataaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCACAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG
                                              |   | || || |  |  || ||||||  |||  | ||   |    |     |  ||| ||  ||| | | |  ||| |      |||  ||||||||||||||||||| || |||||||| || || ||||| || ||||| || |||||||||||||| ||  ||||||||
---------------------------------------------gtgggtgcaaag-caattattcgttttg--ttgctattttttt----tctgagtgaattaactagttcatgctaattgca------tttatagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAG

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 6
gtatacatctttggaaaagaaattataacacattaatattactgattatatacagaggctttccttggttttggtttgtcaattcagtaggataaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCACAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG
                                                         |  |   |  |  |||      || |   |     |  |   ||||| |  ||||  |  |  |           |   ||||||| ||||||||||| || |||||||| || || |||||||| || || || |||||||||||||| || |||||||||
---------------------------------------------------------gtgtgtttaagcattgcacaaacactattgagctctgcaccaatattcagtggtt--aacttgtgccttttgtactcatagGAATTATCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCATCGGTTATTATGGGAATGGCTCCTGTATTGGGAAAG

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 6
gtatacatctttggaaaagaaattataacacattaatattactgattatatacagaggctttccttggttttggtttgt-caattcagtaggataa-atttatatttac-aggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCACAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG
                                          |    |  || ||| |  |   ||| |||    || | |||   |  |  |||   |   | ||| | | | |||    || | || | ||    | ||||||| |||||||| ||||| ||||| ||| | ||||| ||||| ||||| |||||||||||||||||||| ||||| |||
-----------------------------------------gtacacactta-agaagagtgtgttgatttcatattatgcaaaggaccaaaatactgtcggtgtttgctaagctta---cctataaatctacac--gtagGAATTATCATCAGACTCTTCTCAGCACGTCAGATCTGCATTGGCATCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 5
gtatacatctttggaaaagaaattataacacattaatattactgattatatacagaggctttccttggttttggtttgtcaattcagtaggataaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCACAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG
                                   | ||   | |    || ||   | |||||  | |  |        |     |||   |   |  ||||| || | |     ||| |   ||       || ||||  | |||||||| ||||| ||||||||| | ||||| ||||| ||||| |||||||||||||||||||| ||||| |||
---------------------------------gtacatgcttaagagaattcaattgttttccaagttccttacagaaaatcaacgtatagttgttgcatatt-actgat---gattcctcttaatgctacctgtagGAGCTATCATCAGACTCTTCTCAGCATGTCAGATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatacatctttggaaaagaaattataacacattaatattactgattatatacagaggctttccttggttttggtttgtcaattcagtaggataaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCACAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG
                                                       | |  | | |   || |   |   | | |   | |        | | |    |  ||    | | |    |    | | ||||||||| ||||| |||||||| || |||||||| |||||| | ||||||||||||||||| ||||||||  |  | || |||
-----------------------------------------------------gtaagactccttaaattctatataaacgagttgtttgatgtcccctgtctcgtaatattctgatacatactgatg--tctggcagGAATTATCATCGGATTCTTCTCAACATGTCCGCTCTGCTCTAGCTTCAGTAATAATGGGGATGGCTCCTATCCTTGGGAAG

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 5
gtatacatctttggaaaagaaattataacacattaatattactgattatatacagaggctttccttggttttggtttgtcaattcagtaggataaatttatatttacaggtttaagttctttgaaacaac-ttttgcagGAATTGTCATCAGATTCTTCACAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG
||   ||  |||   |||  | |             | |  |||  | |||| |  | ||    ||| |   |   |  | ||| ||    ||       | || |    | | | |  || |  |   | ||||| |||||||||||| |||||| || ||||||||||| ||||| |||||||||||  |||||||||||||||| || || ||||||
gtgctcacgtttattaaaagagt------------gtttctctgtat-tatataatgtctccttttgttcacgaacttactattgagcta-atgtgcacctgttgagctttctcaatatttggtgatgtcattttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTTTTAATGGGAATGGCTCCCGTCTTAGGAAAG

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|207745402|gb|GD715448.1|GD715448
EST:     TTCAGCATATTCTTCCTTGTGTGAAG                         GAATTGTCATCAGATTCTTCACAGCATGTCCGGTCTGCTTTGGCTTCAGTA
genomic: TTCAGCATATTCTTCCTTGTGTGAAGgtatacatct ... acttttgcagGAATTGTCATCAGATTCTTCACAGCATGTCCGGTCTGCTTTGGCTTCAGTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagtaggataaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCACAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG
                                              cttttgc  CT-rich tract
        ataaatttatatttac  TA-rich tract