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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttgtcttgttccctgtcacgtgtaattaattgctattttcttttggaatgctggttttgtcagttattgcaaattcgaaagatgatatactatggtaacagtggactgatgattcttttattaatgatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAACACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC

Basic information

species Glycine max
transcript GLYMA04G01220.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G01220.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 6
gtgtgttgtcttgttccctgtcacgtgtaattaattgctattttcttttggaatgctggttttgtcagttattgcaaattcgaaagatgatatactatggtaacagtggactgatgattcttttattaatg-atacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAACACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC
                                                     | |||  ||   |     | ||  ||  | |   |  | |  ||   |    |   |||  |  ||| |   || |||  | ||||| || |  |||||||||||| | |||||||| || || ||| |||| || ||||||||||| ||||| ||||| || || ||||| ||||| ||||| |
----------------------------------------------------gtactgtcttctactcaattcgctgataagcacagtactgtgttaattttcttgctaacttttttttcgtggttttatgtgttcagACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTATGGAACACTGTGAAGTCCTTTCTGGACCCAAAAACCACTTCCAAGATAC

upper sequence: GLYMA04G01220.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 6
gtgtgttgtcttgttccctgtcacgtgtaattaattgctattttcttttggaatgctggttttgtcagttattgcaaattcgaaagatgatatactatggtaacagtggactgatgattcttttattaatgatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAACACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC
                                                     |    |  |  |   || || ||   ||    | || | |  | || |   | |  | ||  | ||  ||| ||     | |||||||| | ||||||||||||| | |||||||| || || ||  ||||  | ||||||||||| ||||| ||||| ||||||||||| ||  | ||||| |
----------------------------------------------------gtatgagcctcatttttt-ttacactctcttttgttgtttt--tttgcttggaatatattg--ggttaatttgttgcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC

upper sequence: GLYMA04G01220.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G21520.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgtgttgtcttgttccctgtcacgtgtaattaattgctattttcttttggaatgctggttttgtcagtta-ttgcaaattcgaa-agatgatatactatggtaacagtggactgatgattcttttattaatgatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAACACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC
                                                              | | ||||| ||| |  ||| || |  |||| |    |   ||  |   |    ||  | | |  |   | || ||||||||   ||||||||||||||| ||||| |||||||||||||||||  | |||||||||||||||   ||||| || || || ||| || |||| ||||
-------------------------------------------------------------gtattagttaattggagcttctaatacttgatctcaggtatcaaatgctaatct-tggctttgtggtatttcatgcagACTCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTC

upper sequence: GLYMA04G01220.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 3'ss of exon 6
gtgtgttgtcttgttccctgtcacgtgtaattaattgctattttct--tttggaatgctggttttgtcagttattgcaaattcgaaagatgatatactatggtaacagtggactgatgattcttttattaatgatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAACACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC
                          ||| | ||    | | |  |    ||  | |||    |||| |   ||| |||| | || | | |  |    ||     |  ||||      | ||| |||  | || | |||||||| ||||||||||||||||| |||||||| ||||| ||||||||| | ||||||||||| ||| ||||||| ||||||||||||||||| |||||||
--------------------------gtattcaacctttttctgttgacatgataagctatagttgtaatccatttcaaaattgatataggtgactgaatatgtgccctggatcttgaactctctta--actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTCTGGAACACTGTAAAGACTTTTCTAGATCCCAAAACAACTTCCAAGATTC

upper sequence: GLYMA04G01220.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ17479 (Selaginella moellendorffii), 3'ss of exon 4
gtgtgttgtcttgttccctgtcacgtgtaattaattgctattttcttttggaatgctggttttgtcagttattgcaaattcgaaagatgatatactatggtaacagtggactgatgattcttttattaatgatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAACACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC
                                                                         |  |    |   | ||| |  |||||       |   ||||   ||  |   || || || |||||  |    |  |||||||||||||||||||| |||||||||| |||  ||||||||||  |   |   ||| | ||||| |||||| || | || ||  
-------------------------------------------------------------------------gtgagcctgctcgttga-actctatgcctttcttc--ctga--gtttatgcgtttattatgcagACATTGCATCGTATGTTTATTATAAATGCTGGTCCTGGATTTAAGCTTGTGTGGAACACCATACGGGGATTTTTAGATCCGAAAACAGCTACCAAAATAT

upper sequence: GLYMA04G01220.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ28804 (Selaginella moellendorffii), 3'ss of exon 4
gtgtgttgtcttgttccctgtcacgtgtaattaattgctattttcttttggaatgctggttttgtcagttattgcaaattcgaaagatgatatactatggtaacagtggactgatgattcttttattaatgatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAACACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC
                                                                         |  |    |   | ||| |  ||||| |     |   ||||   ||  |   || || || |||||  |    |  |||||||||||||||||||| |||||||||| |||  ||||||||||  |   |   ||| | ||||| |||||| || | || ||  
-------------------------------------------------------------------------gtcagcctgctcgttga-actctatgcttttcttc--ctga--gtttatgcgtttattatgcagACATTGCATCGTATGTTTATTATAAATGCTGGTCCTGGATTTAAGCTTGTGTGGAACACCATACGGGGATTTTTAGATCCGAAAACAGCTACCAAAATAT

upper sequence: GLYMA04G01220.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ23906 (Selaginella moellendorffii), 3'ss of exon 4
gtgtgttgtcttgttccctgtcacgtgtaattaattgctattttcttttggaatgctggttttgtcagttattgcaaattcgaaagatgatatactatggtaacagtggactgatgattcttttattaatgatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAACACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC
                                                                                 | |||    |   || | ||    |||     | ||  | ||| | | || | |||||| |   | |  | |||||||| ||||||||  ||||||| |||||||| |||||||| || |||   || || ||||||||||| |||||||| ||  
---------------------------------------------------------------------------------gtaagtctgttgcctttagtt-ttgtgctgaaaagaaacattt-tgattgttgcagACTTTGCACAAGCTTTTTATTATCAATGCTGGTGCTGGATTCAGGCTGTTATGGAACACAGTGAAGGGGTTCCTAGATCCCAAAACGACTTCTAAAATCA

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|192306575|gb|FG996237.1|FG996237
EST:     GGGAACTTATTACCCGATTGCAGAAGATTGATGGTGATAATTACCC-CA-                         ACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTG
genomic: GGGAACTTATTACCCGATTGCAGAAGATTGATGGTGATAATTACCCTGAGgtgtgttgtc ... aatgatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTG
EST: gi|11274643|gb|BF324980.1|BF324980
EST:     GGGAACTCATTACCCGATTGCAGAAGATTGATGGTGACAATTACCCTGAG                         ACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTG
genomic: GGGAACTTATTACCCGATTGCAGAAGATTGATGGTGATAATTACCCTGAGgtgtgttgtc ... aatgatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTG
EST: gi|151395356|gb|EV265227.1|EV265227
EST:     GGGAACTTATTACCCGATTGCAGAAGATTGATGGTGATAATTACCCTGAG                         ACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTG
genomic: GGGAACTTATTACCCGATTGCAGAAGATTGATGGTGATAATTACCCTGAGgtgtgttgtc ... aatgatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagatgatatactatggtaacagtggactgatgattcttttattaatgatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAACACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC
                                         tattaat  putative branch site (score: 2)
                               atgattcttttattaa  TA-rich tract