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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgccaattgatttcaaggcaagtatttatttggacttgctagttgcttgattctttacttaaatgaagcaattataaatgtgtttctaagGCAATTCTACAAATGGTTGCAGAACAAATGTAATGTTGGCTATGCATTCATCAATATGATTGATCCTGGACAAATTATTCCATTCCACCAG

Basic information

species Glycine max
transcript GLYMA06G17250.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G17250.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 12
gtatttgccaattgatttcaaggcaagtatttatttggacttgctagttgcttgattctttacttaaatgaa-gcaattataaatgtgtttctaagGC--AATTCTACAAA------TGGTTGCAGAACAAATGTAATGTTGGCTATGCATTCATCAATATGATTGATCCTGGACAAATTATTCCATTCCACCAG
                                          |     |  ||  |||||    |||| ||  |||| | | | |    ||  | | |  | || | |||       |  |  ||||||||||||||||| || ||||| || |||||||||| ||||||    || || || |||||| |  ||
------------------------------------------gtctactttttttttcttagtgtaaaagattgcaactgtgagtacaatttcaggactgacttttgcaatgttcacttttctcagAACAAATGTAATGTGGGGTATGCTTTTATCAATATGACTGATCCGCAGCACATAATCCCATTCTATAAG

upper sequence: GLYMA06G17250.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 12
gtatttgccaattgatttcaaggcaagtatttatttggacttgctagttgcttgattctttacttaaatgaagcaa---ttataaatgtgtttctaagGCAATTCTACAAATGGTTGCAGAACAAATGTAATGTTGGCTATGCATTCATCAATATGATTGATCCTGGACAAATTATTCCATTCCACCAG
            |  ||| ||     | |||||     |||    ||   |  |   |||   |||  |||  | |   || |     |||| ||||   |  || |       || ||||| |||||||||||||||||||| |||||||| ||||   || ||   || || ||||||||  | |||
-----------gtagtttgaaactttgaattta-----actcataagcgaccggggccttgtattagttgagactacttttgtgttcatgttactaaatgagatcaatctcctttt-cagAATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAG

upper sequence: GLYMA06G17250.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 12
gtatttgccaattgatttcaaggcaagtatttatttggacttgctagttgcttgattctttacttaaatgaagcaattataaatgtgtttctaagGCAATTCTACAAATGGTTGCAGAACAAATGTAATGTTGGCTATGCATTCATCAATATGATTGATCCTGGACAAATTATTCCATTCCACCAG
   |  |  |||   || || ||   | |||| |||||    |  | |  | |          | | ||      ||     ||  |  | |  |  ||||||        |||||||||||||| ||||| |||||||| ||  |||| ||||||||||||   || ||| |||||||||| |||
--gtaagtaaatc--ttgcatggattgaatttctttggggaagaaaatcacata---------tgacatatgcacatatctgattcgcctttttgcaaattctgt-----tttgcagAACAAATGCAATGTGGGCTATGCTTTTGTCAACATGATTGATCCTCTTCATATTGTTCCATTCCATCAG

upper sequence: GLYMA06G17250.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ29695 (Selaginella moellendorffii), 3'ss of exon 7
gtatttgccaattgatttcaaggcaagtatttatttggacttgctagttgcttgattctttacttaaatgaagcaattataaatgtgtttctaagGCAATTCTACAAATGGTTG--CAGAACAAATGTAATGTTGGCTATGCATTCATCAATATGATTGATCCTGGACAAATTATTCCATTCCACCAG
                                                               | |  | | || |  | || ||| |  ||         |  |   ||  ||  ||||| ||||| || |||||||||||||||||||| ||||  || || |  || ||  | || ||  || ||
--------------------------------------------------------------gtgattttaggcgagcaaaagtgtttccctggtattgaccggcttttgcctgtgcagAATAAATGCAACGTTGGCTATGCATTCATCAACATGACCGAGCCAGCTCACATCGTCCCCTTTTACAAG

upper sequence: GLYMA06G17250.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ28200 (Selaginella moellendorffii), 3'ss of exon 9
gtatttgccaattgatttcaaggcaagtatttatttggacttgctagttgcttgattctttacttaaatgaagcaattataaatgtgtttctaagGCAATTCTACAAATGGTTG--CAGAACAAATGTAATGTTGGCTATGCATTCATCAATATGATTGATCCTGGACAAATTATTCCATTCCACCAG
                                                               | |  | | || |  | || ||| |  ||        ||  |   ||  ||  ||||||||||| || |||||||||||||||||||| ||||  || || |  || ||  | || ||  || ||
--------------------------------------------------------------gtgattttaggcgagcaaaagtgtttccctggtattgatcggcttttgcctgtgcagAACAAATGCAACGTTGGCTATGCATTCATCAACATGACCGAGCCAGCTCACATCGTCCCCTTTTACAAG

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|16105757|gb|BI893497.1|BI893497
EST:     ATGCTTCTTGTTGCCATAGATGAGCAATGTCGAGGAACTTATGATTTTCT                         GTA-TT-TGCCAATTGATTTCAAGAACAAATGTAATGTTGGCTATGCATTC
genomic: ATGCTTCTTGTTGCCATAGATGAGCAATGTCGAGGAACTTATGATTTTCTgtatttgcca ... tgtttctaagGCAATTCTACAAATGG-TTGCA-GAACAAATGTAATGTTGGCTATGCATTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctagttgcttgattctttacttaaatgaagcaattataaatgtgtttctaagGCAATTCTACAAATGGTTGCAGAACAAATGTAATGTTGGCTATGCATTCATCAATATGATTGATCCTGGACAAATTATTCCATTCCACCAG
         gcttgat  putative branch site (score: 5)
                                             tgtttct  putative PPT
                       ttaaatgaagcaatta  TA-rich tract