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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatgacaaatgtttagaagactttagctatctggtctactgttttatctgggttttgaatgggaagggcatttattgtaaagggagctagatcattttttttgtttctgtagtttatttatttccttaatgcatttgttattgatagtaatgcatatgttggggattcccaactcttcctttttgcagTTTCATTCCAATTGTATGATCTCAAACAACAAGGTTTTATTGAAAGACAGGAG

Basic information

species Glycine max
transcript GLYMA07G39940.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 5
gtaagaatgacaaatgtttagaagactttagctatctggtctactgttttatctgggttttgaatgggaagggcatttattgtaaagggagctagatcattttttttgtttctgtagtttatttatttccttaatgcatttgttattgatagtaatgcatatgttggggattcccaactcttcc-tttttgcagTTTCATTCCAATTGTATGATCTCAAACAACAAGGTTTTATTGAAAGACAGGAG
                                                                                    || |  | |||      || | || |    |      ||| | |  || |   || | || |  | |  ||     ||  ||  ||     | || | |  ||||||||||||||||||| || ||||||||||| |||||||| | |||||| ||||| |||
------------------------------------------------------------------------------------aaagttgatagtctgacttctatgctgtcctccaggttttctcttgtttacttatcttttctcaacaaaaa-----attctgaaga-----agctatgcaatttttgcagTTTCATTCCAGTTATATGATCTCAAGCAACAAGGCTATATTGAGAGACAAGAG

upper sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 4
gtaagaatgacaaatgtttagaagactttagctatctggtctactgttttatctgggttttgaatgggaagggcatttattgtaaagggagctagatcattttttttgtttctgtagtttatttatttccttaatgcatttgttattgatagtaatgcatatgttggggattcc---caactcttcc-tttttgcagTTTCATTCCAATTGTATGATCTCAAACAACAAGGTTTTATTGAAAGACAGGAG
                                                                                                |  ||| |||  | |||||   ||||    | | ||| ||  ||| || ||  |     ||            || ||     ||||| |  |  ||||||||||||||||| | ||||| ||||| |||||||| || |||||||||||||||
------------------------------------------------------------------------------------------------ttctttctttcttctctgtgccttatgc-ctgctttagtgttttttttttttttgtatttgagggcaaaaaatatcccttctgactctacaatccttgcagTTTCATTCCAACTTTATGACCTCAAGCAACAAGGCTTCATTGAAAGACAGGAG

upper sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 4
gtaagaatgacaaatgtttagaagactttagctat-ctggtctactgttttatctgggttt-tgaatgggaagggcatttattgtaaagggagctagatcattttttttgtttctgtagtttatttatt--tccttaatgcatttgttattgatagtaat--gcatatgttggggattcccaactcttcctttttgcagTTTCATTCCAATTGTATGATCTCAAACAACAAGGTTTTATTGAAAGACAGGAG
|||||  |   |  |  | ||| |||   |    | || || |     | | | || ||   ||| || ||  |  |   |    | |   |  | | | ||   ||| ||||       |||| |  |  | | | ||| ||||  |  ||||  | ||     |||||| ||||| || ||   || ||||| ||||||||||| ||| |||||||||| || |||||||| || |||||||||||||||
gtaag--ttgtagttagtaagaggacaaaataagttcttgtgtgtgtgtgtgtgtgagtgagtgagtgagagagagagagaggacagaca-atttggtttatgactttagtttactactcttatcttctacttcctgatg-atttcatgctgatgcttattgatgtatgtttgggatgccaaatcatttctttt-gcagTTTCATTTCAACTGTATGATCTAAAGCAACAAGGGTTCATTGAAAGACAGGAG

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|298196422|gb|HO041165.1|HO041165
EST:     TGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGT                         TTTCATTCCAATTGTATGATCTCAAACAACAAGGTTTTATTGAAAGACAGG
genomic: TGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGTgtaagaatga ... ctttttgcagTTTCATTCCAATTGTATGATCTCAAACAACAAGGTTTTATTGAAAGACAGG
EST: gi|151404635|gb|EV274449.1|EV274449
EST:     TGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGT                         CTTCATTCCAATTTGTATGATCTCAAACAACAAGGTTTTATTGAAAGACAG
genomic: TGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGTgtaagaatga ... ctttttgcagTTTCATTCCAATT-GTATGATCTCAAACAACAAGGTTTTATTGAAAGACAG
EST: gi|192304195|gb|FG993507.1|FG993507
EST:     TGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGT                         TTTCATTCCAATTGTATGATCTCAAACAACAAGGTTTTATTGAAAGACAGG
genomic: TGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGTgtaagaatga ... ctttttgcagTTTCATTCCAATTGTATGATCTCAAACAACAAGGTTTTATTGAAAGACAGG
EST: gi|9259434|gb|BE347581.1|BE347581
EST:     TGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGT                         TTTCATTCCAATTGTATGATCTCAAACAACAAGGGTTTATTGAAAGACAGG
genomic: TGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATAAGATTGAGTgtaagaatga ... ctttttgcagTTTCATTCCAATTGTATGATCTCAAACAACAAGGTTTTATTGAAAGACAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttattgatagtaatgcatatgttggggattcccaactcttcctttttgcagTTTCATTCCAATTGTATGATCTCAAACAACAAGGTTTTATTGAAAGACAGGAG
     tattgat  putative branch site (score: 3)
                                ttcccaactcttcctt  putative PPT
     tattgata  TA-rich tract