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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtttctcttacagcattctcctcttcctttttgacctatttatttcttacttagtctttcatttttatttcggatttgaaaggttttttaaaatttgactgacaattatctcattttaattgagttatctgcctagtgggataagactttgttgttattgtatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA

Basic information

species Glycine max
transcript GLYMA06G09320.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
gtcagtttctcttacagcattctcctcttcctttttgacctatttatttcttacttagtctttcatttttatttcggatttgaaaggttttttaaaatttgactgacaattatctcattttaattgagttatctgcctagtgggataagactttgttgttattgtatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
                                        ||   || |  |  ||| | ||  ||| |   | |  ||  | |  | |  ||  || |  |||     |||| |   | | | | |  |  ||    | ||    || |      |||||||     || |||||||||| |||||||| || ||||||||||||||||||||||||||||||||||| ||||| || || || |||||  | ||||| |||||||| || ||
---------------------------------------gtaaagatcttgttttta-tgttcaattctcgatgcacatgcggagtgctagtttgaagt--actactttttatatgtatctgagt-atctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 12
gtcagtttctcttacagcattctcctcttcctttttgacctatttatttcttacttagtctttcatttttatttcggatttga-aaggttttttaaaatttgactgacaattatctcattttaattgagttatctgcctagtgggataagactttgttgttattgtatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
                                                         ||   | || |||  |||  |   || |||||| ||  | || | | |   | |  ||||  ||  | | |||| |                 | ||   | |||||  || ||| |||||| || |||||||| || || |||||||||||||||||||||||||||||||| || || || || || |||||  | |||||||||||||| || ||
---------------------------------------------------------gtaact-atgtttgcttcacacaggataaggttgttacacatcttatt---actggtctctattgtactaagttgt---------------gaagttccctattatt--atttgc-agATCCTACCTACATGATCCGAGCTATTCCAAGCAATGCATCAGACAATGTCTACTGCACGCTGCTGGCCCACAGTGCTATTCATGGTGCAATGGCCGGCTA

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 12
gtcagtttctcttacagcattctcctcttcctttttgacctatttatttcttacttagtctttcatttttatttcggatttgaaaggttttttaaaatttgactgacaattatctcattttaattgagttatctgcctag--tgggataagactttgttgttattgtatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
                                                                                      |   |||  || |    |      |||     | || |||    |  |  ||||  |||  |  |||  | ||   || | |  || ||||||| || |||||| | || || ||||||||||||||||||||||||||||||||||||||||| || || |||||  |||||||||||||||| |||||
-----------------------------------------------------------------------------------gtagccatttgtaactcttatttttgctatt--gatatagttgtaacacatttctagattggtctgtgacaatatt-ccatcggaattggcagATCCTACATACATGGTCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTAGCCCACAGTGCTATCCATGGTGCAATGGCGGGGTA

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 12
gtcagtttctcttacagcattctcctcttcctttttgacctatttatttcttacttagtctttcatttttatttcggatttgaaaggttttttaaaatttgactgaca-attatctcattttaattgagttatctgcctagtgggataa-gactttgttgttattgtatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
                                                                           | | | |     |||||||    |||    ||  | | |    || ||||| | |    || | ||     | | ||  |   ||  ||| | |     |||||||||||||||||| || || ||||||||||||||||||||||||||||| || || || || || || |||||  | |||||||||||||| || ||
---------------------------------------------------------------------------gtaatcgtcttctttttta---cttggtgaacgcagtgttagtttgtaattta-tagcatgtcaaggaatctgatgaagtgcctgccatttttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTATTGCACCCTGCTCGCACATAGTGCCATTCATGGTGCAATGGCGGGATA

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 12
gtcagtttctcttacagcattctcctcttcctttttgacctatttatttcttacttagtctttcatttttatttcggatttgaaaggttttttaaaatttgactgacaattatctcattttaattgagttatctgc-ctagtgggataagactttgttgttattgtatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
                                                                                | |  | |||| |     | |  | |   ||   | |    ||  || ||    ||   |      | |||   || ||||||  || |||| ||||||||| |||||||| || || ||||| ||||| || || || ||||||||||| ||||| || ||||| ||||  |||||||| || ||||| || ||
-------------------------------------------------------------------------------gtcagtgattttct----ctggtatcatgcttgctttacggcaa--gaattgctagcatcaaatatctcaga---tgctgttatccta-ctgc-agATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 10
lower sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 11
gtcagtttctcttacagcattctcctcttcctttttgacctatttatttcttacttagtctttcatttttatttcggatttgaaaggttttttaaaatttgactgacaattatctcattttaattgagttatct-gcctagtgggataagactttgttgttattgtatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
                                                                                                 |  |  || |  |   |  |||  | | ||| ||  | |  |  ||   ||  | | ||   | |    || |  ||||||| || |||||||| || || ||||||  ||||||||| ||||| |||||||  || || ||||| || || |||||||||||||||||||| || ||
------------------------------------------------------------------------------------------------gtacgtttgtcc-tccccaaattcaagtcgagctacatagattcatgaattagaaatatgac-tcaaaccatgtttcagATCCGACATACATGATCCGAGCTATTCCAGCCAATGCATCTGACAACGTCTACTCAACTCTCCTTGCCCAAAGCGCAGTCCATGGTGCAATGGCTGGCTA

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 11
gtcagtttctcttacagcattctcctcttcctttttgacctatttatttcttacttagtctttcatttttatttcggatttgaaaggttttttaaaatttgactgacaattatctcattttaattgagttatctgcctagtgggataagacttt--gttgttattg--tatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
                                                                                      ||   || | |||||  |     |||| |  ||||  ||      |  || ||||   |  ||| | |  | | |  |    | |||  ||||||| || |||||||| || || |||||| |||||||||| |||||||| ||||| ||||| |||||||| ||||| || ||||| ||||||||||| ||
----------------------------------------------------------------------------------gtcagtgacttcagatttgtgtt-tgtttatttatttttccttttagatttggcttagtaacaatagattctaagctatcctgagttgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGTACTGCACACTCCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGTTA

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
gtcagtttctcttacagcattctcctcttcctttttgacctatttatttcttacttagtctttcatttttatttcggatttgaaaggttttttaaaatttgactgacaattatctcattttaattgagttatctgcctagtgggataagactttgttgttattgtatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
                           |  |  | || ||  || |   |||  || || |||  |||     | || | |     ||  ||  | |||    |||     |  || ||||| | |  || |  | ||    | ||| || |   |    |    ||    |||||||||| ||||||||||| ||  ||||||||||||| || ||||| || ||||| ||  | |||||||| || ||  ||||||| || |||||||||||
--------------------------gtggccatatgcccagttgaaaactt--ttggttttttctttgctgcttggttctc----gtgcttctatattca--tga-----aattccttttagtcg--tttttaggct---tgaatatgagtac-tcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA

upper sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S282_45V6.1 (Physcomitrella patens), 3'ss of exon 12
gtcagtttctcttacagcattctcctcttcc--tttttgacctatttatttcttacttagtctttcatttttatttcggatttgaaaggttttttaaaatttgactgacaattatctcattttaattgagttatc-tgcctagtgggataagactttgttgttattgtatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
         |     |||  ||  || |||    | ||||   ||     ||   |||  |  |  |  | | |    |||||   |   | |    ||||   || ||| |     ||  |  || | | | |         |  ||     | || | |  || || ||||| |||||| || || |||||||| ||||||||||||||||| || |||||||||||||| ||| | || ||||| || ||  ||||||| || |||||||||||
--------gtacagtagccgtcaactgttctaactgttgagtgatggtgatccgtcttcctggtctacatctgtc---gattttttacactgtggggaatt--gcttacattctggccacgtccatggtgatcttgcattcgataagactgctcattat-gccatagt-tctgc-agATCCGACGTATATGATTCGAGCAATTCCAAGCAATGCTTCGGACAATGTCTACTGCACATTGCTGGCTCATAGCGCCATCCATGGGGCTATGGCAGGGTA

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|254330797|gb|GR842062.1|GR842062
EST:     GATCACTTTGCAAGGAAGGATAAAATGCCCATCAATCTTAAATATATAG                         ATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATCACTTTGCAAGGAAGGATAAAATGCCCATCAATCTTAAATATATAGgtcagtttct ... tatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|57576052|gb|CX549023.1|CX549023
EST:     GATCACTTTGCAAGGAAGGATAAAATGCCCATCAATCTTAAATATATAG                         ATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATCACTTTGCAAGGAAGGATAAAATGCCCATCAATCTTAAATATATAGgtcagtttct ... tatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|15814347|gb|BI786622.1|BI786622
EST:     ATAAAATGCCCATCAATCTTAAATATATAG                         ATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCT
genomic: ATAAAATGCCCATCAATCTTAAATATATAGgtcagtttct ... tatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|7234213|gb|AW569552.1|AW569552
EST:     GATCACTTTGCAAGGAAGGATAAAATGCCCATCAATCTTAAATATATAG                         ATCCAACTTACATGATTCCGGCAATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATCACTTTGCAAGGAAGGATAAAATGCCCATCAATCTTAAATATATAGgtcagtttct ... tatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|254334741|gb|GR844526.1|GR844526
EST:     GATCACTTTGCAAGGAAGGATAAAATGCCCATCAATCTTAAATATATAG                         ATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATCACTTTGCAAGGAAGGATAAAATGCCCATCAATCTTAAATATATAGgtcagtttct ... tatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|298176657|gb|HO026778.1|HO026778
EST:     GATCACTTTGCAAGGAAGGATAAAATGCCCATCAATCTTAAATATATAG                         ATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATCACTTTGCAAGGAAGGATAAAATGCCCATCAATCTTAAATATATAGgtcagtttct ... tatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|254334742|gb|GR844527.1|GR844527
EST:     TAAATATATAG                         ATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCT
genomic: TAAATATATAGgtcagtttct ... tatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|254320046|gb|GR830962.1|GR830962
EST:     GATCACTTTGCAAGGAAGGATAAAATGCCCATCAATCTTAAATATATAG                         ATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATCACTTTGCAAGGAAGGATAAAATGCCCATCAATCTTAAATATATAGgtcagtttct ... tatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|193351916|gb|FK315455.1|FK315455
EST:     GATCACTTTGCAAGGAAGGATAAAAATGCCCATCAATCTTAAATATATAG                         ATCCAACTTACATGATTCGGGCAATTCCAAGCAA
genomic: GATCACTTTGCAAGGAAGGATAAAA-TGCCCATCAATCTTAAATATATAGgtcagtttct ... tatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAA
EST: gi|208260274|gb|GE060640.1|GE060640
EST:     GATCACTTTGCAAGGAAGGATAAAATGCCCATCAATCTTAAATATATAG                         ATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGAC
genomic: GATCACTTTGCAAGGAAGGATAAAATGCCCATCAATCTTAAATATATAGgtcagtttct ... tatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGAC
EST: gi|58024605|gb|CX711346.1|CX711346
EST:     GATCACTTTGCAAGGAAGGATAAAATGCCCATCAATCTTAAATATATAG                         ATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATCACTTTGCAAGGAAGGATAAAATGCCCATCAATCTTAAATATATAGgtcagtttct ... tatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaattgagttatctgcctagtgggataagactttgttgttattgtatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
 ttttaat  putative branch site (score: 3)
                                       ttattgtat  TA-rich tract