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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtttctcttacagcattctcttcctttttgacctatttatttcttggtctttcatttttatttcggatttcaaaggttttttaaaatttgacaattatctaattttaaccaagttatctacatcgtgggataaggctttgttgttgttgtatctgccagATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA

Basic information

species Glycine max
transcript GLYMA04G09180.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
gtcagtttctcttacagcattctcttcctttttgacctatttatttcttggtctttcatttttatttcggatttcaaaggttttttaaaatttgacaattatctaattttaaccaagttatctacatcgtgggataaggctttgttgttgttgtatctgccagATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
                | |      |  |||||    | || | |||| | |    |||    | | |   ||| ||    |  ||     || | |  ||||| | | |  ||    |||  | ||  ||  ||||     |||| ||  |     || |||||||||| ||||||||||| ||||| | ||||||||||||||| ||||||||||| ||||| || || || |||||  | ||||| |||||||| || ||
----------------gtaaagatcttgttttta---tgttcaattctcgatgca-catgcggagtgctagtttgaagtactactt-----tttatatgtatctgagtatctcc---ctatgga-atgttgcaataacagcctgttatttctaa---tggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA

upper sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 12
gtcagtttctcttacagcattctcttcctttttgacctatttatttcttggtctttcatttttatttcggatttcaaaggttttttaaaatttgacaattatctaattttaaccaagttatctacatcgtgggataaggctttgttgttgttgtatctgccagATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
                                                  ||   | || |||  |||  |    | | | || ||| |  |     |||| ||  | |  |         |||  | |||   |    |  | || || ||     ||| |||||| || ||||||||||| || || | ||||||||||||||| ||||||||||| || || || || || |||||  | |||||||||||||| || ||
--------------------------------------------------gtaact-atgtttgcttcacacaggataaggttgttacacatc--ttatta-ctggtctctattgta----ctaagttgtgaagtt---ccctattattatt-----tgc-agATCCTACCTACATGATCCGAGCTATTCCAAGCAATGCATCAGACAATGTCTACTGCACGCTGCTGGCCCACAGTGCTATTCATGGTGCAATGGCCGGCTA

upper sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 12
gtcagtttctcttacagcattctcttcctttttgacctatttatttcttggtctttcatttttatttcggatttcaaaggttttttaaaatttgacaattatctaattttaaccaagttatctacatcgtgggataaggctttgttgttgttgtatctgccagATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
                                                                 |    ||||  ||   || ||    ||||  | | || || || ||||  | ||  ||| ||  |||  |  | |  | ||    | | |  || ||||||| || |||||| |||| || || | ||||||||||||||| |||||||||||||||||||| || || |||||  |||||||||||||||| |||||
----------------------------------------------------------------gtagccatttgtaactcttatt----tttgctattgatatagttgtaacacattt--ctagat--tggtctgtgacaatatt-ccatcggaattggcagATCCTACATACATGGTCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTAGCCCACAGTGCTATCCATGGTGCAATGGCGGGGTA

upper sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 12
gtcagtttctcttacagcattctcttcctttttgacctatttatttcttggtctttcatttttatttcggatttcaaaggttttttaaaatttgacaattatctaattttaaccaagttatctacatcgtgggataaggctttgttgttgttgtatctgccagATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
                                             |  | |||||   ||||  ||   ||   ||  | |  |||  |||||          ||   |    ||||  ||||        |   |||    ||   || || ||| |   ||||||||||||||||||||| || || | ||||||||||||||| |||||||| || || || || || || |||||  | |||||||||||||| || ||
--------------------------------------------gtaatcgtcttcttttttacttggtgaacgcagtgttagtttgtaattta---------tagcat--gtcaaggaatct--------gatgaagtgcctgccatttttttatgt---agATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTATTGCACCCTGCTCGCACATAGTGCCATTCATGGTGCAATGGCGGGATA

upper sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 12
gtcagtttctcttacagcattctcttcctttttgacctatttatttcttggtctttcatttttatttcggatttcaaaggttttttaaaatttgacaattatctaattttaaccaagttatctacatcgtgggataaggctttgttgttgttgtatctgccagATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
                                                                         |||  | |||| |    | | |   ||   | |    ||   | ||     ||||          | |  | |||| |  || |||| ||||||||| |||||||| || || || |  ||||| || || |||||||||||||| ||||| || ||||| ||||  |||||||| || ||||| || ||
------------------------------------------------------------------------gtcagtgattttctctggtatcatgcttgctttacggcaa--gaattgctagcatcaaatatctcagat--gctgttatccta-ctgc-agATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA

upper sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 11
lower sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 11
gtcagtttctcttacagcattctcttcctttttgacctatttatttcttggtctttcatttttatttcggatttcaaaggttttttaaaatttgacaattatctaattttaaccaagttatctacat-cgtgggataaggctttgttgttgttgtatctgccagATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
                                                                                       |  |||| |  |   | ||||  |  | || ||  || || | ||   ||    | ||   |      || |  ||||||| || ||||||||||| || || | |  ||||||||| || || |||||||  || || ||||| || || |||||||||||||||||||| || ||
-------------------------------------------------------------------------------------gtacgtttgtcc-tccccaaattcaagtcgagctacatagattcatgaattagaaatatgac-tcaaaccatgtttcagATCCGACATACATGATCCGAGCTATTCCAGCCAATGCATCTGACAACGTCTACTCAACTCTCCTTGCCCAAAGCGCAGTCCATGGTGCAATGGCTGGCTA

upper sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 11
gtcagtttctcttacagcattctcttcctttttgacctatttatttcttggtctttcatttttatttcggatttcaaaggttttttaaaatttgacaattatctaattttaaccaagttatctacatcgtgggataaggctttgttgttgttgtatctgccagATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
                                                  |||  | | ||    || |  |||     |||| || |  |||        | ||  |||  |  ||| | | | |    |     | ||| |  ||  ||||  |||  ||||||| || ||||||||||| || || | | |||||||||| || ||||| ||||| ||||| |||||||| ||||| || ||||| ||||||||||| ||
--------------------------------------------------gtcagtgacttcagatttgtgttt-----gtttatttattttt-----ccttttagatttggcttagtaa-caata----gattctaagctatcctga-gttg--tcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGTACTGCACACTCCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGTTA

upper sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ23976 (Selaginella moellendorffii), 3'ss of exon 11
gtcagtttctcttacagcattctcttcctttttgacctatttatttcttggtctttcatttttatttcggatttcaaaggttttttaaaatttgacaattatctaattttaaccaagttatctacatcgtgggataaggctttgttgttgttgtatctgccagATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
                                                                                                     ||      ||  | |||| |      | |    |    ||    | ||| | |      |||||||||| || |||||||| |||||||  ||||| || || || ||||||||||| || || || ||||| |||||  |||| || |||||||| || ||
----------------------------------------------------------------------------------------------------gtcagtgccta--cgagtttttcttgccttctcttttctctcaacttttgattt-----tcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA

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|207836632|gb|GD806629.1|GD806629
EST:     TCACTTTGCAAGGAAGGATTAAGTATTCCCCATCAATCTTAAATATATAG                         ATCCAACTTACAT
genomic: TCACTTTGCAAGGAAGGAT-AAG-ATTCCC-ATCAATCTTAAATATATAGgtcagtttct ... tatctgccagATCCAACTTACAT
EST: gi|193473086|gb|FK436675.1|FK436675
EST:     CACTTTGTTCTAAGGTAAGGATAAGATTCCCATCAATCTTAAATATATAG                         ATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCT
genomic: CACTTTG--C-AAGG-AAGGATAAGATTCCCATCAATCTTAAATATATAGgtcagtttct ... tatctgccagATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCT
EST: gi|207767243|gb|GD739655.1|GD739655
EST:     GATCACTTTGCAAGGAAGGATAAGATTCCCATCAATACTTAAATATATAG                         ATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCT
genomic: GATCACTTTGCAAGGAAGGATAAGATTCCCATCAAT-CTTAAATATATAGgtcagtttct ... tatctgccagATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCT
EST: gi|193437677|gb|FK403516.1|FK403516
EST:     AAGGATAAGATTCCCATCAATCTTAAATATATAG                         ATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCT
genomic: AAGGATAAGATTCCCATCAATCTTAAATATATAGgtcagtttct ... tatctgccagATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCT
EST: gi|193309643|gb|FK276717.1|FK276717
EST:     GATCACTTTGCAAGGAAGGATAAGATTCCCATCAATCTTAAATATATAG                         ATCCAACTTACATGA
genomic: GATCACTTTGCAAGGAAGGATAAGATTCCCATCAATCTTAAATATATAGgtcagtttct ... tatctgccagATCCAACTTACATGA
EST: gi|193403000|gb|FK366496.1|FK366496
EST:     GATCACTTTGCAAGGAAGGATAAGATTCCCATCAATCTTAAATATATAG                         ATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCT
genomic: GATCACTTTGCAAGGAAGGATAAGATTCCCATCAATCTTAAATATATAGgtcagtttct ... tatctgccagATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCT
EST: gi|193363314|gb|FK328350.1|FK328350
EST:     GATCACTTTGCAAGGAAGGATAAGATTCCCATCAATCTTAAATATATAG                         ATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCT
genomic: GATCACTTTGCAAGGAAGGATAAGATTCCCATCAATCTTAAATATATAGgtcagtttct ... tatctgccagATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCT
EST: gi|208318731|gb|GE111170.1|GE111170
EST:     GATCACTTTGCAAGGAAGGATAAGATTCCCATCAATCTTAAATATATAG                         ATCCAACTTACAT
genomic: GATCACTTTGCAAGGAAGGATAAGATTCCCATCAATCTTAAATATATAGgtcagtttct ... tatctgccagATCCAACTTACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaccaagttatctacatcgtgggataaggctttgttgttgttgtatctgccagATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA
 ttttaac  putative branch site (score: 2)
      aagttat  TA-rich tract