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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggagaatctattctttgacattgctgttctttaagcatgctaatcttttttttcttgcttctatttactccttttatgttgtttgaatagGAATTTGAGGACAACTCTGCCTCCAGCCAGATATTTTGGCTATTGAAAGAAAGTGAGCTAACTCCCAGTAATGCCAATATATTGGATGGTCGATATGCAG

Basic information

species Glycine max
transcript GLYMA13G23850.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G23850.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os08g29370.1 (Oryza sativa), 3'ss of exon 6
---------gtgaggagaatctattctttgacattgctgttctttaagcatgctaatcttttttttcttgcttctatttactccttttatgttgtttgaatagGAATTTGAGGACAACTCTGCCTCCAGCCAGATATTTTGGCTATTGAAAGAAAGTGAGCTAACTCCCAGTAATGCCAATATATTGGATGGTCGATATGCAG
          |||      |  | | |     ||      |||  |   |||   ||  ||      || ||   ||| |    ||  || |  |      |||||||||| ||||| ||||| || ||||| || |||||| | || ||||| ||||||||||| || || |||||||||||| ||||||| || ||||| |
gtaagtatcatgatactgcttcagtgtaatgtatcaagcatctgcagatatgggcatgcttcagcattttctaacattaaacgtttgaatatcat---ggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAGAGTGAGCTAACACCAAGCAATGCCAATATACTGGATGGGCGGTATGCCG

upper sequence: GLYMA13G23850.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G015967_T01 (Zea mays), 3'ss of exon 6
--gtgaggagaatctattctttgacattgctgt-tctttaagcatgcta-atcttttttttcttgcttctatttactccttttatgttgtttgaatagGAATTTGAGGACAACTCTGCCTCCAGCCAGATATTTTGGCTATTGAAAGAAAGTGAGCTAACTCCCAGTAATGCCAATATATTGGATGGTCGATATGCAG
    |||    ||  |   ||  ||||  | |  | |  |  |   ||  ||| | | |    |  |   |  |        |    ||  |||  |||||||||| ||||| ||||| || |||||  |||||||||| |||||||| ||||||||||| || || ||||||||||||||||| || || || ||||
gtaagagagacatgcaagattgcacatatcagcatatgcagacgatctgcatcgtatctaatgtattctaacctgagataacttcactgcatga-cagGAATTTGATGACAATTCTGCTTCTAGCCAAGTATTTTGGCTCTTGAAAGAGAGTGAGCTAACACCAAGCAATGCCAATATATTGGACGGGCGGTACGCAG

upper sequence: GLYMA13G23850.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0066g01410.t01 (Vitis vinifera), 3'ss of exon 6
gtgaggagaatctattctttgacattgctgttctt-taagcatgctaatcttttttttcttgcttctatttactccttttatgttgtttgaat---------agGAATTTGAGGACAACTCTGCCTCCAGCCAGATATTTTGGCTATTGAAAGAAAGTGAGCTAACTCCCAGTAATGCCAATATATTGGATGGTCGATATGCAG
  |     | |||| |   |  ||| ||| ||  |  |    ||       ||  |  ||   |  |||||  || |||| |||| ||| | |         |||||||||| || || || || || |||||||||||||||||| ||||||||||||| || ||||| ||||||||||||||||||||||| || |||||||
--gtaagaactctaattcataccatggctatttctacatatgtgtatggacttgatggctaaatgatatttgttctttttttgttttttcattttactctgcagGAATTTGACGATAATTCCGCGTCAAGCCAGATATTTTGGCTACTGAAAGAAAGTGAACTGACTCCTAGTAATGCCAATATATTGGATGGCCGTTATGCAG

upper sequence: GLYMA13G23850.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ25643 (Selaginella moellendorffii), 3'ss of exon 7
gtgaggagaatctattctttgacattgctgttctttaagcatgctaatcttttttttcttgcttctatttactccttttatgttgtttgaatagGAATTTGAGGACAACTCTGCCTCCAGCCAGATATTTTGGCTATTGAAAGAAAGTGAGCTAACTCCCAGTAATGCCAATATATTGGATGGTCGATATGCAG
                                      | | |  || |    | ||  ||  |||||| |    |||  |  ||||||   |||| |||||| || |||| || |||||||||||||||||||||||||                                                      
--------------------------------------gtaagaaaaacggcctctttatg--tctattgaagATTTTCTT--TGTTTG--CAGGAGTTTGAGAACGACTCGGCTTCCAGCCAGATATTTTGGCTATTGA------------------------------------------------------

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|31474483|gb|CD416511.1|CD416511
EST:     AAACGAAGCTTCCCTTTAATGCTTTCGGTACAATGGCAATGGCTAGAGAT                         GAATTTGAGGACAACTCTGCCTCCAGCCAGATATTTTGGCTATTGAAAGAA
genomic: AAACAAAGCTTCCCTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGATgtgaggagaa ... gtttgaatagGAATTTGAGGACAACTCTGCCTCCAGCCAGATATTTTGGCTATTGAAAGAA
EST: gi|209701690|gb|BW673137.1|BW673137
EST:     AAACAAAGCTTCCCTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGAT                         GAATTTGAGGACAACTCTGCCTCCAGCCAGATATTTTGGCTATTGAAAGAA
genomic: AAACAAAGCTTCCCTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGATgtgaggagaa ... gtttgaatagGAATTTGAGGACAACTCTGCCTCCAGCCAGATATTTTGGCTATTGAAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgctaatcttttttttcttgcttctatttactccttttatgttgtttgaatagGAATTTGAGGACAACTCTGCCTCCAGCCAGATATTTTGGCTATTGAAAGAAAGTGAGCTAACTCCCAGTAATGCCAATATATTGGATGGTCGATATGCAG
  tgctaat  putative branch site (score: 2)
     taatcttttttttctt  TA-rich tract